Chromosome Analysis Suite (ChAS) v4.

4
USER GUIDE

Publication Number MAN0027798

Revision 18

For Research Use Only. Not for use in diagnostic procedures.

 Affymetrix, Inc.
3450 Central Expressway
Santa Clara, CA 95051
USA

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 Contents
 CHAPTER 1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

Features in v4.4 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
About this user guide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Customer support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21

 CHAPTER 2 Installing ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Recommended and minimum requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22

Requirements and prerequisites for arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Zip file contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
Installing ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
New Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Upgrade installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Copying analysis files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Analysis file locations in Windows 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Viewing Hidden Files and Folders . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Displaying hidden files and folders in Windows 10 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Analysis file download . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Downloading ChAS analysis files from NetAffx for use with the ChAS Browser . . . . . . 26
Downloading ChAS analysis files from NetAffx using the Analysis Workflow . . . . . . . . 27
Updating NetAffx Genomic Annotation files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Setting up proxy server access . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Access to NetAffx from the analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Access to NetAffx from the ChAS browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
Access to a remote ChAS database server from the ChAS browser . . . . . . . . . . . . . . . . 29
Uninstalling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29

 CHAPTER 3 Getting started. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30

Starting ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
Logging into the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
Analysis workflow module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
First time setup . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
Assigning an Input sample path(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
Assigning an Output results path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Assigning a Central QC history path . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
File types and data organization in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
ChAS file types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

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File Types Supported in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34

Region information files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
Analysis and visualization library files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Data organization in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Basic workflow for cytogenetics analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
Array processing workflow (using instrument control software) . . . . . . . . . . . . . . . . . . . . 37
Probe-level Analysis of CEL file data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
Loading data into ChAS for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
CytoScan array (CYCHP files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
CytoScan XON array (XNCHP files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
CytoScan HTCMA array (RHCHP files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
Genome-wide SNP array 6.0 (CNCHP files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
OncoScan array (OSCHP files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
ReproSeq aneuploidy (zip files) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Viewing data and features of interest using the ChAS display controls . . . . . . . . . . . . . . 41
Working with ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Accessing functions in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Changing pane sizes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
Opening panes in separate windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

 CHAPTER 4 CN/LOH/Mosaicism analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44

Single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45

ChAS analysis file compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Introduction to single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
Copy number segments on the X and Y chromosomes . . . . . . . . . . . . . . . . . . . . . . . . 48
Mosaic copy number segments on the X chromosome . . . . . . . . . . . . . . . . . . . . . . . . 48
LOH segments on X and Y chromosomes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
CytoScan arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Performing a single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Setting up and running a single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
Adding sub-folders to your assigned result path/folder . . . . . . . . . . . . . . . . . . . . . . . . 53
Creating your own custom QC setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Viewing results in the browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58
Recentering CytoScan HD, 750K and Optima arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
Method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
Determing the median Log 2 ratio for the region in the sample that is truly diploid . . . 61
Method 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
Determining the median Log 2 ratio for the region in the sample that is truly diploid . . 62
No gender single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
Setting up and running a normal diploid analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Viewing the recommended QC metrics (listed above) . . . . . . . . . . . . . . . . . . . . . . . . . . 67
Setting up and running an OncoScan single sample analysis . . . . . . . . . . . . . . . . . . . . . . 67

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Adding sub-folders to your assigned Output Results folder . . . . . . . . . . . . . . . . . . . . . 69

Creating your own custom QC settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Viewing results in the browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
Recentering OncoScan CNV and OncoScan CNV Plus arrays . . . . . . . . . . . . . . . . . . . . . 74
Method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
Determining the median Log 2 ratio for the region in the sample that is truly diploid . . 74
Method 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
Determining the median Log 2 ratio for the region in the sample that is truly diploid . . 75
Setting up and running an OncoScan matched normal analysis . . . . . . . . . . . . . . . . . . . . 78
Adding CEL files to analyze . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
Manually adding CEL files to analyze . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
CEL file displaying options (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Selecting a File Name display attribute . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Importing CEL files using batch import . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Converting CEL files to CHP files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
How it works . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Supported array types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 84
Launching the tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
Setting up the tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Assigning your input folder(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Assigning your output folder(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Assigning an archive folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
Assigning a QC History file folder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Selecting a target genome version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Normal diploid analysis check box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Running the tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
Opening the newly generated CHP file(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
Reference files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89
Creating a reference file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90

 CHAPTER 5 Analysis workflow exports and QC tools . . . . . . . . . . . . . . . . . . . 93

Displaying and exporting data from the analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . 93

Adding files to the QC results table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Exporting QC table information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Viewing analysis files in the ChAS browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Exporting probe-level data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Exporting CytoScan Probe-Level Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Exporting OncoScan probe-level data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Exporting a gene report (CytoScan or OncoScan arrays) . . . . . . . . . . . . . . . . . . . . . . . . . 95
Exporting a XON region report (CytoScan XON only). . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
Exporting a copy number expression overlap report . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Exporting genotype data using the analysis workflow . . . . . . . . . . . . . . . . . . . . . . . . . . 103

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Exporting options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104

Exporting a SNP List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Exporting a specific chromosome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Selecting an output path and filename . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Multiple file output options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
Saving and importing attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Exporting to Integrative Genomics Viewer (IGV) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 105
Principle component analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
PCA plot generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Sample display options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
Additional PCA graph display options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Concordance checks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Performing a concordance check . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
Concordance table filter and display options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
Filtering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
Changing the view and/or order of sample and reference columns . . . . . . . . . . . . . . 111
Exporting the currently displayed table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Mendelian error checking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Running an error checking analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
Interpreting an error checking analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Analysis workflow troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Log rollover . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
Log collection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117

 CHAPTER 6 Loading data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

Introduction to loading data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118

Loading files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
Using the search feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Copy number segment smoothing and joining (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Viewing what segments were smoothed/joined . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Setting smoothing and joining parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
Segment data tab options and descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
About smoothing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
Copy Number State for Smoothed Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
About joining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
XON segment merging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Turning off XON merging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Setting QC parameters in the ChAS browser . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
Viewing QC thresholds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
QC Thresholds tab options and descriptions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
Adding a QC property. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
Editing an existing QC threshold . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

Chromosome Analysis Suite (ChAS) User Guide 6

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Histogram data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138

Loading histogram data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Changing the default histogram filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Changing the default histogram colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Adding filtered histogram data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Removing a histogram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

 CHAPTER 7 Viewing data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Displaying options of analysis results data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143

Overview of ChAS window components . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
Files list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
Data types list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Named settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Status bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
Display area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
Upper panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Selected chromosome view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Lower panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
Changing the NetAffx genomic annotation file version . . . . . . . . . . . . . . . . . . . . . . . . . . . 151

 CHAPTER 8 Displaying data in graphic views . . . . . . . . . . . . . . . . . . . . . . . . 152

Graphic views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152

Karyoview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Whole genome view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Displaying the Whole Genome View for a sample(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . 158
Changing graph types. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Changing colors of the data points or line data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 160
Setting a default WGV state display and colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Creating WGV states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
Applying a saved WGV state(s). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Deleting a saved WGV state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Using the WGV zoom feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
Adding a reference line to the WGV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Adding a comparison file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165
Selecting a new comparison file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Exporting a WGV . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
Selected chromosome view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
Detail view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
Viewing CytoScan XON region segments in detail view. . . . . . . . . . . . . . . . . . . . . . . . . . 171
Viewing CytoScan XON whole genome segments in the detail view . . . . . . . . . . . . . . . . 173

Chromosome Analysis Suite (ChAS) User Guide 7

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Annotation color codes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174

Annotation OMIM color codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Changing an annotation color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
Data in the detail view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 175
Navigation controls in detail view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
Obtaining summary metrics for a zoomed in region . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Selecting a chromosome section for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Karyoview and selected chromosome view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Selecting a chromosome for detailed examination . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Examining a section of the chromosome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Coordinate range box . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Going to a specific coordinate or coordinate range . . . . . . . . . . . . . . . . . . . . . . . . . . 182
Returning to a previous location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Zooming to a selected item . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
Setting a vertical highlight . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Edit configurations in the misc tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Accessing the Misc tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
Autosave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Coordinated box format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Chromosome sorting order. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Zoom buffer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
CHP file colors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Changing a CHP file color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
Remapped segment patterns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Microarray nomenclature configuration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188
Controlling the display of data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Selecting data for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 190
Selecting and deselecting files for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Changing the order of the Sample lanes or reference annotations . . . . . . . . . . . . . . . 191
Viewing data properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Closing a file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
Selecting data types for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Selecting and deselecting data types for display . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Changing the order of the data types: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Turning the symbols used for segments on or off: . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Changing the grouping of samples and data types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Changing the grouping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
Lanes grouped by sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
Selecting display schemes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Selecting a dark scheme display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Expanding and contracting annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
Toggling between collapsed and expanded display of annotations: . . . . . . . . . . . . . 196
Changing graph appearance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

Chromosome Analysis Suite (ChAS) User Guide 8

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Opening the Graph Settings window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196

Changing the settings for a graph type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Selecting different graph styles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Changing the graph style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
Changing graph attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Changing graph attributes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
Changing scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Setting specific minimum and maximum values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 202
Changing the vertical height of a graph . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Learning more about features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Pop-ups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
Turning pop-ups on or off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Right-click menu options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
Selection details table. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Linking to external websites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Viewing a selected area at a public site . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Linking to TaqMan copy number and genotyping assays . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Viewing and ordering TaqMan assays for CN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Viewing and Ordering TaqMan assays for genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . 215

 CHAPTER 9 Filtering segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217

Applying segment parameter filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218

Opening the Segment Filters window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
Using segment parameter filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
Bypassing segment filters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222

 CHAPTER 10 Segment modification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Editing segment data overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 223

Using edit mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
Types of segment editing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
Tracking original calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Merging all segments types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Merging segment groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 226
Segment to segment merge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
Un-Merging . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
Merged Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
Deleting all segments types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
Un-deleting a deleted segment(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 234
Editing the start/end Coordinates of all segment types . . . . . . . . . . . . . . . . . . . . . . . . . . . 235
Un-doing the edited start/end coordinates of a segment . . . . . . . . . . . . . . . . . . . . . . . . 236
De Novo segment drawing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Un-doing a segment De Novo drawing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239

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Changing all copy number segment types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241

Un-doing a copy number change . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
Promoting mosaic segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
Modified segments in the segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Editing mode on . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
Editing mode off . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Removing all edits made to a sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Editing the Microarray Nomenclature (ISCN 2013) and Microarray Nomenclature fields . . 246

 CHAPTER 11 Sample and segment annotations . . . . . . . . . . . . . . . . . . . . . . 248

Sample annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248

Adding, removing, and changing the order of sample type text . . . . . . . . . . . . . . . . . . . 248
Adding a Sample Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
Deleting a Sample Type . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Re-arranging the order currently displayed Sample Types . . . . . . . . . . . . . . . . . . . . . 249
Restoring the factory default Sample Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 249
Adding, removing, and changing the order of phenotype text . . . . . . . . . . . . . . . . . . . . 249
Adding a short Phenotype text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Deleting a short Phenotype text . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Re-arranging the currently displayed Phenotypes order . . . . . . . . . . . . . . . . . . . . . . . 250
Restoring the factory default Phenotypes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Adding annotations at the sample (xxCHP) file level . . . . . . . . . . . . . . . . . . . . . . . . . . . . 250
Segment annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Setting up the calls feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Adding and removing calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 252
Adding, deleting, and re-arranging calls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Adding calls to the Call drop-down list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Deleting calls from the Call drop-down list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Re-arranging the order of Calls in the Call drop-down list . . . . . . . . . . . . . . . . . . . . . 253
Restoring the factory default Calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Using the calls feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Method 1: At the segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
Method 2: At the View/Edit Annotation Properties Window . . . . . . . . . . . . . . . . . . . . 254
Adding or removing interpretation snippets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Removing a saved snippet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 256
Removing multiple saved snippets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Using the interpretation snippets feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Method 1: At the segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 257
Method 2: At the View/Edit annotation properties window . . . . . . . . . . . . . . . . . . . . . 258
Adding or removing inheritance calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 259
Adding an Inheritance call to the Inheritance drop-down list . . . . . . . . . . . . . . . . . . . 260
Deleting a call from the Inheritance drop-down list . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
Re-arranging the order of calls displayed in the Inheritance drop-down list . . . . . . . . 260

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Using the inheritance feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261

Method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 261
Method 2: From the View/Edit annotation properties window . . . . . . . . . . . . . . . . . . 261
Adding Oncomine Reporter annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
Tracking and reviewing the log file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263

 CHAPTER 12 Using CytoRegions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

CytoRegions overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267

Selecting a CytoRegions information file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
Viewing CytoRegions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
CytoRegions in the graphic views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
CytoRegions table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
Highlighting regions in the CytoRegions table and details view . . . . . . . . . . . . . . . . . 272
CytoRegions tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Searching CytoRegions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 274
Using filters with CytoRegions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Using restricted mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Selecting/De-selecting Restricted Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
Assigning a CytoRegion for targeted XON analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277
Creating an AED File from a gene list . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 277

 CHAPTER 13 Using the overlap map and filter. . . . . . . . . . . . . . . . . . . . . . . . 279

Overlap map and filter overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279

Using the overlap filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
Selecting the overlap map file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
Viewing overlap regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Viewing overlap map regions in the graphic displays . . . . . . . . . . . . . . . . . . . . . . . . . . . 282
Viewing the overlap map table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283
Highlighting overlap regions in the overlap map table and details view . . . . . . . . . . . 283
Overlap map tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 284
Using the overlap filter . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286

 CHAPTER 14 Creating and editing AED files . . . . . . . . . . . . . . . . . . . . . . . . . 287

Creating an AED file of annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287

Adding annotations to an AED file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289
Creating an AED file of regions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Creating a new CytoRegions file in AED file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 290
Adding regions to an existing AED file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
Adding a section to a new region (AED) file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 292
Deleting regions from an AED file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294
Viewing or Editing AED File Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294

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Viewing file properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 294

Viewing the genome assembly version . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
Adding a property . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296
Removing a property . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Editing a property value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Viewing and editing annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Entering general information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Editing the General tab properties in AED annotations . . . . . . . . . . . . . . . . . . . . . . . . 299
Customizing properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Adding Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Adding custom properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Adding a curation (Optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
New user annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
Viewing and batch editing AED file contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
Protecting an AED file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
AED/BED color rules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
Selecting a new default color for loaded AED or BED files . . . . . . . . . . . . . . . . . . . . . . . 310
Creating a color rule . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
Changing an annotation color. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 317
Exporting information in AED or BED format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
Exporting position data as an AED or BED file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
Merging and exporting feature position information for multiple files . . . . . . . . . . . . . 320
Expression analysis AED file generation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321
Viewing a Gene Expression AED file in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 321

 CHAPTER 15 VCF files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322

Loading VCF files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322

Exporting VCF files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 325
Exporting CN and/or variant data as a VCF file (for use in 3rd party browsers) . . . . . . . 325

 CHAPTER 16 Displaying data in table views . . . . . . . . . . . . . . . . . . . . . . . . . 327

Display overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327

Common table operations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 327
Standard tool bar controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Sorting by columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Sorting a table by a single column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
Performing a multi-column sort . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Changing the order of table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Selecting columns to display or hide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
Using the right-click menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 330
Using a column header’s right-click menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

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Sum, mean, and median calculator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331

Calculating multiple numeric values in a column . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 331
Saved table states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 332
Saving the current segment table state to its default . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Adding columns to table states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Removing (hiding) columns in a table (for report use) . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
Saving a newly edited segment table state . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Applying previously saved table states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
Deleting previously saved table states . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336
Segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 337
Segments table tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
Segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
Segment table columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
Obtaining all annotations associated with a segment . . . . . . . . . . . . . . . . . . . . . . . . . . . 343
Graphs table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
Graphs table properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 346
Graph Table Tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
Exporting genotype calls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 347
Variants table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 351
Tool bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
Variants table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
CytoScan HTCMA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
OncoScan CNV Plus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
QC and sample info tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
QC and sample information table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
CytoScan QC view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
Default QC view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 356
CytoScan HTCMA QC view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
OncoScan QC view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
ReproSeq QC view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
SMN Sample Info view . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Gender call algorithms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360
Loaded AED/BED files table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361
Chromosome summary data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 362
Auto-generated Autosome LOH percentage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
Searching results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
Searching within a selected file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 367
Finding intersections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370

 CHAPTER 17 Prioritizing segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373

ChAS Professional version of Franklin by Genoox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373

ChAS AIR tokens . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373

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Uploading your sample(s) to Franklin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 374

Returning to an open case in Franklin from ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375
Tier-based prioritization in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376
Configuring the tier-based option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 376
Tier to call settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
Viewing segment prioritization in the segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Score-based prioritization in ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
Configuring the score-based option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 381
View/Edit Score-Based Rules for Gain Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 382
View/Edit Score-Based Rules for Loss Segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . 384
Configuring the score-based option . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
Viewing segment prioritization in the segments table . . . . . . . . . . . . . . . . . . . . . . . . . . . 388

 CHAPTER 18 Interacting with the ChAS database . . . . . . . . . . . . . . . . . . . . . 390

Setting up a ChAS DB query . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 390

Setting up query parameters for a copy number search . . . . . . . . . . . . . . . . . . . . . . . . . 391
Setting up query parameters for an LOH segment search . . . . . . . . . . . . . . . . . . . . . . . 391
Setting up query parameters for an XON region segment search . . . . . . . . . . . . . . . . . . 391
Querying a segment from the segment table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 392
Segment intersections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 393
Additional segment intersection information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 397
Downloading segments from a sample file in ChAS DB . . . . . . . . . . . . . . . . . . . . . . . . . . . 399
Downloading and viewing Segments from a sample(s) stored in ChAS DB . . . . . . . . 399
Updating downloaded segment annotations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
Filtering DB count columns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 401
Querying overlapped segments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
Changing or refining the DB query criteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
Publishing data to the database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Publishing data or multiple data to the database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Method 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Method 2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
Publishing to database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
Important rules and restrictions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
Manual or automatic connection mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408
Querying samples in the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Editing column contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409
Editing multiple cells with the same value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 410
Removing a sample from the query window . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Deleting sample(s) from the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Deleting a single sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411
Deleting multiple samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 412

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Querying segments to the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413

Editing column contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 413
Editing multiple cells with the same value . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 414

 CHAPTER 19 Exporting results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415

Exporting graphic views . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416

Exporting as a PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 416
Creating signature and background profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418
Signature profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418
Creating a new signature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418
Editing a saved Signature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
Deleting a signature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
Background profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
Creating a new background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 419
Editing a saved background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420
Deleting a background . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420
Exporting as Word (DOCX) format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 420
Exporting as PNG . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
Exporting table data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
Exporting table data into a PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
Exporting table data into a PDF file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
Exporting tables tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 425
Exporting views and tables as a DOCX file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426
Exporting tables as TXT file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426
Exporting table information as a text file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426
Exporting a segments table with modified segments to a TXT file . . . . . . . . . . . . . . . . . 428
Transfer to clipboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
Combining PDFs into a single PDF . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Adding a new PDF export to an existing PDF file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Combining two existing PDF files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
Exporting with ClinVar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434
Creating a ClinVar submission profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 434
Editing an existing ClinVar profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Deleting a profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Adding vocabulary content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Removing vocabulary content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Exporting in ClinVar format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 435
Exporting a deletion log . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 437

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 CHAPTER 20 User profiles and named settings . . . . . . . . . . . . . . . . . . . . . . . 438

Types of settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438

User profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 438
Named settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439
Creating and using user profiles . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
Deleting a user profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
Creating and using named settings . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
Saving a named setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
Selecting a named setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 442
Deleting a named setting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 443
Exporting and importing preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444
Exporting preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 444
Importing preferences . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445
Importing hyperlinks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446
Configuring the HTTP service . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446

 CHAPTER 21 Database tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447

Connecting to a remote ChAS DB server . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447

Accessing the ChAS DB server tools . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 448
Status page . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450
Maintenance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 450
Backing up a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
Restoring a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 451
Merging ChAS databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452
Merging two ChAS databases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 452
Merging an older ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453
Cleaning up a database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453
Downloading deletion logs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454
Creating a blank ChAS DB . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 454
Deidentifying Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455
Administration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 456
Permission Guidelines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Using a shared ChAS database while off-line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Working off-line using a ChAS database that resides on a shared server . . . . . . . . . 457
Publishing data you have analyzed in off-line mode to the shared ChAS DB server . 457
Remapping a hg19 ChAS DB to hg38 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 458

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 CHAPTER 22 ChAS Database Loader (CDL) . . . . . . . . . . . . . . . . . . . . . . . . . . 460

Starting CDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461

Adding files to CDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 462
Sample info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463
Adding files to be published using a text file . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Publishing to the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Testing your connection (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Verifying the ChAS database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 465
Before publishing files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466
Changing segment filters (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466
Managing data types (optional) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467
Publishing your files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468
Clearing Table Data . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471
Clear Published . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471
Clear All . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471
Closing CDL . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 471

 APPENDIX A Analysis parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Analysis parameters for single sample analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

Reference model file creation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472

 APPENDIX B AED file format . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

AED file description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 473

Header row . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 474
Metadata records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 475
Annotations Rows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Property name elements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Namespaces . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477
AFFX properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477
AED properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 477
Biology properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
Style properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 479
Compatibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480
UCSC Browser Extensible Data (BED) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 480
Microsoft Excel and other spreadsheet applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
Microsoft Notepad and other Text editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
Text Editors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 481

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 APPENDIX C ChAS properties and types . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482

Identifying properties within ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482

Standard AED property style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 482
ChAS property style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483
Full URI property style . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483
Identifying value types within ChAS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Automatic conversion of xxCHP headers to properties . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Header name conversion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 484
Converted properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485
Derived properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 485

 APPENDIX D ChAS browser NetAffx Genomic Annotations. . . . . . . . . . . . . . 487

Homo Sapiens database files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487

NetAffx Genomic Annotation files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
Source of content . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487

 APPENDIX E Genomic position coordinates . . . . . . . . . . . . . . . . . . . . . . . . . . 488

Genome assemblies . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488

SNP and marker positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488
Segment positions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489

 APPENDIX F Editing BED files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490

 APPENDIX G CytoScan algorithms and QC metrics . . . . . . . . . . . . . . . . . . . . 492

Algorithm overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492

Feature identification and signal extraction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492
Single sample CytoScan workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492
Signal-level covariate adjustors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
Fragment adapter covariate adjustor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
Fragment length covariate adjustor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
Dual quantile normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
Copy number workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Log2 ratio calculation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
High pass filter image correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Log2 ratio-level covariate adjustors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Super GC covariate adjustor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Reference intensity covariate adjustor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Marker Type Covariate Adjustor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
Median Autosome normalization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496

Chromosome Analysis Suite (ChAS) User Guide 18

 Contents

Systematic residual variability removal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496

Signal restoration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497
Segmentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497
Copy Number Calls for each Marker based on Log2 Ratios . . . . . . . . . . . . . . . . . . . . 497
Segment Formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
Enforce Minimal Segment Length . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
Smoothing & Joining . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 498
Segment table output . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499
Mosaicism segment algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499
Limitations in mosaicism segmentations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 499
SNP marker workflow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Signal summarization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Allelic signal computation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Genotyping . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Allelic difference GC correction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Detection of LOH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
Array data QC metrics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501
Median of the Absolute values of all Pairwise Differences (MAPD) . . . . . . . . . . . . . . . . . 501
Waviness SD . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501
SNPQC . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501
ndSNPQC (SNP Quality Control of Normal Diploid Markers) . . . . . . . . . . . . . . . . . . . . . . . 501
ndWavinessSD (Normal Diploid Waviness Standard Deviation) . . . . . . . . . . . . . . . . . . . . . 501
MAPD – Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 502
Effect of MAPD on functional performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 502
Waviness-SD – Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 503
SNPQC – Detailed Description . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 504
Effect of SNPQC on Functional Performance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 505
TuScan algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
Manual re-centering algorithm (OncoScan) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
Copy number effect on somatic mutations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 508
CytoScan XON region calling algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 510

 APPENDIX H Recommended CytoScan XON array workflows . . . . . . . . . . . 511

Whole exome analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511

Recommended workflow for analyzing the whole exome . . . . . . . . . . . . . . . . . . . . . . . . 511
Loading XNCHP file(s) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511
Targeted analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513

Chromosome Analysis Suite (ChAS) User Guide 19

 Introduction
1
The Chromosome Analysis Suite (ChAS) software for cytogenetic analysis enables you to
view and summarize chromosomal aberrations across the genome.
Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss of
heterozygosity (LOH).
ChAS provides tools to:
 Perform single sample analysis of CEL files from CytoScan™ Arrays and OncoScan
Arrays.
 Analyze segment data at different levels of resolution.
 View results data (CYCHP, XNCHP, and OSCHP files) that summarize chromosomal
aberrations in table and graphical formats.
 Display CNCHP data from Genome-Wide Human SNP 6.0 Array.
 Customize and load your own annotations and regions for focused analysis.
 Display ReproSeq Aneuploidy data from Ion Reporter™.
 Apply separate filters to the entire genome and user-specified regions of interest to
remove irrelevant information such as segments in areas that are not of interest.
 Perform detailed comparisons between different samples.
 Directly access external databases such as UCSC Genome Browser, NCBI,
DECIPHER, ClinVar, and ClinGen.
 Export user-selected data in graphical and tabular formats.
 Store and query segment data for streamlined analysis.
 Check for Mendelian Inheritance errors across related samples.
 Combine gene expression and copy number data in both tabular and graphical
formats.
 Export data for viewing in Integrative Genome Viewer (IGV).
 Directly access the TaqMan website for follow up analysis.

IMPORTANT! The results from ChAS are for Research Use Only and not for use in diagnostic
procedures.

Chromosome Analysis Suite is not a secondary analysis package. However, it does create
CYCHP, OSCHP, XNCHP, and tab-delimited text files required for secondary analysis
packages.

Chromosome Analysis Suite (ChAS) User Guide 20

 Chapter 1 Introduction
Features in v4.4 1

Features in v4.4
 Seamless integration with Franklin by Genoox for enhanced sample data
TM TM

interpretation.
 Whole Genome Segmentation Visualization for large copy number abberations on
CytoScan XON arrays.
 Flag Segments to bypass Filter settings.
 Display LOH segments in different colors based on median copy number.
 Ability to filter out LOH segments having a copy number < 2.
 Addition of pHaplo and pTriplo scores.
 Included the ClinGen Curated Regions in a Recurrent/Curated Regions track.
 Download Library Files from the NetAffx Server securely, via https.

About this user guide

This user guide provides step-by-step instructions for performing the procedures required
to use ChAS and can also be accessed from the software by clicking on the top menu
bar’s Help drop-down.
The steps outlining procedures through out this User Guide are frequently supplemented
with screen captures to further illustrate the instructions.
Note: The screens that were captured for this User Guide may not exactly match the
windows displayed on your screen.

Customer support
Visit thermofisher.com/support for the latest in service and support, including:
 Worldwide contact telephone numbers
 Product support, including:
 Product FAQs
 Software, patches, and updates
 Order and web support
 Product documentation, including:
 User guides, manuals, and protocols

Chromosome Analysis Suite (ChAS) User Guide 21

 Installing ChAS
2
ChAS is a stand-alone application that supports the analysis and/or visualization of
the following results data files:
 CytoScan (CYCHP)
 OncoScan (OSCHP)
 CytoScan XON (XNCHP)
 Genome-Wide Human SNP 6.0 (CNCHP)
 ReproSeq Aneuploidy (.zip)
 BED/AED files
 VCF files

IMPORTANT! Due to the amount of memory that ChAS requires to operate, Thermo Fisher
Scientific VERY STRONGLY recommends that you DO NOT install the ChAS software on
instrumentation computers being used for scanning and operating fluidics systems.

Recommended and minimum requirements

Note: The full Database and Browser software must be installed on at least one or
more 64-bit analysis workstations to create results data files.

Table 1 Software

System Properties Recommended System Requirements Minimum System Requirements

Processor 3 GHz (or greater) Pentium Quad 3 GHz (or greater) Pentium Dual Core
Core Processor Processor

64-bit Windows® Operating System Windows 10/11 Windows 10/11

and Web Browser Windows Edge Windows Edge

Available Disk Space 250 GB HD + data storage 150 GB HD + data storage

Free Disk Space Required at > 5 GB > 5 GB

Installation

RAM 32 GB 16 GB

Chromosome Analysis Suite (ChAS) User Guide 22

 Chapter 2 Installing ChAS
Requirements and prerequisites for arrays 2

Table 2 Server

System Properties Recommended System Requirements Minimum System Requirements

Processor 3.1 or 3.3 GHz Quad Core Processor 2.7GHz Quad core processor

Windows Operating System Windows Server 2022 Standard 64-bit Windows Server 2022 Standard 64-bit

Available Disk Space 1 TB HD + data storage 512 GB HD + data storage

Free Disk Space Required at > 5 GB > 5 GB

Installation

RAM >24 GB 16 GB

Requirements and prerequisites for arrays

IMPORTANT! A Windows 64-bit Operating System is required for all array types.

IMPORTANT! Chromosome Analysis Suite requires AGCC 4.3/GCC 6.1 or higher to produce
CytoScan/Oncoscan CEL files.

IMPORTANT! The larger file sizes associated with the CytoScan HD Array should be taken into
account when calculating the necessary free space requirement. A CytoScan HD Array CYCHP file
is ~155 MB. A CytoScan XON Array XNCHP files is ~174MB.

IMPORTANT! The ChAS software has been verified for use on a Windows 64-bit Operating
System. ChAS may work on other Windows Operating Systems, but only the 64-bit version has
been verified.

Zip file contents

Go to thermofisher.com ChAS product page to downloaded the zip files.
To analyze the CytoScan HD array CEL files and visualize the data in ChAS, you must
download the following ChAS v4.4 files:
 CytoScanHD_Array_Analysis_Files_hg19_NA33.r9.zip (and/or)
CytoScanHD_Array_Analysis_Files_hg38_NA36.r6.zip

Before performing an analysis, you must download the appropriate zip file package(s)
listed in the table below.

Chromosome Analysis Suite (ChAS) User Guide 23

 Chapter 2 Installing ChAS
Installing ChAS 2

Table 3 Available Library file packages

Array name hg19 hg38

CytoScan HD CytoScanHD_Array_Analysis_Files_hg19_NA33.r10.zip CytoScanHD_Array_Analysis_Files_hg38_NA36.r7.zip

CytoScan 750K CytoScan750K_Array_Analysis_Files_hg19_NA33.10.zip CytoScan750K_Array_Analysis_Files__hg38_NA36.r7.zip

CytoScan CytoScanOptima_Array_Analysis_Files_hg_19_NA33.r10.zip CytoScanOptima_Array_Analysis_Files_hg_38_NA36.r7.zip

Optima

CytoScan XON CytoScan_XON_Array_Analysis_files_hg19_NA33.r8-Part1.zip CytoScan_XON_Array_Analysis_Files_hg38_NA36.r8-Part1.zip

CytoScan_XON_Array_Analysis_files_hg19_NA33.r8-Part2.zip CytoScan_XON_Array_Analysis_Files_hg38_NA36.r8-Part2.zip

OncoScan CNV OncoScan_Array_Analysis_Files_hg_19_NA33.r9.zip OncoScan_Array_Analysis_Files_hg38_NA36.r7.zip

Plus

OncoScan CNV OncoScan_CNV_Analysis_Files_hg_19_NA33.r7.zip OncoScan_CNV_Analysis_Files_hg38_NA36.r7.zip

CytoScan CytoScan_HTCMA_96_ChAS_Files_hg19.r3.zip CytoScan_HTCMA_96_ChAS_Files_hg38.r3.zip

HTCMA

After downloading and extracting the Chromosome_Analysis_Suite_4.4zip file, a

Chromosome Analysis Suite 4.4 folder appears containing the following files:
 ChAS4.4_setup.exe
 ChAS_4.4_Manual.pdf
 ChAS_4.4_Release_Notes.pdf
 ChASDB_adgv_hg19_Gold.backup
 ChASDB_adgv_hg38_Gold.backup
 ChASDB_adgv_hg19_Gold_HD.backup
 ChASDB_adgv_hg38_Gold_HD.backup
 ChASDB_adgv_hg19_Gold_XON.backup
 ChASDB_adgv_hg38_Gold_XON.backup

Installing ChAS
Note: The installation process also installs additional required components, which
includes Java components and Visual C++ runtime.

New Installation 1. Double click on the ChAS4.4_setup.exe file from the “Chromosome Analysis
Suite 4.4” folder.
The Install Shield Wizard for Chromosome Analysis Suite begins.
2. At the Welcome window, click Next.
The License Agreement window appears.
3. Please read the license agreement carefully, click the “I accept the terms of the
license agreement” radio button, then click Next.
The Setup Type window appears.

Chromosome Analysis Suite (ChAS) User Guide 24

 Chapter 2 Installing ChAS
Installing ChAS 2
4. Click the appropriate drive’s check box, then click Next.
The PostgreSQL Database Server Installation window appears.
Note: Make sure you select a drive with the most available space. Consider 1 GB
of space is required for every 1000 samples you add to the database.
The installer auto-detects and displays a default Port number. It is recommended
that you do not change this number.
5. Click Next.
The Start Copying Files window appears.
6. Click Next, then follow the on-screen instructions to complete the installation.
7. After all software installation is complete, you must download the new Analysis
files from the NetAffx site or copy them into your ChAS Library folder. If you are
unable to connect to the Internet, refer to "Copying analysis files" on page 25.

IMPORTANT! If your Windows Firewall is enabled during the installation of ChAS and you want
to Backup the ChAS Database and Restore it to your local ChAS DB (see "Using a shared ChAS
database while off-line" on page 457) a message may appear indicating that you cannot connect
to the shared folder.

If this message appears, contact your IT department for help in allowing file sharing through the
Windows Firewall.

Upgrade
installation
IMPORTANT! The ChAS 4.4 Installer does NOT support upgrade from previous versions. Due to
an updated version of the ChAS DB, previous versions of ChAS must be uninstalled using add/
remove programs prior to running the ChAS 4.4 installer. Be sure to make a backup of your ChAS
DB prior to uninstalling your previous version of ChAS.

To keep current preferences, see "Exporting and importing preferences" on page 444.

Copying analysis The CytoScan Analysis Library Files zip package download contains the Analysis Files
files required to process their respective CytoScan Array CEL files into CYCHP files.
The OncoScan Analysis Library Files.zip package download contains the Analysis
Files required to process their respective OncoScan Array CEL files into OSCHP files.
The CytoScan XON Analysis Library Files.zip package download contains the Analysis
Files required to process their respective CytoScan XON Array CEL files into XNCHP
files.
Also included in the CytoScan HD Analysis Library Files. zip are the files for
GenomewideSNP_6 files (required in ChAS to view GenomeWideSNP_6 CNCHP
files).
If you are unable to download library files through the software, you can download the
zipped library files from the ChAS product page at www.thermofisher.com, then
extract (unzip) the files into the following location: C:\Affymetrix\ChAS\Library

Chromosome Analysis Suite (ChAS) User Guide 25

 Chapter 2 Installing ChAS
Viewing Hidden Files and Folders 2
Analysis file  Library: C:\Affymetrix\ChAS\Library
locations in  Preference file: C:\ProgramData\Affymetrix\ChAS\preferences.xml
Windows 10  All other user profile related preference files and saved settings:
C:\ProgramData\Affymetrix\ChAS\users

Viewing Hidden Files and Folders

The ChAS preference files may be placed in folders and files that are normally hidden
from the user in Windows.

Displaying hidden 1. At the Windows 10 Desktop, move your mouse to the bottom right of the Task
files and folders in bar (right of the clock).
Windows 10 Five large icons appear.
2. Click on the Settings icon.
3. Click Control Panel.
The Control Panel window opens.
4. Click Appearance and Personalization in Control Panel. Under Folder Option,
click “Show hidden files and folders”.
5. In the Folder Options window that appears, click the View tab. Under Hidden files
and folders, click Show hidden files and folders.
Hidden files and folders are dimmed to indicate they are not typical items. If you
know the name of a hidden file or folder, you can search for it.
6. Click OK.
7. Close all open windows.

Analysis file When you start ChAS for the first time, you will be prompted to:
download 1. Create a user profile. (See "Creating and using user profiles" on page 440)

Note: To process the CytoScan Arrays in AGCC/GCC, you must install the
appropriate library files for AGCC/GCC on the AGCC/GCC workstation (see the
specific array product page at www.thermofisher.com for details).
You can download the ChAS analysis files from NetAffx using either the ChAS
Browser or the Analysis Workflow. The files will be saved into the same folder whether
downloading through the ChAS Browser or the Analysis Workflow.

Downloading ChAS analysis files from NetAffx for use with the ChAS
Browser

1. Start ChAS.

Chromosome Analysis Suite (ChAS) User Guide 26

 Chapter 2 Installing ChAS
Updating NetAffx Genomic Annotation files 2
If no annotations are installed, a Download Annotations notice appears. (Figure 1)

Figure 1 Download Annotations notice

2. Click OK.
The Library File Download Service window opens.
Note: You can also open the Library File Download Service window by selecting
Update Library and Annotation Files from the Help menu.
3. From the Library File Download Service window, click OK to view available Library
Files for download.
4. Select the library and annotation files you want to download.
5. Click Download.
The Download Progress window displays the progress of the downloading and
unpacking of the files.
6. Click OK when the download is complete.
7. The NetAffx Authentication window remains open, click Close when finished
downloading the library files.

Downloading ChAS analysis files from NetAffx using the Analysis Workflow
1. Select Analysis → Perform Analysis Setup.
2. Select Utility Actions → Download library Files.
3. From the Library File Download Service window, click OK to view available Library
Files for download.
4. Select the array type check box(es) for the analysis files that you want to download,
then click Download.

Updating NetAffx Genomic Annotation files

The publicly available annotations in the NetAffx Genomic Annotation file are updated
quarterly. When launching the ChAS Browser or Analysis Workflow, the software will
check for the availability of new NetAffx Genomic Annotation files.
If more current files are available, you will be prompted to download the files from NetAffx
using the instructions from either of the previous two sections.
If you are unable to download from NetAffx through the software, please contact Technical
Support for access to the current NetAffx Genomic Annotation file.

Chromosome Analysis Suite (ChAS) User Guide 27

 Chapter 2 Installing ChAS
Setting up proxy server access 2

Setting up proxy server access

Note: If you do not know what the proxy settings are, contact your IT department.
Follow the steps below if your system has to pass through a Proxy Server before it can
access the NetAffx server.
To change from a Local Disk (C: or D:) Database to a dedicated remote Database
Server, see "Access to a remote ChAS database server from the ChAS browser" on
page 29.

Access to NetAffx 1. Launch the Analysis Workflow by selecting Analysis → Perform Analysis Set
from the analysis Up in the ChAS Browser.
workflow 2. Click Utility Actions → Download Library Files.

The Library File Download Service window appears.

3. Click the Proxy Settings tab. (Figure 2)

4. Click the Enable Custom Proxy Server check box.

5. Enter the Host Address, Port (if not listed), User and Password.

IMPORTANT! This proxy user ID and password is NOT the same ID and password used to
connect to NetAffx.

Figure 2 Proxy Settings window

6. Click Save.

Access to NetAffx 1. From the Help drop-down menu, click Update Library and Annotation Files…
from the ChAS The Library File Download Service window appears.
browser
2. Click the Proxy Settings tab. (Figure 2)
3. Click the Enable Custom Proxy Server check box.
4. Enter the Host Address and Port information, then enter your user name and
password.

Chromosome Analysis Suite (ChAS) User Guide 28

 Chapter 2 Installing ChAS
Uninstalling 2

IMPORTANT! This proxy user ID and password is NOT the same ID and password used to
connect to NetAffx.

5. Click Save.

Access to a 1. From the Preferences drop-down menu, click Edit Application Configuration…
remote ChAS The Configuration window appears. (Figure 3)
database server
from the ChAS Figure 3 Proxy Settings window
browser

2. Click the Use custom proxy button.

3. Contact your IT department for help with entering the Host and Port information.
4. After you have completed the appropriate fields, click OK.

Uninstalling
IMPORTANT! It is strongly recommended you backup your database BEFORE uninstalling
ChAS.

1. From the Windows Start Menu, navigate to the Windows Control Panel,

2. Select Uninstall or change a program.

3. Locate the Chromosome Analysis Suite application, then perform the uninstall as
you normally would.

4. Click OK to acknowledge the message box that warns the ChAS application must be
closed (before removing it).

Chromosome Analysis Suite (ChAS) User Guide 29

 Getting started
3
Starting ChAS
1. Double-click on the Desktop ChAS icon.
The Select User window appears. (Figure 4)

Figure 4 Select User window

2. Use the drop-down button to select a user or click Create New to create a new
user profile. For more information, see "Creating and using user profiles" on page
440.
3. Optional: Click the Manual connection check box. For information on manual
connections, see "Manual or automatic connection mode" on page 408.
4. Click OK.
The Chromosome Analysis Suite application opens. as shown in Figure 5 on
page 31 after logging into the ChAS DB. To login, see "Logging into the ChAS
database" (below).
Note: A message may appear indicating a more current version of the NetAffx
Genomic Annotation file is available for download. To download the newer
version of the file, see "Analysis file download" on page 26. If you are unable to
download the files via the NetAffx dialog, please contact Technical Support for
alternative downloading options.

Chromosome Analysis Suite (ChAS) User Guide 30

 Chapter 3 Getting started
Logging into the ChAS database 3

Logging into the ChAS database

See Chapter 21, "Database tools" on page 447 for steps on how to log into the
ChAS Database.
Note: The ChAS installation automatically generates a default user name (admin)
and password (admin). To change these default passwords and/or create
additional user names, see "Administration" on page 456. Also, your sign in
(login) information is retained throughout a working session, however, if the ChAS
application is closed, then opened again, you must login again.

Figure 5 Chromosome Analysis Suite with CYCHP file loaded

Menu Bar
Tool Bar

Files List

Named Karyoview in
Settings Upper Display Area

Data Types
List

Detail View in
Lower Display Area

Selected chromosome view

The ChAS browser window has the following components:

 Menu Bar - Provides access to the functions of the software.
 Tool Bar - Provides quick access to commonly used functions. Note: Some
features that were previously in the Tool bar (such as Dark/Light Schema) have
been removed, but continue to be available under the View menu item.
 Files List - Shows the data and annotation files that are available for display. See
“Files list” on page 145.
 Data Types List - Displays the type of data available in the files. See “Data types
list” on page 147.
 Named Settings - Displays a list of the previously saved display settings for ChAS.
See “Named settings” on page 148.

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 Status Bar - Displays information on the status of the software, the ChAS Browser
NetAffx Genomic Annotation file version, the hg version, information about the
annotation or probe that the mouse pointer is nearest to in the Detail View, and the
user profile name. See “Status bar” on page 148.
 Display Area - Displays the following data in graphical and table formats:
 CYCHP, CNCHP, XNCHP, OSCHP, RHCHP, and/or ReproSeq Aneuploidy data
 Detected segments
 Region information file data
 Histogram data (representing segments uploaded to the database)
 Reference annotations
For more display area information, see "Viewing data" on page 143.

Analysis workflow module

The Analysis Workflow generates xxCHP files from CEL files and tracks ongoing ChAS
analysis tasks.
You can access the Analysis Workflow at any time by clicking on its icon.

First time setup After installation, you must configure your data paths.
The Analysis Workflow requires the following steps:
1. From the Analysis menu, select Perform Analysis Setup. (Figure 6)

Figure 6 Analysis drop-down menu

The Analysis Workflow Configuration window tab appears. (Figure 7)

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If it does not appear, click Utility Actions → Configuration.

Figure 7 Analysis Workflow Module - Setup example

Assigning an A minimum of two sample paths is recommended.

Input sample 1. Click Add.
path(s)
The Add Input sample files window appears. (Figure 8)

Figure 8 Add Input sample files window

2. Click the Up one level button to navigate to the recommended C:\Users

directory, then click the Create new folder button to label a new input sample
folder.
(Example: C:\Users\YourUserName\CytoScan Data)
3. Repeat Step 2 to create a second input folder in an easy to access area.
(Example: C:\Users\YourUserName\Collaborator_OncoScan Data)

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Assigning an 1. Click the Browse button.
Output results A good practice is to navigate to your current ChAS data folder location, then
path click Create New Folder to create an output results path folder inside this folder.
(Example: C:\Users\YourUserName\CytoScan Data\CytoScan_Results_Files)
2. Click Save.

Assigning a 1. Click the Browse button, then navigate to a folder in which to store the QC
Central QC history file. (Example: C:\Cytoscan_data\)
history path 2. Click Create New Folder to create a central QC history path folder. (Example:
QC_History)

File types and data organization in ChAS

To fully use the capabilities of ChAS, you need to understand the ChAS file types and
data organization in ChAS.

ChAS file types ChAS uses the following types of files:

 Data files
 Region Information files
 Support files

File Types Supported in ChAS

Some data files that ChAS uses are generated by other Thermo Fisher Scientific
software, as shown in Table 4.
Table 4 Supported file types
File Type Created In ChAS…
Sample file (ARR) AGCC/GCC Uses this information to associate sample attribute information with CEL and
xxCHP or CNCHP files.
Intensity Data file (CEL) AGCC/GCC Analyzes the intensity data in the CEL file, then generates a xxCHP files.
Note: A 64-bit system is required to analyze intensity data.
Analysis Results (CYCHP) ChAS Displays results in graphical and tabular formats.
CytoScan array: CYCHP
contains copy number, LOH,
mosaicism, and genotype call
information
Analysis Results (RHCHP from RHAS Displays results in graphical and tabular formats.
HTCMA) contains copy
number, LOH, Carrier Variant,
and SMN results
Analysis Results (OSCHP) ChAS Displays the probe-level analysis, segment level data, and somatic mutation
OncoScan FFPE and data.
OncoScan_CNV arrays,
OSCHP contains copy
number/LOH and somatic
mutation information (FFPE
Assay only)

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Table 4 Supported file types
File Type Created In ChAS…
Analysis Results (XNCHP) ChAS Displays probe-level analysis, segment level data in graphical and tabular
CytoScan XON array: XNCHP formats.
contains LOH, Exon Region,
and Genotype information.
Analysis Results (CNCHP) GTC Displays probe-level analysis data and generates segment data on-the-fly.
GenomeWide SNP 6.0 array
contains copy number and
LOH segments
CHP Change Archive ChAS Stores user-annotated segment and sample annotations as well as
(CHPCAR) modifications made to the segment data.
Analysis Results (.zip) ION Reporter Displays copy number segment data and sequence tile information.
ReproSeq Aneuploidy
contains copy number and
tiling information
Region Information File (BED ChAS or Text Allows users to display their own custom data and optionally use the
or AED) Editor information to define CytoRegions or an Overlap Map. ChAS can export data
in BED format for use with the UCSC Browser and other programs which
understand this format.
Tab-separated values (TSV, ChAS Exports data in this format for use in a spreadsheet program or other user-
TXT, and DOCX) defined uses. This format is for export only. ChAS does not import TSV or
TXT files.
VCF Files Other Allows users to view genotype and indel data in the Detail View.
software
packages

Region information files

The region information files in Browser Extensible Data (BED) and Affymetrix
Extensible Data (AED) format provide lists of regions in the genome with position
information and other annotations. To open a BED or AED file, click the button or
select File → Open on the menu bar. All BED or AED files that are opened during a
session will reload when you start a new session with the same user profile.
Note: You can use the reference annotations to provide region information or use the
Export feature to export data in existing BED files to an AED file. See "Exporting
information in AED or BED format" on page 318.

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Analysis and
visualization
library files
IMPORTANT! Every feature in ChAS requires support files.

 Array-type specific Library file sets with files for running Copy Number/LOH/Mosaicism
analysis and Reference Creation workflows (Analysis files)
 Files for visualizing and exporting data from xxCHP results data files.
 Reference Annotation files
 Browser Annotation files are named using the following format:
<NetAffxGenomicAnnotations.Homo_sapiens.hgXX.naYYYYMMDD.db>

Data organization ChAS enables you to keep your CEL and Analysis Results files in any folder on your
in ChAS computer. As long as you know where the files are, you can load them from anywhere and
move them around at your convenience.

IMPORTANT! It is recommended that you perform analysis operations with all analysis files
stored on a local disk drive.

Basic workflow for cytogenetics analysis

Note: xxCHP is used when referring to CYCHP, CNCHP, XNCHP, and OSCHP files.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

ChAS can be used to:

 Perform probe-level analysis of CEL file data for CytoScan and OncoScan Arrays.
 Display probe-level analysis data (xxCHP) from:
 CytoScan arrays (CYCHP)
 Genome-Wide Human SNP array 6.0 (CNCHP)
 OncoScan arrays (OSCHP)
 CytoScan XON arrays (XNCHP)
 CytoScan HTCMA arrays (RHCHP)
Note: There are some differences in the way the ChAS handles these different types
of arrays and how it treats the data from these four types of files. The basic
cytogenetic analysis workflow includes the following steps:
 "Array processing workflow (using instrument control software)" on page 37.
 "Probe-level Analysis of CEL file data" on page 37.
 For CytoScan arrays, this analysis is performed in CHAS and produces CYCHP or
XNCHP files depending on array type. See "CN/LOH/Mosaicism analysis" on page
44.

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 For CytoScan HTCMA arrays, analysis is performed in the RHAS and produces
RHCHP files.
 For the Genome-Wide Human SNP Array 6.0, this analysis is performed in
Genotyping Console (GTC) software and produces CNCHP files. For more details,
please refer to the GTC User Guide.
 For the OncoScan files, this analysis can be performed in ChAS and produces
OSCHP files.
 "Viewing data and features of interest using the ChAS display controls" on page 41.

Array processing Array processing is performed in AGCC 4.1.2/GCC 5.0 or higher for the CytoScan Arrays,
workflow (using OncoScan Arrays, and Genome-Wide Human SNP 6.0 Array.
instrument Note: You need to have the appropriate library files installed on the instrument control
control software) workstation to perform these analyses for the different array types.

The array processing includes the following steps:

1. Registering samples and arrays.
2. Washing and staining the arrays.
3. Scanning arrays and generating intensity (CEL) file data.
The following file types are produced:
 Sample (ARR files)
 DAT Files
 CEL Files
 Audit
 JPG
See the Instrument Control Console Users Guide for more information.

Probe-level Copy number data is handled differently from genome-wide genotyping data in this step.
Analysis of CEL Note: You need to have the appropriate ChAS library files installed to perform these
file data analyses for different array types. A 64-bit system is required to analyze CytoScan CEL
files.

 For CytoScan arrays, this analysis is performed in ChAS and produces CYCHP or
XNCHP files (depending on array type) and contain the data shown in Table 5. See
“CN/LOH/Mosaicism analysis” on page 44.
 For CytoScan HTCMA arrays, the analysis is performed in the RHAS which produces
a RHCHP file for viewing in ChAS.
 Genome-Wide Human SNP Array 6.0 Data: The probe level analysis on CEL file data is
performed in GTC and produces the CNCHP file data types shown in Table 5. See the
GTC User Guide for more information.

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 For OncoScan Data: The probe level analysis on CEL file data is performed in ChAS
and produces the OSCHP file data types show in Table 5.

Table 5
Analysis Results *

CytoScan Genome-Wide OncoScan 3 CytoScan

Array 1 Human SNP XON 4
Array 6.0 2
Graph Data for the individual CN and SNP probes
Copy Number State Yes Yes Yes No
Log2 Ratio Yes Yes Yes Yes
Weighted Log2 Ratio Yes No Yes Yes
LOH Yes Yes Yes Yes
Allele Difference Yes Yes Yes Yes
Genotype Calls Yes No No Yes
Smooth Signal Yes Yes Yes Yes
Variant Data No No Yes No
(CNV Plus only)
B-allele Frequency Yes No Yes Yes
Segment data
Gain and Loss segments based on runs of aberrant Yes Yes Yes Yes
Copy Number State data
Mosaic Gain and Loss segments of non-integer Copy Yes No No No
Number States between CN=1 and CN=3
LOH (Loss of Heterozygosity) based on runs of SNPs Yes Yes Yes Yes
where heterozygote calls are absent
Exon Region Gain and Loss segments No No No Yes

* CYCHP for CytoScan, CNCHP for Genome-Wide Human SNP 6.0 Array, XNCHP for CytoScan XON
Array, and OSCHP for OncoScan Array.
1) For more details on CytoScan Array data, see Table 14 on page 175.
2) For more details on Genome-Wide SNP Array 6.0 data, see Table 17 on page 178.
3) For more details on OncoScan FFPE Assay Data, see Table 18 on page 178.
4) For more details on CytoScan XON array data, see Table 16 on page 177.

Note: Segment types drawn with flat ends (Gain and Loss) are the result of algorithms
which can ascertain precise marker-to-marker breakpoints. Segment Types drawn with
rounded ends (LOH, GainMosaic, LossMosaic) are the output of algorithms which closely
approximate breakpoints based on the data.)

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Loading data into You perform the same steps for the different types of analysis data (CYCHP, CNCHP,
ChAS for display XNCHP, OSCHP and .zip (ReproSeq Aneuploidy), but ChAS handles these types of data
differently.

CytoScan array (CYCHP files)

When loading CYCHP files into ChAS for viewing, the software:
1. Selects the segments in the CYCHP file to display as segments.
2. Applies any smoothing or joining that would alter the length and other properties of
segments.
3. Displays the segments and graph data:
 Segment Data
• Copy Number Gain/Loss
• Loss of Heterozygosity (LOH)
• Mosaic Gain/Loss
 Graph Data
• Copy Number State
• Log2 Ratio
• Weighted Log2 Ratio
• Smooth Signal
• Loss of Heterozygosity (LOH)
• Allele Difference
• B-allele Frequency
• Genotype calls

CytoScan XON array (XNCHP files)

When loading XNCHP files into ChAS for viewing the software:
1. Selects the segments in the XNCHP file to display as segments.
2. Displays the segments and graph data:
 Segment Data
• Loss of Heterozygosity
• XON Region Gain/Loss
• Whole Genome Gain/Loss Segments
 Graph Data
• Log2 Ratio
• Weighted Log 2 Ratio
• Smooth Signal
• Loss of Heterozygosity (LOH)
• Allele Difference
• B-allele Frequency (BAF)
• Genotype Calls

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CytoScan HTCMA array (RHCHP files)
When loading RHCHP files into ChAS for viewing, the software:
1. Selects the segments in the RHCHP file to display as segments.
2. Displays the segments and graph data:
 Segment Data
• Copy Number Gain/Loss
• Loss of Heterozygosity (LOH)
 Graph Data
• Copy Number State
• Log2 Ratio
• Smooth Signal
• Loss of Heterozygosity (LOH)
• Allele Difference
• B-allele Frequency
• Variant Data

Genome-wide SNP array 6.0 (CNCHP files)

When loading CNCHP files into ChAS for viewing, the software:
1. Performs segment generation by analyzing the CN and LOH graph data in the
CNCHP file.
2. Applies any smoothing or joining that would alter the length and other properties of
Copy Number segments.
In GTC software, these steps were performed in the Segment Reporting Tool.
3. Displays the segments and graph data:
 Segment data
• Copy Number Gain/Loss
• Loss of Heterozygosity (LOH)
 Graph Data
• Copy Number State
• Log2 Ratio
• Allele Difference
• SmoothSignal
• Loss of Heterozygosity (LOH)

OncoScan array (OSCHP files)

When loading OSCHP files into ChAS for viewing, the software:
1. Selects the segments in the OSCHP file to display as segments.
2. Displays the segments and graph data:
 Segment data
• Copy Number Gain/Loss
• Loss of Heterozygosity

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 Graph Data
• Copy Number State
• Log2 Ratio
• Weighted Log2 Ratio
• Allele Difference
• B-allele frequency
• Smooth Signal
• Loss of Heterozygosity
• Variants/Somatic Mutations (OncoScan CNV Plus only)

ReproSeq When loading zip files from Ion Reporter into ChAS for viewing, the software displays
aneuploidy (zip the following segments and graph data:
files)  Segment data
 Copy Number Gain/Loss
 Graph Data
 Copy Number State (sequence tiles)

Viewing data and ChAS provides the following options for viewing and studying your loaded analysis
features of results data:
interest using the  Graphic Displays
ChAS display
See “Displaying data in graphic views” on page 152.
controls
 Tables
See “Displaying data in table views” on page 327.
After the data is loaded, you can:
 Filter the segments by Segment Parameters to hide segments that do not meet
your requirements for significance. mSee “Filtering segments” on page 217.
 Select a region information file for use as a CytoRegion file and:
 Perform differential filtering for segments in CytoRegions and in the rest of the
genome. See “Using CytoRegions” on page 267.
 Display only segments that appear in CytoRegions using Restricted Mode.
 Query segments from a loaded sample against segments previously uploaded to
a ChAS Database. See "Querying a segment from the segment table" on page 392.
 See which samples had segments similar to the current sample.
 View the Calls and Interpretations of previous segments to help in the analysis
of the current sample.
 Select a region information file for use as an Overlap Map and use the Overlap filter
to identify or conceal segments that appear in the Overlap Map regions. See
“Using the overlap map and filter” on page 279.
 Add selected features of the genome to new or existing Region (AED) files, and edit
annotation data on existing annotations. (To open a BED or AED file, click the
button or select File → Open on the menu bar.) See “Creating and editing AED
files” on page 287.

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 View genotype data from Next Generation Sequencing data via VCF files. See
“VCF files” on page 322.
 Prepare reports on your findings by exporting graphics and table data in PDF and
other formats. See “Exporting results” on page 415.
 Save setups of ChAS for different tasks in user profiles and named settings. See
“User profiles and named settings” on page 438.

Working with ChAS

Accessing Commands in ChAS can be accessed in the following ways:

functions in ChAS  Main menus
 Tool bar
 Right-click menu options in:
 Files List
 Data Types List
 Karyoview
 Selected Chromosome View
 Detail View
 Table Headers

Changing pane Do one of the following to change the size of the panes in the ChAS window, as shown
sizes in Figure 9 on page 43.
 Click and drag the dividers between panes.
 Click the arrows in the dividers ( or ) to hide or maximize an entire pane.

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Figure 9 Resize or show/hide panes

Click arrows to
show/hide a pane

Click, then drag a divider

bar to resize a pane

Opening panes in You can display a pane in a separate window by clicking the icon on the tab. To
separate close the window and return the information to the tab panel, click the icon in the
windows window.

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4
ChAS analyzes the intensity data (CEL file) from both CytoScan and OncoScan Arrays.
The software performs a single sample analysis which compares the data in a CEL file
to a previously created reference file, using analysis parameters specified in the
.chasparam file. The analysis generates a CYCHP/XNCHP/OSCHP data file that you
load and view in ChAS. The analysis detects segments that exhibit are as follows:
 Copy Number State Gain or Loss: Regions of integer copy number gain or integer
copy number loss.
 Mosaic Gain and Loss (CytoScan HD, CytoScan 750k and CytoScan Optima
only): Regions of non-integer copy number gain or loss (CN states between 1 and
3).
 XON Region Gain and Loss (CytoScan XON only): Regions of gain or loss at the
exon level.
Note: The mosaicism segmentation analysis is currently only available for CytoScan
Array CEL files. However, xxCHP files for the other array types contain the
SmoothSignal data type which displays non-integer copy number changes.
 Loss of Heterozygosity (LOH): Regions where the preponderance of SNPs do not
display heterozygosity.
For more details on loading and viewing CHP data, see "Loading data" on page 118.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

Note: Reference files are provided as part of the complete Library file packages. You
can also create your own reference file using ChAS.
Load Genome-Wide Human SNP Array 6.0 CNCHP into ChAS to display and detect
Copy Number and Loss of Heterozygosity segments. See "Loading data" on page
118.
Load CytoScan HTCMA Array RHCHP into ChAS to display and detect Copy Number
segments, Loss of Heterozygosity segments, variant data, and SMN data. See
"Loading data" on page 118.

IMPORTANT! It is recommended to perform analysis operations with all associated analysis files
in a locally stored folder(s).

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Single sample analysis 4

Single sample analysis

Single Sample Analysis compares the values in one or more user-selected CEL files with
the values in a reference file that is created from a set of sample files. You can use the
included default reference file or create your own (For more details, see "Creating a
reference file" on page 90)

ChAS analysis file Table 6 lists the compatibility between ChAS Analysis file versions for the CytoScan
compatibility Arrays.
Note: ChAS automatically prevents you from selecting an incompatible analysis file
version for analysis or when viewing analysis results.

Table 6 Compatibility table

CytoScan Array ChAS ChAS ChAS ChAS ChAS ChAS

Analysis File Set 4.4 4.3 4.2.1 4.2 4.1 4.0
Version

NA36 (hg38) Yes Yes Yes Yes Yes Yes

NA36 (hg19) Yes Yes Yes Yes Yes Yes

NA33(hg19) Yes Yes Yes Yes Yes Yes

NA32.3(hg19) No No No No No No

NA32.1(hg19) No No No No No No

NA32(hg19) No No No No No No

Note: Refer to the ChAS Release Notes for data equivalency information between the
ChAS software and the Library file versions used to create CHP files.

Introduction to Single sample analysis requires:

single sample  ChAS analysis files for the array. See "Analysis file download" on page 26.
analysis
 A previously created reference model file
You can use the included reference model file or create one using your own CEL file
data and the Reference File creation function. The Reference Model file in the
CytoScan Array set includes 380 microarrays which were run as part of a larger set
of microarrays by nine operators processing ~48 unique samples in two rounds each,
with randomization of the placement of sample DNAs across the PCR plates and
randomization of the reagents and instruments used. The source DNA includes:
 284 HapMap samples including at least one replicate of each of 270 HapMap
samples: 90 from each of the Yoruban, Asian, and Caucasian ethnic groups, from
cell-line derived DNAs from the Coriell Institute of Medical Research.
 96 DNA samples from blood of phenotypically healthy male and female individuals
obtained from BioServe Biotechnologies.
 CEL file data
During the analysis, ChAS generates CYCHP files with:

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 Graph Data
 Copy Number State
 Log2 Ratio
 Weighted Log2 Ratio
 LOH
 Allele Difference
 Smooth Signal
 Genotype Calls
 B-allele Frequency
 Segment Data
 Copy Number Gain/Loss
 Mosaicism Gain/Loss
 Loss of Heterozygosity (LOH)
The CYCHP files can be loaded into ChAS for viewing and study.
Figure 10 on page 47 shows an overview of single sample analysis for the CytoScan
Array.

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Single sample analysis 4

Figure 10 CytoScan Single Sample Analysis workflow example

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Copy number segments on the X and Y chromosomes

The expected copy number state on the X chromosome in normal males is not
constant over its entire length. This is due to the structure of the sex chromosomes,
and the fact that they share extensive homology with each other only in the Pseudo
Autosomal Regions (PARs) that they each have at either end. PAR1 is at the top of the
p-arm and PAR2 at the bottom of the q-arm.
Markers occurring in the PAR regions are mapped exclusively to the X Chromosome.
Therefore, in normal males the PAR regions of the X are expected to be CN=2 (probes
on the X and Y contribute to the signal), while the rest of the Chr X is expected CN=1
for normal males. As a result, we treat the two X PARs in males as independent units
(CN=2 expected) from the rest of the X chromosome (CN=1 in males) when generating
Copy Number Segments.
Aberrant segments that cross PAR/non-PAR boundaries may be normalized into one
segment if they have equivalent type (Gain or Loss) and CN State. During this
normalization process, ChAS will not combine an aberrant (Gain or Loss) segment
with a normal segment across PAR/non-PAR boundaries, even if they have the same
CN State. If smoothing is subsequently applied, aberrant segments with different copy
number state may be combined. If joining is subsequently applied, aberrant segments
separated by a non-aberrant segment may be combined.
Because only Y-specific probes are mapped to the Y chromosome, the expected
state of the entire Y chromosome is 1 for males and is 0 for females.

Mosaic copy number segments on the X chromosome

The expected copy number state on the X chromosome in normal males is not
constant over its entire length. This is due to the structure of the sex chromosomes
and the fact that they share extensive homology with each other only in the Pseudo
Autosomal Regions (PARs) that they each have at either end. PAR1 is at the top of the
p-arm and PAR2 at the bottom of the q-arm.
Markers occurring in the PAR regions are mapped exclusively to the X Chromosome.
Therefore, in normal males the PAR regions of the X are expected to be CN=2 (probes
on the X and Y contribute to the signal), while the rest of the Chr X is expected CN=1
for normal males.
Mosaic Segments whose boundaries start and end entirely in one of the PAR regions
will use CN=2 as normal to determine the type (GainMosaic or LossMosaic) of Mosaic
segment to draw.
Because the Mosaicism algorithm can generate segments which cross the PAR
boundaries, Mosaic Segments that touch the non-PAR region of the X chromosome
use the gender call of the sample to determine the Type of Mosaic segment to draw.
Because only Y-specific probes are mapped to the Y chromosome, the expected
state of the entire Y chromosome is 1 for males and is 0 for females.

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LOH segments on CytoScan arrays
X and Y
For normal XY male samples, the X chromosome will have single-copy based LOH
chromosomes calls (CN = 1). Male samples with more than one X chromosome (for example, XXY)
may have LOH calls on the X chromosome, depending on the constitution of the X
chromosomes’ origins.
The tables below briefly describe how the array-specific algorithms call LOH
segments for the X or Y chromosome.

Table 7 Expected LOH calls on the X and Y chromosomes for the CytoScan arrays

LOH Segments X Chromosome Y Chromosome

Normal male sample (XY) LOH calls that are single copy-based LOH
call (CN = 1).

Male sample with multiple X LOH calls are possible, depending on the
chromosomes (for example, XXY) constitution of the X chromosomes’ origins.
No LOH calls are made for the Y
Normal female sample (XX) LOH calls are possible, depending on the chromosome. Genotype calling is not
constitution of the X chromosomes’ origins. performed on the Y chromosome.

Female sample with a single X LOH calls on X regions which have only a
chromosome (X0) single copy. Heterozygous SNP genotypes
are possible, but are due to the low inherent
Heterozygote call error rate noise, not the
true presence of two alleles.

Table 8 Expected LOH calls on the X and Y chromosomes for the Genome-Wide Human SNP Array 6.0

LOH Segments X Chromosome Y Chromosome

Normal male sample (XY) LOH calls on the non-PAR region of the X
chromosome resulting from “forced”
homozygote-only calls due to the presence
of the Y chromosome.

Heterozygous calls are ignored on the X

chromosome in males. LOH calls that are due to single copy
genotyping calls (CN = 1).
Male sample with multiple X LOH calls are possible, depending on the
chromosomes (for example, XXY) constitution of the X chromosomes’ origins.

SNP genotypes are not constrained to

homozygous calls.

Heterozygous calls are ignored on the X

chromosome in males.

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Table 8 Expected LOH calls on the X and Y chromosomes for the Genome-Wide Human SNP Array 6.0

LOH Segments X Chromosome Y Chromosome

Normal female sample (XX) LOH calls are possible, depending on the
constitution of the X chromosomes’ origins. LOH analysis is not performed on the Y
chromosome since it is assumed that
Female sample with a single X LOH calls on X regions with only a single
there not substantial Y chromosomal
chromosome (X0) copy. Heterozygous SNP genotypes are
possible, but are due to the low inherent Female sample with a single X material.
Heterozygote call error rate noise, not the
true presence of two alleles.

Table 9 Expected LOH calls on the X and Y chromosomes for the OncoScan arrays

LOH Segments X Chromosome Y Chromosome

Normal male sample (XY) LOH calls that are single copy-based LOH
call (CN = 1).

Male sample with multiple X LOH calls are possible where there is either
chromosomes (for example, XXY) loss or low heterozygosity.
No LOH calls are made for the Y
Normal female sample (XX) LOH calls are possible depending on the chromosome.
constitution of the X origins or in regions of
either loss or low heterozygosity.

Female sample with a single X LOH regions on X which have only a single
chromosome (X0) copy. Will be called LOH where there is
single copy X.

Performing a single sample analysis

You only need to perform the following steps once, as the data and selections you
input (throughout this section) are retained for your convenience with future single
sample analysis runs.

Setting up and Note: If you want to setup and run an OncoScan Analysis, see "Setting up and running
running a single an OncoScan single sample analysis" on page 67. If your samples are cancer samples
sample analysis and you suspect aberrations for at least 50% of the genome, then running a Normal
Diploid Analysis is recommended. For more information, see "Setting up and running
a normal diploid analysis" on page 65.
1. From the Analysis menu, select Perform Analysis Setup. (Figure 11)

Figure 11 Analysis drop-down menu

The Analysis Setup window tab opens. (Figure 12)

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]

Figure 12 Analysis Workflow

2. From the Select array type drop-down list, click to select CytoScan array type.
(Example: CytoScanHD_Array)

Note: Once you select the array type, analysis workflow, and reference model file,
then the annotation file will be auto selected for you based on your earlier selections.
The Select array type drop-down list includes only the array types for which library
(analysis) files have been downloaded from NetAffx or copied from the Library
package provided with the installation.

3. Choose a Genome Build. (Example: hg38)

4. From the Select analysis workflow drop-down list, click to select an analysis
workflow. (Example CytoScanHD_Array Single Sample Analysis: NA33 or higher)
5. By default, the Set workflow name is Workflow. Click inside the Workflow’s
(upper right) text box to enter a different workflow name.
6. From the Select the reference model file for the analysis drop-down list, click
to select a reference model file for the analysis. (Example:
CytoScanHD_Array.na33.r2.REF_MODEL or higher).
Note: For Single Sample Analysis, the Annotation to be used for analysis field
is auto-populated and set with the annotation filename used when the reference
model file was generated.
7. At the Select the intensity (CEL) file(s) to analyze pane, click Add.

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Note: The Workflow Analysis window retains the drop-down selections used in your
last submitted analysis. However, it does not display a previously set workflow name,
CEL files to analyze list, or any suffix used to append your last analysis results. These
three fields must be completed again.
The following window appears: (Figure 13)

Figure 13 CEL file folder

8. If your CEL files are located somewhere other than your input path location, navigate
to the desired folder. Single click, Ctrl click, Shift click or Ctrl a (to select multiple CEL
files).
9. Click Open.
The Select the intensity (CEL) file(s) to analyze pane is now populated with your
CEL files, as shown in Figure 14.
Note: You can load several CEL files at a time for a Single Sample Analysis.

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Figure 14 Select the intensity (CEL) file(s) to analyze pane

To remove a CEL file from this list, click to highlight it, then click Remove.

10. At the Output result information pane, confirm the path shown for your output
...
file folder. To change the current path/folder, click button to select a different
output path/folder.
Note: To better organize your output results, you can add sub-folders to your
assigned output result path/folder.

Adding sub-folders to your assigned result path/folder

 Click the
... button to return to your assigned output path and/or folder.

 Click Create New Folder.

 Enter a sub-folder name.
 Click OK. Repeat the above steps to add more sub-folders.

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The newly created sub-folders now appear in the output result information
window. (Figure 15)

Figure 15 Output result information window with sub-folders example

11. If you are using a previously analyzed CEL file(s) to verify new CHP data (against
CHP data generated from previous versions of ChAS and Library files), you may
want to use a suffix to append the new resulting CHP file(s). To do this, click
inside the Select a suffix to append to the analysis results field to enter an
appending file suffix. (Figure 16)

IMPORTANT! If you are saving the same .CYCHP file into the same output file folder that
contains your originally run CYCHP file, a “1” is automatically added into the filename (in
addition to any suffix you may add) to differentiate the two runs of identical CEL file names.
Example: na33(1).cyhd.cychp

Figure 16 Adding a suffix

12. Optional: If you have a CEL file(s) in which the Y chromosome is partially/fully
deleted and therefore determined to be female by the gender calling algorithm,
go to the Analysis Setup’s Optional pane (Figure 17), click the Set Gender
Manually check box, then click to select the appropriate radio button.

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Figure 17 Set Gender option

13. Optional: If you want to have an automatic export of the Karyoview, Segments
Table, and Detail View for Copy Number and LOH Segments in the CHP file, click
the check box Generate a Results Summary File, then and select the output
format of either PDF or DOCX. (Figure 18)
Note: You can assign a CytoRegion and Overlap Map region file that will
highlight these regions in the export. The export is placed in the same folder as
the CYCHP file. This automatic export feature is only available for CytoScan
arrays.

Figure 18 Results Summary File

14. Click Submit.

If the following warning message appears (Figure 19), acknowledge it, then click
OK.

Figure 19 CEL warning message

The Workflow dashboard window appears and your annotation files begin to
load. (Figure 20).

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The Analysis Workflow Dashboard tracks ongoing analysis tasks for ChAS. It also
delivers the results of the analyses and can restart the Browser (if it was shut
down to free up memory for the analysis).

Figure 20 CEL files loading inside the Workflow dashboard

After loading is complete, a Workflow completed successfully message appears.

(Figure 21)

Figure 21 Workflow Dashboard example with multiple Single Samples loaded

Note: The View Logs button will access the algorithm pipeline logs which may
be useful if you have a Workflow that fails to complete.

15. Click to choose the analysis you want to view, then click View Results List.
The QC Results tab window appears showing the Basic View QC settings. A
Detail View QC setting, which provides more columns of data, is also available in
the QC Settings drop-down list. (Figure 22)
Note: QC parameters can also be viewed in the ChAS Browser see setting QC
parameters in ChAS Browser.

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Figure 22 QC Results window tab

16. Click each sample's check box or click the 'Select All' button to select all
samples.

Creating your own custom QC setting

1. Click on the Edit or Create QC Settings button.

The New QC Setting window appears. (Figure 23)

Figure 23 New QC Setting window

2. Click Add Threshold (Figure 23) to create a new row.

3. Select the threshold you want to view in your custom QC Setting.
Note: The threshold metric you select is not required to have a threshold value.

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4. Name your custom QC settings. (Example: My Custom Settings) (Figure 23),
then click Save.
Your custom QC Setting is now available from the QC Settings drop down menu,
as shown in Figure 24.

Figure 24 New QC Settings menu item

Viewing results in the browser

At the QC Results window, click the View in Browser button or the View in MSV
button. For more MSV information, see the RHAS User Guide.
If the following warning message appears (Figure 25), acknowledge it, then click
OK.

Figure 25 Recommended maximum exceeded message

If the following warning message appears (Figure 26), acknowledge it, then click
OK.

Figure 26 Duplicated files message

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If the following warning message appears (Figure 27), click Yes to acknowledge
it.

Figure 27 NetAffx versions message

A progress bar appears. (Figure 28)

Figure 28 Progress bar

Note: The ChAS Browser allows for loading of xxCHP files analyzed from
different versions of ChAS. However, xxCHP files analyzed from different
genome versions (hg18, hg19, hg38) cannot be loaded at the same time.

After a few moments, the ChAS browser featuring your selected samples
appears. (Figure 29)

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Figure 29 ChAS browser

Recentering Due to the complexity and low diploid count in a small fraction of cancer samples,
CytoScan HD, there may be a need to manually assign the diploid region of the sample or recenter it.
750K and Optima In Figure 30, Chromosome 1 is called as a mosaic copy number loss, the log 2 ratio
arrays data is shifted downward, the smooth signal averages 1.75 copies, but the Allele
Difference (AD) and B- Allele Frequency (BAF) Graphs are displaying three tracks.
Note: Since it is unlikely to have three tracks in AD/BAF data in a region of loss (unless
the loss is CN=0), this sample needs to be recentered.

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Figure 30 Need for re-centering example

If the region that is true diploid is a whole chromosome, use Method 1. If the region
that is true diploid is part of a chromosome, use Method 2.

Method 1 Determining the median Log 2 ratio for the region in the sample that is truly
diploid

1. Open the ChAS Browser.

2. Click on the Chromosome Summary Data tab, then click the drop-down to
select MedianSignal. (Figure 31)

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Figure 31 Chromosome Summary tab - median log2 ratio value for Chromosome 16
example

Method 2 Determining the median Log 2 ratio for the region in the sample that is truly
diploid

1. Open the ChAS Browser.

2. In the Detail View (Figure 30), zoom into the region determined to be diploid.
3. Go to the Graphs tab, then click to include only the selected view.
4. Highlight the Log2 Ratio column, then right-click to select Sum, mean and
median. (Figure 32)

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Figure 32 Graphs tab - Log 2 Ratio column

A Sum, mean and median window appears. (Figure 33)

Figure 33 Sum, mean and median message

5. Acknowledge the message, then click OK.

6. In the Analysis Workflow, set up the CEL file in the Single Sample Workflow, as
described in "Performing a single sample analysis" on page 50.
7. Check the Use Manual Recentering check box to enable the parameter fields,
then enter the value of the median Log2 (determined by the browser) into the
Adjust this log 2 to 0 text field. (Optional) Enter a suffix. Note: A suffix is
recommended in order to differentiate the re-centered CYCHP file from the
original.

Figure 34 Use Manual Recentering check

box

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8. Click Submit.
Note: By entering a median Log2 Ratio value (for the region you have determined
to be diploid, The Recentering Algorithm has re-centered the log2 ratio data (for
the region determined to be diploid) around 0 and there is no longer a mosaic loss
segment called in this region, as shown in the Chromosome 1 example below.
(Figure 35)

Figure 35 Re-centered Chromosome 1 example

No gender single The No Gender Single Sample Analysis (Figure 36) is the same analysis as
sample analysis described previously for Single Sample Analysis with the exception that no
gender information is displayed in ChAS. The gender will not be reported and no
segment or probe level data from X or Y chromosomes are displayed.
The metric, Sex Chromosomes Aberrated can be added to the QC table and
reports either a Yes or No.
 Yes: Indicates that the sample does have segments meeting the following
default thresholds: 50 Markers/200kb for copy number and 50 Markers/
10,000kb for LOH segments.
 No: Indicates no copy number or LOH segments meet the previously defined
thresholds.

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Figure 36 No gender workflow

Setting up and The Normal Diploid Analysis for CytoScan is recommended for cancer samples
running a normal in which >50% of the genome is likely to be rearranged. This analysis will
diploid analysis automatically determine the normal diploid regions and normalize the rest of the
sample based on those regions resulting in properly centered data.
A Normal Diploid Analysis has the identical setup steps as "Setting up and
running a single sample analysis" on page 50. The only difference is you must
select Normal Diploid Analysis from the Select analysis workflow drop-down
menu, as shown in Figure 37.

Figure 37 Normal Diploid Analysis

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Figure 38 Example: Sample with and without a Normal Diploid Analysis

The data shown above is from a cancer sample in which >50% of the genome was non-diploid. The top
graph (purple) shows the sample run through the traditional single sample analysis. There are no Copy Num-
ber Segments called, the weighted log2 is centered around 0, but there are 4 allele difference tracks indi-
cating more than two copies of this chromosome. In the bottom graph (pink), this same sample is run
through the Normal Diploid normalization algorithm. The Copy Number Gain segment is called, the weighted
log2 is shifted above the 0 line which is in agreement with the four allele difference tracks.

Recommended QC metrics for Normal Diploid Analysis

 ndSNPQC
 MAPD
 ndwavinessSD
 SNPQC
 wavinessSD

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Viewing the recommended QC metrics (listed above)

Note: For samples run through the Normal Diploid Analysis, the following QC metrics
are recommended:
 MAPD < 0.25
 SNPQC or ndSNPQC >= 15
 wavinessSD or ndwavinessSD < 0.12
1. From the Analysis Workflow, click the QC Results window tab.
2. Click the Settings drop-down menu, then select NDN View.r1, as shown in
Figure 39.

Figure 39 NDN View.r1 from the Setting drop-down menu

Setting up and 1. From the Analysis menu, select Perform Analysis Setup. (Figure 40)
running an
OncoScan single Figure 40 Analysis drop-down menu
sample analysis

The Analysis Setup window tab opens. (Figure 41)

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Figure 41 Analysis Workflow

2. From the Select array type drop-down list, click to select OncoScan.
Note: Once you select the array type, analysis workflow, and reference model
file, then the annotation file will be auto selected for you based on your earlier
selections.

IMPORTANT! The Select array type drop-down list includes only the array types for which
library (analysis) files have been downloaded from NetAffx or copied from the Library package
provided with the installation.

3. Select the appropriate Genome Build.

4. From the Select analysis workflow drop-down list, click to select an
appropriate analysis workflow.

IMPORTANT! For FFPE samples use the FFPE Analysis NAXX workflow. For Control DNA
use the Control DNA Analysis.

5. By default, the Set workflow name is Workflow. Click inside the Workflow’s
(upper right) text box to enter a different workflow name.

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6. Click the Copy number reference model file from the drop-down list, then click
to select an appropriate file.
7. Click the Somatic mutation reference model file from the drop-down list, then
click to select an appropriate file.
8. At the Select the intensity (CEL) file(s) to analyze pane, click the Add CEL
Files drop-down, then click to select AT Channel.
An Explorer Window appears.
9. Highlight the CEL file(s) using Ctrl click or Shift click, then click Open.
10. At the Select the intensity (CEL) file(s) to analyze pane, click the Add CEL
Files drop-down, then click to select GC Channel.
An Explorer Window appears.
11. Highlight the CEL file(s) using Ctrl click or Shift click, then click Open.
The Select the intensity (CEL) file(s) to analyze pane is now populated with AT
and GC Channel CEL files.

IMPORTANT! After loading the CEL files, check that the AT lines up with the matching GC
CEL file.

12. Click the Result File Names drop-down menu to enable ChAS to automatically
generate Output Names.
Note: Output file names are only auto-generated if the two CEL files have the
same root name. It is recommended to use an “A” or “C” as the last character to
designate the channel in the CEL file naming convention. Example:
“_AS_05A.CEL” is an AT Channel file, while “_AS_05C.CEL” is a GC Channel file.
You can also clear this (populated) column by clicking Clear Column.
13. OPTIONAL: To choose a different output folder from the saved output path that
is displayed, click the Output result information’s Browse button.
An Explorer window appears.
14. Navigate to an output folder location, then click OK.
Note: To better organize your output results, you can add sub-folders to your
assigned output result path/folder.

Adding sub-folders to your assigned Output Results folder

1. Click the
... button to return to your assigned output path and/or folder.

2. Click Create New Folder.

3. Enter a sub-folder name.
4. Click OK. Repeat the above steps to add more sub-folders.
The newly created sub-folders now appear in the output result information
window.

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5. If you are using a previously analyzed CEL file(s) to verify new CHP data (against
CHP data generated from previous versions of ChAS and Library files), you may
want to use a suffix to append the new resulting CHP file(s). To do this, click
inside the Select a suffix to append to the analysis results field to enter an
appending file suffix. (Figure 42)

IMPORTANT! If you are saving the same OSCHP file into the same output file folder that
contains your originally run OSCHP file, a “1” is automatically added into the filename (in
addition to any suffix you may add) to differentiate the two runs of identical CEL file names.
Example: na33(1).oschp

Figure 42 Adding a suffix

6. Optional: If you have a CEL file(s) in which the Y chromosome is partially/fully

deleted and therefore determined to be female by the gender calling algorithm,
go to the Analysis Setup’s Optional pane (Figure 43), click the Set Gender
Manually check box, then click to select the appropriate radio button.

Figure 43 Set Gender option

7. Click Submit.

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If the following warning message appears (Figure 44), acknowledge it, then click
OK.

Figure 44 CEL warning message

The Workflow dashboard window appears and your annotation files begin to
load. (Figure 45).
The Analysis Workflow Dashboard tracks ongoing analysis tasks for ChAS. It also
delivers the results of the analyses and can restart the Browser (if it was shut
down to free up memory for the analysis).

Figure 45 CEL files loading inside the Workflow dashboard

After loading is complete, a Workflow completed successfully message appears.

(Figure 46)

Figure 46 Workflow Dashboard with Single Samples loaded

Note: The View Logs button will access the algorithm pipeline logs which may
be useful if you have a Workflow that fails to complete.
8. Click to choose the analysis you want to view, then click View Results List.

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The QC Results tab window appears showing the Basic View QC settings.
(Figure 47) A Detail View QC setting (which provides more columns of data) is
also available in the QC settings drop down list.
Note: QC parameters can also be viewed in the ChAS Browser see "Setting QC
parameters in the ChAS browser" on page 133.

Figure 47 QC Results window tab

9. Click each sample’s check box or click the Sample File check box to select ALL
samples.

Creating your own custom QC settings

See "Creating your own custom QC setting" on page 57

Viewing results in the browser

1. At the QC Results window, click View In Browser.

If the following warning message appears (Figure 48), click Yes to acknowledge
it.

Figure 48 Recommended maximum exceeded message

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If the following warning message appears (Figure 49), acknowledge it, then click
OK.

Figure 49 Duplicated files message

If the following warning message appears (Figure 50), click Yes to acknowledge
it.

Figure 50 NetAffx versions message

A progress bar appears. (Figure 51)

Figure 51 Progress bar

Note: The ChAS Browser allows loading files analyzed using different NetAffx
version at the same time (as long as the versions are all from all the same
reference and genome builds). If NetAffx versions are from different builds of the
genome (for example Hg18 and Hg19), The ChAS Browser does not load the files.
After a few moments, the ChAS browser featuring your selected samples
appears.

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Recentering Due to the complexity and low diploid count in a small fraction of cancer samples,
OncoScan CNV there may be a need to manually assign the diploid region of the sample or "recenter"
and OncoScan it.
CNV Plus arrays In Figure 52, Chromosome 16q is called as a loss, the log 2 ratio data is shifted
downward, but the Allele Difference Graph is displaying three tracks representing AA,
AB, BB calls. Having an Allele Difference graph with three tracks means this region
must have at least two copies. Since you cannot have three Allele Difference tracks in
a region of loss, this sample needs to be recentered. For more information, see
"Manual re-centering algorithm (OncoScan)" on page 507.

Figure 52 Example of 3 Allele Difference tracks in a Region of Loss

If the region that is true diploid is a whole chromosome, use Method 1. If the region
that is true diploid is part of a chromosome, use Method 2.

Method 1 Determining the median Log 2 ratio for the region in the sample that is truly
diploid

1. Open the ChAS Browser.

2. Click on the Chromosome Summary Data tab, then click the drop-down to
select MedianSignal. (Figure 53)

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Figure 53 Chromosome Summary tab - median log2 ratio value for Chromosome 16
example

Method 2 Determining the median Log 2 ratio for the region in the sample that is truly
diploid

1. Open the ChAS Browser.

2. In the Detail View (Figure 52), zoom into the region determined to be diploid.
3. Go to the Graphs tab, then click to include only the selected view.
4. Highlight the Log2 Ratio column, then right-click to select Sum, mean and
median. (Figure 54)

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Figure 54 Graphs tab - Log 2 Ratio column

A Sum, mean and median window appears. (Figure 55)

Figure 55 Sum, mean and median message

5. Acknowledge the message, then click OK.

6. Open the ChAS Analysis Workflow, then click on the QC Results tab.
(Figure 56)

Figure 56 ChAS Analysis Workflow - QC Results window tab

7. Load the OSCHP file into the QC Results tab by clicking on the Add Files
button. (Figure 56)
8. From the QC Settings drop-down menu, select Recenter View, then make a
note of the TuScan L2R Adj value. (Figure 56)
9. Click on the Analysis setup tab. (Figure 57)

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Figure 57 ChAS Analysis Workflow - Analysis setup window tab

10. Select the FFPE or non-FFPE analysis based on the sample type.
11. Load in the two CEL files into the appropriate channel.
12. Check the Manual Recenter check box to enable the parameter fields.
(Figure 57)
13. Enter the TuScan Log2 Adjustment value you noted earlier.
14. Enter the value of the median Log2 determined from the browser into the Adjust
this log 2 to 0 field.
15. Enter a suffix if desired.
Note: An RC will automatically be appended onto any OSCHP file that goes
through Manual Recentering for an RC.OSCHP extension.

Figure 58 shows the original OSCHP file (pink data) and the manually recentered
RC.OSCHP (green data).
By inputting both the TuScan Log2 Ratio value (derived from the algorithm) and the
median Log2 Ratio value (for the region you have determined to be diploid,
Chromosome 16q for our example), the Recentering Algorithm has recentered the
log2 ratio data (for the region determined to be diploid) around 0 and there is no longer
a loss segment called in this region.

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Figure 58 Example original OSCHP file (pink data) and the manually re-centered RC.OSCHP (green data)

Setting up and As long as your library file folder contains the necessary analysis files for the array,
running an your configuration paths are established (Figure 59) your Array Information fields will
OncoScan auto-populate. (Figure 60)
matched normal
analysis

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Figure 59 Matched Normal Analysis Setup window/tab - Overview

Figure 60 Matched Normal Analysis Configuration

1. From the Select array type drop-down list, select OncoScan.

Note: The Select array type drop-down list includes only the array types from the
library (analysis) files that have been downloaded from NetAffx or copied from the
Library package provided in the OncoScan installation package.

IMPORTANT! After adding new library files to the library file folder, always close and re-
launch OncoScan Console to ensure the newly added files are recognized by the software.

2. From the Select analysis workflow drop-down list, click to select FFPE
Analysis including Matched Normal NAXX.
Other available Analysis Workflow options are:
Control DNA Analysis NAXX - Use this workflow for the Control DNA in the
OncoScan Kit.
Non-FFPE Analysis NAXX - Use this workflow with cell line DNA.
FFPE Analysis NAXX - Use this workflow for a standard analysis.
3. Enter a Workflow name (optional). By default, the Set workflow name is
Workflow. Click Workflow (upper right) to enter a different workflow name.

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Note: Customizing a Workflow name can be a useful tool in keeping track of
analysis workflows as all the related output files (outside of the OSCHP file) are
pre-fixed with this workflow name.
The Annotation file is automatically selected for you and is based on your
selected reference model file. (Example: OncoScan.na33.v1.annot.db)
Note: The Annotation to be used for analysis field is auto-populated based on
your Ref Model file selection. The analysis is not be permitted to run if the
appropriate annotation file is not available in your Library folder.
4. Select a Somatic mutation reference model file. By default, it is set to
OncoScan.na33.v1.SOM_REF_MODEL. If you created your own reference
model file, click the drop-down list to select your .SOM_REF_MODEL.
5. Confirm the displayed Somatic mutation threshold file to be used is correct. If
you need to change it, click the Browse button, navigate to the appropriate
threshold TXT file, then click OK.

IMPORTANT! If the Reference Model File and Somatic mutation Reference Model File were
created independently of each other, a warning message appears after you click Submit (to
start the Workflow Analysis process). Click OK to acknowledge the message.

Adding CEL files You can manually add CEL files or import them as a tab-delimited text file.
to analyze
Manually adding CEL files to analyze

1. At the Select the intensity (CEL) file(s) to analyze pane, click the Add CEL files
drop-down.
2. Click Tumor AT Channel.
The CEL file window appears. (Figure 61)

Figure 61 CEL file folder example

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3. Click any header to sort your files or click the Files of type drop-down to filter
your CEL files by AT Channel, as shown in Figure 62.

Figure 62 Files of type drop-down list

4. Single click, Ctrl click, or Shift click (to select multiple Tumor AT Channel files).

IMPORTANT! It is recommended to use an “A” or “C” as the last character to designate the
channel in the CEL file naming convention. Example: “_AS_05A.CEL” is an AT Channel file,
while “_AS_05C.CEL” is a GC Channel file. See Figure 61.

5. Click Open.
The Tumor AT Channel fields are now populated. (Figure 63)

Figure 63 Tumor AT Channel file list

6. Click the Add CEL files drop-down.

7. Click Tumor GC Channel. The CEL file window appears. (Figure 61 on page 80)
8. Single click, Ctrl click, or Shift click (to select multiple Tumor GC Channel files).
9. Click Open.
The Tumor GC Channel fields are now populated. (Figure 64)

Figure 64 Tumor GC Channel file list

10. Click the Add CEL files drop-down.

11. Click Normal AT Channel. The CEL file window appears. (Figure 61)

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12. Single click, Ctrl click, or Shift click (to select multiple Normal AT Channel files).
13. Click Open.
The Normal AT Channel fields are now populated. (Figure 65)

Figure 65 Normal AT Channel file list

14. Click the Add CEL files drop-down.

15. Click Normal GC Channel. The CEL file window appears. (Figure 61)
16. Single click, Ctrl click, or Shift click (to select multiple Normal GC Channel files).
17. Click Open.
The Normal GC Channel fields are now populated. (Figure 66)

Figure 66 Normal GC Channel file list

CEL file displaying options (optional)

The File Name drop-down list (Figure 67) is dynamically populated and based on what
attributes are populated in the ARR file.
To use this display option, you must:
1. Provide the appropriate attributes at the time of sample registration in AGCC.
2. The ARR files must reside in the same folder as the CEL files.

Figure 67 EXAMPLE: File Name

Display Choices

To see “channel” (as an option in the drop down), you must use a template (or the

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OncoScan template provided in the AGCC library files) that contains a “channel”
attribute. The resulting ARR file must also reside in the same folder as the CEL files
you are analyzing.
You can display one of the attributes from the ARR file in the table. For example,
“Channel” can be chosen (Figure 67) to confirm the assignment of a CEL file to its
appropriate channel.

Selecting a File Name display attribute

1. Click the File Name drop-down button, then click to select the attribute you want
displayed along with your CEL file names.
The two examples (Figure 68 and Figure 69) show how the table appears with the
display set to Filename, then to Channel.

Figure 68 Table with Filename displayed

Figure 69 Table with Channel displayed

Importing CEL The batch file must be saved as a text (Tab-delimited) format and include the full
files using batch directory path for your CEL files, as shown in Figure 70.
import Note: The resulting OSCHP files are saved to your output path location, therefore it is
not necessary to include a path under RESULT. Simply enter the desired results
filename in this column.
The format for this tab-delimited file is 5 columns (A,B, C, D, and E) with the headers:
 ATCHANNELCEL
 GCCHANNELCEL
 ATChannelMatchedNormalCel
 GCChannelMatchedNormalCel
 RESULT
You must provide the full path to the CEL files for each Channel column.

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(Example: C:\Desktop\OncoScan\Data\Sample1.cel)

Figure 70 List from Windows Excel

1. Click Import Batch File

A File window appears.
2. Navigate to your text (tab delimited) file location, then click on the file you want
to import.

IMPORTANT! Excel must be closed before you import.

3. Click Open.
The Tumor AT, Tumor GC, Normal AT, Normal GC and Result File Name fields
are now populated. (Figure 71)

Figure 71 Tab-delimited text file imported into OncoScan Console

Converting CEL files to CHP files

The Automatic CEL File Analysis tool in ChAS converts CEL files into ChAS Browser
compatible CHP files automatically.

How it works The Automatic CEL File Analysis tool continually scans up to five designated input
folders for new CEL files to analyze. Once a CEL file is detected, it is analyzed resulting
in a CHP file (which is auto-saved to a designated output folder). Once a CEL file is
processed, the ARR and CEL files are moved to the designated Archive folder.

Supported array  CytoScan HD (Single Sample Analysis or Normal Diploid Analysis only)
types  CytoScan XON (Single Sample Analysis only)
 CytoScan 750K (Single Sample Analysis or Normal Diploid Analysis only)
 CytoScan Optima (Single Sample Analysis only)
 OncoScan CNV (FFPE Analysis only)

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 OncoScan CNV Plus (FFPE Analysis only)
Note: In order to properly match up CEL files when running OncoScan CNV or
OncoScan CNV Plus arrays, the CEL files from the "AT" and "GC" channels must have
the exact same root name and include the array type. Each CEL file must indicate
which channel they are using a concluding A or C. For example, the following CEL files
will be paired properly for OncoScan FFPE analysis:
 OncoScan_Sample1_(OncoScanCNV_Array)A.cel
 OncoScan_Sample1_(OncoScanCNV_Array)C.cel
The following CEL files will NOT be paired properly for OncoScan FFPE analysis
because the root names do not match:
 OncoScan_Sample1_(OncoScanCNV_Array)A.cel
 OncoScan_Sample2_(OncoScanCNV_Array)C.cel
The following CEL files will NOT be paired properly for OncoScan FFPE analysis
because the array names are not included:
 OncoScan_Sample1_A.cel
 OncoScan_Sample1_C.cel

Launching the 1. Click the Utility Actions button (top right of the Analysis Workflow window)
tool 2. Click Automatic CEL File Analysis.
The window opens. (Figure 72)

Figure 72 AutoCelAnalysis window

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Setting up the tool
IMPORTANT! Input, Output, and Archive folder names and their assigned paths should not
contain spaces. If a space is needed, use the underscore symbol [_].

Any non-ARR and non-CEL files detected in your assigned input folder will remain in this folder.
Any detected ARR and CEL files will be processed and moved into your assigned Archive
folder.

Assigning your input folder(s)

The Input folder is where your CEL files reside.

1. Click the Input folder 1 the

... button.

An Explorer window appears.

2. Navigate to your CEL file folder.

3. Click on the folder to highlight it, then click Select Folder.

Your CEL file folder path is displayed.

4. Optional: Once the first Input folder is assigned, an option to designate a second
Input folder appears (Input folder 2). Repeat steps above to assign a second
Input folder. Up to five Input folders can be assigned.

Assigning your output folder(s)

After the tool produces a CHP file, it is placed in an Output folder.

1. Click the Output folder 1 the

... button.

An Explorer window appears.

2. Navigate to an existing folder where you want your newly converted CHP files
saved or click New Folder to create a new Output folder.

3. Click Select Folder.

Your Output folder 1 path is displayed.

4. Optional: Once the first Output folder is assigned, an option to designate a
second Output folder appears (Input folder 2). Repeat steps above to assign a
second Output folder. Up to five Output folders can be assigned.

Assigning an archive folder

Copies of the processed CEL files are placed in the Archive folder.

1. Click the Archive folder the

... button.

An Explorer window appears.

2. Navigate to the folder where you want the CEL files saved or click New Folder
to create a new Archive folder.

3. Click Select Folder.

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Your Archive folder path is displayed.

Assigning a QC History file folder

1. Click the QC History folder button.

An Explorer window appears.
2. Navigate to the folder where you want the CEL files saved or click New Folder
to create a new QC History folder.
3. Click Select Folder.
Your QC History folder path is displayed.

Selecting a target genome version

1. By default, hg19 is selected. If needed, click the Target Genome Version drop-
down to select hg38, a shown in Figure 73.

Figure 73 Version drop-down

Normal diploid analysis check box

1. Click the check box to use the Normal Diploid algorithm. Leave unchecked to run
the default single sample analysis.

Running the tool 1. Click .

The CEL file analysis begins and the Time and Message pane populates with
information, as shown in Figure 74. Click Cancel to stop an analysis in progress.
Note: The time for CEL file analysis to complete should be comparable to
analysis times when manually setting up CEL files in the Analysis Workflow.
Note: During the analysis process, the tool detects the array type, then auto-
generates an appropriately named array staging folder. As each CEL file analysis
completes, the tool moves the newly created CHP file from its staging folder to
the output folder you assigned earlier.
Note: If the Automatic CEL File Analysis stops for any reason (such as losing
connection to the input folder or is inadvertently canceled) a log file of processed
CEL files can be found in the designated Archive folder.

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Figure 74 AutoCelAnalysis window - Populated

Opening the 1. From the ChAS Browser window, click File → Open.
newly generated An Explorer window appears.
CHP file(s)
2. Navigate to your assigned Automatic CEL File Analysis output folder(s). See
"Assigning your output folder(s)" on page 86.

3. Click or Ctrl click to highlight the CHP files you want to open in the ChAS
Browser, then click Open.

The file(s) appear in the ChAS Browser.

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Reference files
This section explains how to create a reference file which is required to perform single
sample analysis in ChAS. The software analyzes a sample file by comparing it to a
reference file. You can use the reference file provided with ChAS, or you can create a
reference file using your own sample data.
See Figure 75 for an overview of the analyses involved in creating a reference file for
the CytoScan Arrays.

Figure 75 Overview of creating a reference file

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Creating a
reference file
IMPORTANT! When creating a CytoScan reference file, it is recommended that you use a
minimum of 44 CEL files. These CEL files must include at least 20 male and 20 female samples.

1. From the Analysis menu, select Perform Analysis Setup. (Figure 76)

Figure 76 Analysis drop-down menu

The Analysis Workflow window tab opens. (Figure 77)

Figure 77 Analysis Workflow

2. From the Select array type drop-down list, click to select an array type
(Example: CytoScanHD_Array.
Note: The Select array type drop-down list includes only the array types for
which library (analysis) files have been downloaded from NetAffx or copied from
the Library package provided with the installation.
3. Select a Genome Build. (Example: hg19)

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4. From the Select analysis workflow drop-down list, click to select an analysis
workflow. (Example: CytoScanHD_Array Reference Model Creation:NA33)
5. By default, the Set workflow name is Workflow. Click inside the Workflow’s
(upper right) text box to enter a different workflow name.
6. Click the Assay Preparation type used drop-down button, then select one of
the following:
 Manual (CEL files whose assays were performed by hand)
 Automation (CEL files whose assays were assisted by a robot)
 Automation, Manual (a mix of CEL files whose assays were performed either
by hand or with the assistance of a robot.
Note: The Annotation file for analysis is auto-selected once the array type,
analysis workflow and assay preparation type used fields are selected.
7. From the Select the annotation file for this analysis drop-down list, verify the
selection of the annotation file. (Example, CytoScanHD_Array.na.33.annot.db)
8. At the Select the intensity (CEL) file(s) to analyze pane, click Add.

IMPORTANT! The same annotation file you used to create a Reference Model File MUST also
be used with future Single Sample Analyses runs that utilize your created Reference Model File.

The following window appears: (Figure 78)

Figure 78 >CEL file folder

9. Single click, Ctrl click, or Shift click (to select multiple CEL files), then click Open.
The Select the intensity (CEL) file(s) to analyze pane is now populated with
your CEL files. (Figure 79)

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Figure 79 Select the intensity (CEL) file(s) to analyze pane

To remove a CEL file from this list, click to highlight it, then click Remove.
10. At the Output result information pane, enter a name for your reference model
file. (Figure 80)

Figure 80 Name your Reference Model File name

11. Click Submit.

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Displaying and exporting data from the analysis workflow

Adding files to the 1. Click the QC results tab. (Figure 81)

QC results table The QC results window tab appears.
2. Click Add Files.
A Chromosome Analysis Suite window appears.
3. Navigate to your folder’s location, then select the xxCHP files you want to add.
4. Click Open.
Your selected files appear in the Export QC Table window tab, as shown in
Figure 81.

Exporting QC 1. Check the adjacent check box next to the file(s) you want to export or click the
table information Select All button (atop the check boxes) to auto-check all the displayed
files.

2. Click on the Export QC Table tab.

Figure 81 Workflow Dashboard loaded

An Explorer window appears.

3. Navigate to the export location you want, then enter a name for your QC file.
4. Click Save.

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Viewing analysis 1. Check the adjacent box next to the file(s) you want to open in the ChAS Browser.
files in the ChAS 2. Click the View in Browser button to open the files in the ChAS Browser or click the
browser View in MSV button to open the files in the Multi-Sample Viewer. For more
information on the MSV see, the RHAS User Guide.

Exporting probe- Exporting CytoScan Probe-Level Data

level data 1. In the QC Results tab, click the check box adjacent to the Results File(s) you want
to generate a report for or click the Select All button (atop the check boxes), as
shown in Figure 82.

2. To export probe-level data, click the Generate Report drop-down. (Figure 82)
The following export reporting options appear: (Figure 82)

Figure 82 Generate Report drop-down menu

3. Click to select Export Probe Level Data. (Figure 82)

Your previously assigned Output folder file window appears.
Note: The default root filename is Result. Click inside the File Name field to enter a
different root filename.
4. Enter a File Name for your text (tab-delimited) reporting file, then click Save, or
navigate to different save location.

Exporting OncoScan probe-level data

1. In the QC Results tab, click each check box next to the Results File(s) you want to
generate a report for. Click the Select All button (atop of the check boxes)
(Figure 83) to auto-check all the displayed files.

2. To export probe-level data, click the Generate Report drop-down.

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The following export reporting options appear: (Figure 83)

Figure 83 Generate Report drop-down menu

3. If you want to export all 4 available reports at once, click to select Export All
Probe Level Data. (Figure 83) Otherwise, click to select the specific report(s) you
want export.
The appropriate (previously assigned) folder file window appears.
Note: The default root filename is Result. Click inside the File Name field to enter
a different root filename.
4. Enter a File Name for your reporting file, then click Save or navigate to a different
save location.

Exporting a gene This report summarizes the copy number segments that overlap user defined
report (CytoScan regions of interest (e.g., Genes) as defined in the selected BED file.
or OncoScan 1. From the QC Results tab, click the Generate Report drop-down menu and
arrays) select Export Gene Report. (Figure 84)

Figure 84 Generate Report drop-down menu

CytoScan array report OncoScan array report

The following window appears. (Figure 85)

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Figure 85 Select the BED file for the Gene Report window

2. Click to select the appropriate BED file, then click Open.

Note: Any BED file can be used to generate the Gene Report on any regions of
interest contained within the BED file.
Your previously assigned Output folder file window appears. (Figure 86)

Figure 86 OncoScan Output folder window

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3. The default root filename is Result. Click inside the File Name field to enter a
different root filename, then click Save.
A progress bar appears while your report generates, followed by a message
window. (Figure 87)

Figure 87 Gene Report finished successfully

4. Click Yes.
The Results Output folder window appears.
5. Locate the Gene Report text file, then open it in Microsoft Excel.
The following window appears. (Figure 88)

Figure 88 Gene Report

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Gene Report Description

Column

Filename Name of the xxCHP file containing the data.

Chromosome Chromosome on which the probeset is located.

Start Position Start position of gene or region as defined in the bed file.

End Position End position of gene or region as defined in the bed file.

Genes This column is populated from the name column of the bed file. In most cases, it will contain gene
names.

Threshold Test Displays Outside Bounds if any of the QC metrics fail to meet a threshold test. For more information
on thresholds, see "Creating your own custom QC setting" on page 57.

% Aberr.Cells If % AC = 100%, we return “homogeneous” because it could be 100% normal or 100% tumor.
(OSCHP only) If % AC =NA, the percent aberrant cells could not be determined and TuScan returns non-integer CN
calls. This metric is an algorithmically determined estimate of the % of aberrant cells in the sample.

TuScan Ploidy TuScan Ploidy is the most likely ploidy state of the tumor before additional aberrations occurred.
(OSCHP bnly) TuScan Ploidy is assigned the median CN state of all markers, provided that %AC could be
determined and integer copy numbers are returned. If %AC cannot be determined, NA (Not Available)
is reported for both ploidy and %AC.

Low Diploid Flag An essential part of the algorithm is the identification of “normal diploid” markers in the cancer
(OSCHP only) samples. This is particularly important in highly aberrated samples. The normal diploid markers are
used to calibrate the signals so that “normal diploid markers” result in a log2 ratio of 0 (e.g. copy
number 2). The algorithm might later determine that the "normal diploid" markers identified really
correspond to (for example) CN=4. In this case the log2 ratio gets readjusted and TuScan ploidy will
report 4. Occasionally (in about 2% of samples) the algorithm cannot identify a sufficient number of
“normal diploid” markers and no “normal diploid calibration occurs. This event triggers “low diploid
flag” = YES. In this case the user needs to carefully examine the log2 ratios and verify if re-centering
is necessary.

Median Log2 Ratio Log2 Ratio is the log2 ratio of the normalized intensity of the sample over the normalized intensity of
(OSCHP only) a reference with further correction for sample specific variation. The Median Log2 Ratio is computed
for each segment.

Median BAF B-allele frequency (BAF) is (Signal (B)/{Signal(A) + Signal(B), where signal (A) is the signal from the AT
(OSCHP only) chip and signal (B) is the signal from the G/C chip. Median BAF is reported for each segment and is
the median BAF of the markers identified as heterozygous, after mirroring any marker BAFs above 0.5
to the equivalent value below 0.5. If the number of heterozygous markers in the segment is below 10
or the percent of homozygous markers is above 85% no value is reported,

State This is a comma separated list of the copy number state of the segments that overlap the gene or
region.

LOH Flag to indicate whether the gene or region is in a Loss of Heterozygosity region (0=No, 1=Yes).

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Exporting a XON Note: This export provides XON Region gains/loses for a defined list of genes.
region report 1. From the QC Results tab, select the check box for the sample file(s) for which you
(CytoScan XON would like to generate an XON Region report.
only) 2. Click on the Generate Report drop down menu and select Export XON Region
Report.
3. In the browse window, click to select the appropriate aed/bed file, then click
Open.
4. Click the browse button to assign an output path.
Note that the default root filename is Result.
5. Optional: Click inside the Filename field to enter a difference root filename, then
click Save.
6. Click the appropriate radio button (for each XNCHP file) to either export all data
into a single text file or into individual text files.
7. Locate the XON Region Report text file, then open it in Microsoft Excel.

XON Region Description

Report Column

Filename Name of the XNCHP file containing the data

Gene This column is populated from the name column of the bed file. In most cases, it will contain gene
names.

Chromosome Chromosome on which the probeset is located.

Gene Start Start position of the gene or region as defined in the bed file.
Position

Gene End Position End position of gene or region as defined in the bed file.

XON Region Start Start position of the Exon Region segment as defined in the XNCHP file.
Position

XON Region Stop End position of the Exon Region segment as defined in the XNCHP file.
Position

XON Region Type Gain or Loss

Size (bp) Size of the Exon Region Segment.

Marker Count Number of markers in the Exon Region Segment.

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Exporting a copy This report summarizes the copy number segments with the fold change from
number expression data that overlap user defined regions of interest (e.g. Genes) as defined
expression in the selected AED or BED file.
overlap report 1. In the QC Results tab, click on the Generate Report drop-down menu, then
select Copy Number Expression Overlap Report. (Figure 89)

Figure 89 Generate Report drop-down menu

The following window appears: (Figure 90)

Figure 90 Select files for the Overlap Report window

2. Click the Select the region file Browse button to navigate to and select the
appropriate file.
Note: For the Regions file, you can use the default bed files provided in the in the
library files for use with the Copy Number Expression Overlap report. You may
also create your own AED/BED file containing your custom regions of interest.
3. Click the Select the AED file (TAC output) Browse button to navigate to and
select the appropriate file. Refer to the Transcriptome Analysis Console (TAC) 4.0
User Manual for analyzing and exporting expression data as an AED file.
4. Click the Select output file name Browse button to navigate to an existing report
location, or click inside the text field to enter a different root filename (other than
the default Results filename), then click OK.
A progress bar appears while your report generates.
5. Locate the cnexoverlapreport.txt file, then double-click on it to open it. It is
recommended to open the tab delimited file with Excel for easier viewing.

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The following window appears. (Figure 91)

Figure 91 Expression Gene Report

Expression Gene Description

Report Column

Filename Name of the OSCHP file containing the data

Gene This column is populated from the name column of the bed file. In most cases, it will contain gene
names.

Chromosome Chromosome on which the probeset is located.

Gene Start Start position of gene or region as defined in the bed file.
Position

Gene End Position End position of gene or region as defined in the bed file.

CN State This is a comma separated list of the copy number state of the segments that overlap the gene or
region.

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Expression Gene Description

Report Column

Segment ID The unique identifier for the copy number segment.

Segment Start Start position of the overlapping copy number segment in the xxCHP file.
Position

Segment End End position of the overlapping copy number segment in the xxCHP file.
Position

Segment Size (bp) The Segment Stop Position minus The Segment Start Position.

Percent Gene Gene Boundary Size/Segment Size.

Overlap

% Aberr.Cells If % AC = 100%, we return “homogeneous” because it could be 100% normal or 100% tumor. If %
(OncoScan only) AC =NA, the percent aberrant cells could not be determined and TuScan returns non-integer CN calls.
This metric is an algorithmically determined estimate of the % of aberrant cells in the sample.

TuScan Ploidy TuScan Ploidy is the most likely ploidy state of the tumor before additional aberrations occurred.
(OncoScan only) Algorithmically it is the CN state of the markers identified by the algorithm as normal diploid before
%AC and ploidy are determined. When a high ploidy is determined the "normal diploid" is deemed to
correspond to a higher CN and the log2 ratio gets adjusted appropriately. If ploidy cannot be
determined NA (Not Available) is reported.

Low Diploid Flag An essential part of the algorithm is the identification of “normal diploid” markers in the cancer
(OncoScan only) samples. This is particularly important in highly aberrated samples. The normal diploid markers are
used to calibrate the signals so that “normal diploid markers” result in a log2 ratio of 0 (e.g. copy
number 2). The algorithm might later determine that the "normal diploid" markers identified really
correspond to (for example) CN=4. In this case the log2 ratio gets readjusted and TuScan ploidy will
report 4. Occasionally (in about 2% of samples) the algorithm cannot identify a sufficient number of
“normal diploid” markers and no “normal diploid calibration occurs. This event triggers “low diploid
flag” = YES. In this case the user needs to carefully examine the log2 ratios and verify if re-centering
is necessary.

Median Log2 Ratio Log2 Ratio is the log2 ratio of the normalized intensity of the sample over the normalized intensity of
(OncoScan only) a reference with further correction for sample specific variation. The Median Log2 Ratio is computed
for each segment.

Median BAF B-allele frequency (BAF) is (Signal (B)/{Signal(A) + Signal(B), where signal (A) is the signal from the AT
(OncoScan only) chip and signal (B) is the signal from the G/C chip. Median BAF is reported for each segment and is
the median BAF of the markers identified as heterozygous, after mirroring any marker BAFs above 0.5
to the equivalent value below 0.5. If the number of heterozygous markers in the segment is below 10
or the percent of homozygous markers is above 85% no value is reported,

LOH Flag to indicate whether the gene or region is in a Loss of Heterozygosity region (0=No, 1=Yes).

Fold Change The level of fold change as determined from the TAC software.

TCID The Transcript Cluster ID overlapping the Gene or Region defined in the bed file.

TCID Start Position Start Position: Start position of the overlapping TCID(s).

TCID End Position End Position of the overlapping TCID(s).

TCID P-Value ANOVA p-value (Condition1 vs Condition2)

TCID GeneSymbol Gene Symbol: the Gene Symbol assigned to the TCIS(s) based on the TAC analysis.

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Exporting Note: For exporting genotypes from an entire sample or multiple samples at one time,
genotype data exporting genotypes from the Analysis Workflow is generally faster than from the
using the analysis ChAS browser.
workflow 1. In the QC Results tab, click on the Generate Report drop-down menu, then
select Export Genotyping Data. (Figure 92)

Figure 92 Generate Report drop-down

menu

The following window appears: (Figure 93)

Figure 93 Genotype Export Selections window

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Exporting options Note: The default export is All Chromosomes.

Exporting a SNP List

1. Click the Annotation File drop-down menu (Figure 93), then click to select which
array annotation file you want to use for exporting SNP information (along with
the genotypes).
2. Click the SNP List radio button, then click the SNP List Browse button.
The Select SNP List window appears. An example SNP List can be seen in
Figure 388 on page 349.
3. Navigate to, then click to select the SNP List you want to export.
4. Click Open.
Your SNP List is now set for exporting.

Exporting a specific chromosome

1. Click the Chromosome radio button.
2. Click the Chromosome drop-down menu, then click to select the specific
number or chromosome type you want to export.
3. Optional: Click to check the Select Region check box, then enter a Start and
Stop value in the provided text fields.

Selecting an 1. Click the Output Path Browse button.

output path and The Select Output Path for the Genotype Export Report appears.
filename
2. Navigate to an existing report location, or click inside the text field to enter a
different root filename, then click OK.
3. Click inside the File Name text field to enter a report name.

Multiple file output options

1. Click to check the Separate File for each Chromosome and/or Separate File
for each CHP File check box.
2. Click OK.
A Please Wait...Exporting Genotype Data progress bar appears.
3. After a few moments, the Export Genotype Data finished successfully window
appears. Click Yes to view the report, click No to view the report later.
Clicking Yes opens your previously assigned Output folder window. Locate the
newly exported file, then double-click on it to open it. It is recommended to open
the tab-delimited text file with Excel for easier viewing.

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Saving and Sample attributes can be added to the Results table for use in the PCA and
importing Export IGV functions. A tab-delimited text file containing sample attributes can
attributes also be added to the Results table, however, column A must contain the name of
the xxCHP file. Subsequent columns can contain other sample attributes.
Alternatively, sample attributes listed in an ARR file generated in AGCC will also
be automatically displayed in the Results table (as long as the ARR and xxCHP
files are located in the same directory).
1. In the ChAS Analysis Workflow, select the QC Results tab.
2. Click Add Files to navigate to and load your CHP files.
The Attributes button is enabled.
3. Click on the Attributes drop down, select Import, then navigate to the
corresponding TXT file.
4. Click Open.
The attributes now appear in the table.
5. Optional: To save an individual text file of sample attributes for each loaded chp
file, click the Attributes drop-down, then select Save.

Exporting to The ChAS Analysis Workflow enables you to export a variety of graphs for viewing in
Integrative IGV. To access this viewer, go to: http://software.broadinstitute.org/software/igv/
Genomics Viewer 1. In the ChAS Analysis Workflow, click the QC Results tab.
(IGV) 2. Load results files by clicking on Add Files, then navigate to and highlight the
CHP files.
3. Click Open.
4. Select files by either clicking the Select All, or checking each filename’s adjacent
check box.
5. Click Export to IGV.
The IGV Exporter window appears. (Figure 94)
6. Click the Browse button to assign an output folder.
7. From the IGV Exporter window, click the check box(es) adjacent to the data you
want to export, as shown in Figure 94.
8. Click OK.
Note: To include sample attribute information in the IGV Export, click on
Attribute → Save prior to running the IGV Export.

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Note: XON Region segments are exported as CN segments when working with
CytoScan XON arrays.

Figure 94 IGV Exporter window

Note: The export process may take several minutes to complete, as it is dependent
on your sample(s) and data type(s).
If the export was successful, an IGV Export Complete message appears. (Figure 95)
Acknowledge the message, then click OK.

Figure 95 IGV Export Complete message

Your data is now ready to be imported into IGV’s browser.

For more information on importing and viewing your data in IGV, go to:
http://software.broadinstitute.org/software/igv/UserGuide

Principle ChAS Analysis Workflow enables you to perform Principle Component Analysis (PCA)
component on signal (CHP) data. PCA identifies a new set of variables (PCA1, PCA2, and PCA3)
analysis that account for a majority of the variance in the original data set. The first principal
component (PCA1) captures as much variability in the data as possible. PCA2
captures as much of the remaining variability (not accounted for by PCA1) as possible.
PCA3 captures as much of the remaining variability (not accounted for by PCA2) as
possible.

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PCA plot generation
1. In the ChAS Analysis Workflow, select the QC Results tab. Load results files by
clicking on Add Files, and navigating to xxCHP files, then click Open.
When files are loaded, the Import Attributes, Export to IGV and QC Analysis
buttons will be enabled.
2. Select files, by either clicking Select All button or selecting files individually by
ticking box to left of file.
3. Click on the QC Analysis button and in the resulting drop down menu, select
PCA.
The 3-dimensional PCA graph(s) appears. The graph axes represent the top three
variables (PCA1, PCA2, and PCA3) that account for the majority of the variability
among the samples.

Sample display options

By default, the table is set to a vertical view. Click to change the view to a
horizontal view.
1. The file can be identified by clicking on an icon in the plot.
The corresponding file in the table is highlighted, as shown in Figure 96.

Figure 96 PCA Display

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2. Icons can be lassoed by left-clicking and drawing circle around sample(s) of
interest, as shown in Figure 97. This action also highlights the corresponding files
in the table.

Figure 97 PCA Display

3. Points on the plot can also be hidden by right-clicking, then selecting the
appropriate option.
Note: The selected samples are only hidden from the plot.
4. Use the drop-down menus (Figure 98) to select attributes for display by Color
By Attribute and by Shape By Attribute.

Figure 98 Sample Display

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Additional PCA graph display options
 To rotate the graph, right-click, then drag the graph to change its view perspective.
 Click Export Image to save the displayed plot as a PNG graphics file.

Concordance The ChAS Analysis Workflow enables you to perform pairwise comparison
checks concordance checks on genotype calls for all selected samples.
The concordance between all pairwise comparisons for the samples in the results
table are reported.
A reference sample can be selected. Once selected, concordances are displayed.
Compare to reference allows you to compare every sample to a single reference file.

Performing a concordance check

1. In the ChAS Analysis Workflow, select the QC Results tab.
2. Load results files by clicking on Add Files, then navigate to xxCHP files.
After the files are loaded Import Attributes, Export to IGV, and QC Analysis
buttons are enabled.
3. Select files, by either clicking Select All button or by clicking each file’s (left)
check box.
4. Click on the QC Analysis button.
A drop-down menu appears.
5. Click Concordance.
The concordance table with sample, reference and percent concordance is
generated, as shown in Figure 99.

Figure 99 Concordance table example

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Concordance table filter and display options
 To compare to reference sample, select the sample from drop down-menu.

 The default values are set at >98%, 95-98%, and below 95%.
 The three categories of QC are passing, failing, and marginal.
 Each QC category is represented by its own unique color, as shown in Figure 100.

Figure 100 Displayed concordance QC example

Failing Marginal Passing

 Colors in the table can be changed by clicking on the color drop-down

(Figure 101), then choosing a different color from the pallet.

Figure 101 Concordance

color options

 The default values can be changed by either moving the hash marks on the line bar,
or typing in a number in the designated category (Figure 101).
 The data can also be viewed in matrix format by selecting Matrix in the drop-down
menu, as shown in Figure 102.

Figure 102 Table and Matrix options

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Filtering
1. At the table, place your mouse cursor over a Sample or Reference cell.
A filter icon appears. (Figure 103)

Figure 103 Filter icon

2. Right-click on the Filter icon.

A drop-down list appears. (Figure 104)

Figure 104 Drop-down list

3. Click to select the samples you want to filter from the drop-down list.

Changing the view and/or order of sample and reference columns

1. Left-click the Filter icon.
A menu appears. (Figure 105)

Figure 105 Left-click Filter

icon menu

2. Use the menu selections to customize your sample and reference columns.

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Exporting the currently displayed table
1. Click the appropriate, button, then export the file
as you normally would.

Mendelian error checking

Note: The Mendelian Error Checking feature is for the CytoScan family of arrays only.

Running an error 1. From the Analysis menu, select Perform Analysis Setup.
checking analysis The Analysis Workflow window opens. (Figure 106)

Figure 106 Analysis Workflow

2. From the Select array type drop-down list, click to select an array type
(Example: CytoScanHD_Array.
Note: The Select array type drop-down list includes only the array types for
which library (analysis) files have been downloaded from NetAffx or copied from
the Library package provided with the installation.

3. From the Select analysis workflow drop down, click to select the appropriate
Mendelian Error Check Workflow. (Example: CytoScanHD_Array Mendelian
Error Check)
4. By default, the Set workflow name is Workflow. Click inside the Workflow’s
(upper right) text box to enter a different workflow name.

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5. Click each of the three Results files (CYCHP or XNCHP) to analyze Browse
buttons to navigate to and select the appropriate Results File for Child, Mother,
and Father.
You can also run a Mendelian Error Check using two Results files: Child and
Mother or Child and Father.
6. Click the Allele Frequency File Browse button to navigate to and select the
appropriate Allele text file.
Note: An Allele Frequency file is provided in the library file package or you can
create your own custom Allele Frequency File for use in this analysis.
7. Click the Analysis Output File Browse button to navigate to and enter a name
(tab-delimited text filename) for your Mendelian Error Check output result. By
default, the Output name is based on the CYCHP/XNCHP filename used for the
Child.
8. Click Submit.
An error appears if a male is assigned as mother or a female is assigned as father
or if the gender in the actual cychp file is wrong.
The Workflow Dashboard window appears. (Figure 107).

Figure 107 .Files loading inside the Workflow Dashboard

After loading is complete, a Workflow completed successfully message appears.

(Figure 108)

Figure 108 Workflow Dashboard loaded

9. Click View Results List.

The Output folder window (you assigned earlier) appears.
10. Locate the newly created *.cyhd.txt/cyex.txt (or *.cychp.ND.txt) file, then
double-click it to open it in MS Notepad to view it as tab-delimited text file, as
you normally would.
11. Optional: If you want to view the Workflow’s Log File, click View Logs.
The C:\ProgramData\Affymetrix\ChAS\Log folder window appears.

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Locate the newly created Log.txt file, then double-click it to open it in MS
Notepad to view it as tab-delimited text file, as you normally would.

Interpreting an The Mendelian Error Check analysis provides two key points of information:
error checking 1. Are the input samples related?
analysis
 Mother-Child
 Father-Child
If the samples are related, the Role Validity equals 1. If the samples are not related,
Role Validity equals 0. (Figure 109) The output also indicates which CYCHP/XNCHP
file is assigned as the Mother, Father and Child (Index). The analysis also can be run
as a DUO analysis. (Mother-Child or Father-Child).

Figure 109 Trio Output Tool Validity examples

2. Do any chromosomes have an elevated occurrence of Mendelian Errors?

In Figure 110, chromosome 15 has a higher error rate (7.2%) compared to the
rest of the chromosomes in this trio. In this example, the mother has 0% errors
on chromosome 15, whereas the father has 7%, indicating that both
chromosome 15 (or some portion of) alleles were inherited from the mother. It is
recommended to compare the genotypes on chromosome 15 for these samples
using the Graphs tab. For more information, see "Graphs table" on page 345.

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Figure 110 High Instance of Mendelian Errors Table example

Mendelian Errors Description

Report Column

Analysis Type Provides the samples being run through the analysis based on the sample key.
0 = Proband, 1 = Mother, 2 = Father.

Familial Sample Key Tells you the parent for which relatedness is being tested.
1= Mother only used in the analysis.
2= Father used in the analysis (may be father only (duo) or trio).

Role Validity A logical value with 0 being False and 1 being True. If the Role Index Score is > 1000 then the Role
Validity = 1 (likely related). If the Role Index Score is < 1000 then Role Validity = 0 (likely unrelated).

Role Index Score Role Index Score: This score is basically a Log Odds score that computes the probabilities of the
observed genotype calls for the trio while accounting for potential genotyping error. Assume the
following hypothesis: H1 – alleged father is true H2 – alleged father is random male. For each marker,
compute a likelihood ratio of H1 vs H2. Sum all markers. In theory a value of zero means equally likely
probability for either hypothesis. Positive means more likely Paternity related. Negative means more
likely unrelated.

Chromosome/ Chromosome number

Display

Marker Count Number of genotypeable SNPs on the chromosome.

MIE Trio Mendelian Inheritance Error for the Trio. (Ex 119 errors of 56482 SNPs).

MIE Mat Number of errors for Mom.

MIE Pat Number of errors for Dad.

Percentage MIE Number of raw error turned into a percent 119/56482 *100.
Trio

Percentage MIE Percent of errors for Mom.

Mat

Percentage MIE Pat Percent of errors for Dad.

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Analysis workflow troubleshooting

1. Click the Utility Actions button (top right of the Analysis Workflow window)
2. Click to select Log Collection.
The following dialog window appears. (Figure 111)

Figure 111 Log Collection dialog window

3. Make note of the assigned zip folder filename and its location.
4. Use Windows Explorer to navigate to the location.
Example: C:\ProgramData\Affymetrix\ChAS\log
5. Locate the zip folder you noted earlier, then double-click on it to open it.
The folder opens.

Log rollover When the software determines that the log file for the Analysis Workflow
(C:\ProgramData\Affymetrix\ChAS\log\AnalysisWorkflow.log) has reached a defined size
(approximately 4MB), the following steps will be completed:
 A sub-folder will be created in C:\ProgramData\Affymetrix\ChAS\log called 'Log*'
(the * denotes the current date and time).
 A zip file called RolledLogFile*.zip is created in that folder. The '*' is the same date
and time used for the folder name. The files in the
C:\ProgramData\Affymetrix\ChAS\log folder and all files found in the currently
selected QC History Log folder will be included in this zip file.
 The Analysis Workflow files that are associated with analysis workflows that are no
longer active on the Dashboard will be deleted from
C:\ProgramData\Affymetrix\ChAS\log
 A new AnalysisWorkflow.log file will be created in
C:\ProgramData\Affymetrix\ChAS\log

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Log collection When the Log Collection option is selected from the Utility Actions menu, a file called
LogCollection*.zip (the * denotes the current date and time) is created in the folder
C:\ProgramData\Affymetrix\ChAS\log.
This created file contains the full contents of the folder
C:\ProgramData\Affymetrix\ChAS\log, including the log file for the browser
(ChAS_RUO.log).
If available, the sub-folders of C:\ProgramData\Affymetrix\ChAS\log and all files found
in the currently selected QC History Log folder.
Note: All log files for the ChAS database, ChAS Browser and Analysis Workflow can
be found in: \ProgramData\Affymetrix\ChAS\Log

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ChAS can display data from:

 CytoScan Array CYCHP/XNCHP files, generated in ChAS.
 CytoScan HTCMA files, generated in the RHAS.
 Genome-Wide Human SNP Array 6.0 CNCHP files, generated in Genotyping Console
(GTC).
 OncoScan OSCHP files, generated in OncoScan Console or ChAS.
 ReproSeq Aneuploidy results (.zip) from Ion Reporter.

Note: When referring to steps that apply to both CytoScan CYCHP and SNP 6.0 CNCHP
data files, the CHP files are described as CxCHP files. When referring to steps that apply
to CytoScan CYCHP, CytoScan XNCHP, CytoScan HTCMA RHCHP, SNP 6.0 CNCHP
data, and OncoScan files, the resultant files are described as xxCHP files.

Introduction to loading data

The same steps are used to load results xxCHP files from CytoScan arrays, Genome-Wide
Human SNP 6.0 Array, or OncoScan Arrays.
When loading CYCHP files into ChAS for viewing, the software:
1. Loads the run-length encoded segments in the CYCHP file to display as segments.
2. Applies any smoothing or joining that would alter the length and other properties of
segments.

IMPORTANT! In a new user profile, smoothing and joining are turned on by default for
CytoScan 750K and CytoScan HD arrays. Smoothing and joining are disabled for CytoScan
Optima arrays. Smoothing and joining are OFF by default for OncoScan and CytoScan HTCMA
arrays. The smoothing and joining settings are specific for each array type (for more details on
smoothing and joining, see "Copy number segment smoothing and joining (optional)" on page
127).

3. Displays the segments and graph data:

 Segment Data
• Copy Number Gain/Loss
• Mosaicism Copy Number Gain and Loss
• Loss of Heterozygosity (LOH)
 Graph Data
• Copy Number State
• Log2 Ratio
• Weighted Log2 Ratio
• LOH
• Smooth Signal

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• Allele Difference
• B-allele Frequency
• Genotype Calls

When loading XNCHP files into ChAS for viewing from CytoScan XON arrays, the
software:
1. Selects the segments in the XNCHP file to display as segments.
2. Displays the segments and graph data:
 Segment Data
• Loss of Heterozygosity
• Exon Region Gain/Loss
 Graph Data
• Log2 Ratio
• Weighted Log 2 Ratio
• Smooth Signal
• Loss of Heterozygosity (LOH)
• Allele Difference
• B-allele Frequency (BAF)
• Genotype Calls

When loading RHCHP files into ChAS for viewing, the software:
1. Selects the segments in the RHCHP file to displays as segments.
2. Displays the segments and graph data:
 Segments Data
• Copy Number Gain/Loss
• Loss of Heterozygosity
 Graph Data
• Copy Number State
• Log 2 Ratio
• Smooth Signal
• LOH
• Allele Difference
• B-allele Frequency
When loading SNP6 CNCHP files into ChAS for viewing, the software does the
following:
1. Performs segment detection by analyzing the CN and LOH graph data in the
CNCHP file.

Note: When running the Segment Reporting Tool in GTC on SNP 6 data, the software
sets the end coordinate such that the segment ends at the base position of the last
marker in the segment. When loading SNP 6 data into ChAS, the segment detection
sets the end coordinate for a segment such that the segment ends one base after the
last marker in the segment. This may result in a discrepancy between the end position
for segments when comparing data analyzed in both GTC and ChAS.

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2. Applies any smoothing, removing, or joining that would alter the length and other
properties of segments.
Smoothing is similar to the process applied when running the Segment Reporting
Tool in GTC.
Note: ChAS uses the median of the aberrant markers’ CNStates, as the
recalculated CNState of the smoothed (and/or joined) segment.

IMPORTANT! For CNCHP files from the SNP 6.0 Array, smoothing but not joining is turned
on by default in a new user profile.

Displays the Segments and Graph Data:

 Segment data
• Copy Number Gain/Loss
• Loss of Heterozygosity (LOH)
Note: The expected Copy Number State on the X chromosome of normal males
is not constant over its entire length. This is due to the structure of the sex
chromosomes. For more information see "Copy number segments on the X and
Y chromosomes" on page 48.
 Graph Data
• Copy Number State
• Log2 Ratio
• Allele Difference
• SmoothSignal
• LOH

When loading OncoScan OSCHP files for viewing, the software does the following:
1. Displays segments in the OSCHP created by the TuScan Copy number
algorithm. For details on this algorithm, please refer to the OncoScan Console
User Guide (P/N 703195) or Appendix G.

IMPORTANT! Smoothing and Joining are OFF by default for OSCHP files.

2. Displays the segments and graph data:

 Segment Data
• Copy Number Gain/Loss
• Loss of Heterozygosity
 Graph Data
• Copy Number State
• Log2 Ratio
• Weighted Log2 Ratio
• Allele Difference
• B-allele Frequency
• LOH

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• Smooth Signal
• Variant/Somatic Mutation
• Somatic Mutation (OncoScan FFPE Assay only)

When loading ReproSeq Aneuploidy data for viewing, the software does the following:
1. Displays segments from the Ion Reporter software. For details, refer to the Ion
Reporter User Guide: https://ionreporter.thermofisher.com/ir/
2. Displays the whole genome sequencing tiles on the Copy Number State graph.

Loading files
Loading xxCHP data for viewing in ChAS involves the following steps:
1. Optional: Before loading: Select Segment Smoothing and Segment Joining
parameters for processing the CN Gain and Loss Segment data for CxCHP files.

IMPORTANT! Smoothing and Joining are ON by default for CytoScan 750K and HD arrays.
Both Smoothing and Joining are OFF by default for OncoScan, CytoScan HTCMA, and
GenomeWide Human SNP 6.0 arrays. and is disabled for CytoScan Optima arrays and
ReproSeq Aneuploidy data.

XON Segment Merging is turned ON by default for CytoScan XON arrays. For details, see "XON
segment merging" on page 132.

2. Select analysis results from:

 CytoScan Arrays (generated by analyzing CEL files in ChAS)
 CytoScan HTCMA arrays (generated from CEL files in the RHAS.
 Genome-Wide Human SNP 6.0 Arrays (generated by analyzing CEL files in
GTC)
 OncoScan Arrays (generated by analyzing in ChAS)
 ReproSeq Aneuploidy .zip files (generated in Ion Reporter)
You can also select region information files in AED and BED format for loading.
Use the Open window (click the button) to load xxCHP data files, Affymetrix
Extensible Data (AED), or Browser Extensible Data (BED) annotation files. The
AED and BED files that you open will be automatically loaded when a new
session is started with the same user profile. Note: You may want to edit
smoothing and joining parameters. This can be done before or after loading the
CxCHP data. See "Copy number segment smoothing and joining (optional)" on
page 127 for more information.

3. Select File → Open on the menu bar. Alternatively, click the File Open
button.
The Open window appears. (Figure 112)

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Figure 112 Open window

4. To view information about results, select one or more files, then click Sample
Info.
The Sample Info window opens. (Figure 113)

Figure 113 Sample Info window

Note: If the xxCHP and ARR files are located in the same folder, the Sample Info
window shows information about both the sample and the results. To load files
from the Sample Info window, select the files, then click Open Selected Files.

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Using the search 1. Click Close Dialog (Figure 113) to close the Sample Info window.
feature The Open window appears.
2. Navigate to the folder with the files that you want to search for and load.
3. Enter a text string with an asterisk (*) before and after the search term in the File
Name field. See example in Figure 114 on page 123.
4. Select a file type from the drop-down list. See example in Figure 114 on
page 123.
5. Click Open.
Files with names that include the search term are displayed in the Open window.
See example in Figure 115 on page 124.

Figure 114 Enter a file name search term (*text string*) and select a file type

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Figure 115 The Open window shows files with names that include your search term

6. Select the files (you can use Shift click or CTRL click to select multiple files)
7. Click Open.
If any of the files fail the QC checks, a warning notice appears (Figure 116).
You can click Yes to continue to load the files.

Figure 116 Warning Notice for QC failure

It is recommended you load no more than 3 files at one time.

If the following warning message appears (Figure 117), click OK to acknowledge
it or click Cancel to reselect a maximum of 3 files.

Figure 117 Recommended maximum exceeded message

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If the following warning message appears (Figure 118), acknowledge it, then click
OK.

Figure 118 Duplicated files message

If the following warning message appears (Figure 119), click Yes to acknowledge
it.

Figure 119 NetAffx versions message

Note: The ChAS Browser allows loading different NetAffx versions at the same
time (as long as the versions are all from all the same reference and genome
builds). If NetAffx versions are from different builds of the genome (for example
Hg18 and Hg19), The ChAS Browser does not load the files.
A progress bar appears (Figure 120)

Figure 120 Progress bar

After a few moments, the ChAS browser featuring your selected samples
appears.
The loaded files appear in the Files list pane. (Figure 121).

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Figure 121 Files list shows the loaded data

Loaded
File(s)

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Copy number segment smoothing and joining (optional)

“Smoothing” and “Joining” are non-destructive processes that affect the display of
Copy Number segments. Smoothing and joining are performed on the Copy Number
State data during the loading process, based on settings that are specified before
loading. Any data filtering is applied after smoothing and joining.

IMPORTANT! Smoothing and joining are turned on by default in a new user profile for CytoScan
750k and HD Arrays.

Smoothing and Joining are specified per array type. The processes do not affect the
marker data in the CNCHP or CYCHP file. If these settings are turned off, the Copy
Number segment data is displayed without smoothing or joining.

IMPORTANT! Smoothing and Joining affect only data loaded from CNCHP and CYCHP files.
This ONLY applies to copy number data, NOT LOH or Mosaic types. Smoothing and Joining is OFF
by default for CytoScan Optima, OncoScan, and ReproSeq Aneuploidy files.

Segments which have been smoothed and/or joined are indicated by a blue check
mark in the Smoothed/Joined column of the Segments table (Figure 122). The
segment ID name indicates whether smoothing and/or joining has occurred. A red “X”
indicates no smoothing or joining has been applied.

Viewing what 1. Click the Segments tab.

segments were 2. Use the horizontal scroll bar to move the window to the far right.
smoothed/joined
The Smoothed/Joined column appears. (Figure 122)
For more information:
 See “About smoothing” on page 130.
 See “About joining” on page 131.

Figure 122 Example Segments table with smooth/joined segments

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Setting 1. Click Preferences → Edit User Configuration.
smoothing and The User Configuration window appears.
joining
2. Click the Segment Data tab.
parameters
3. Click the Choose Array Type drop-down menu to select the array type to view
or edit its Smoothing and Joining settings. (Figure 123 on page 128)
Note: If you change the smoothing or joining parameters, the new rules are
applied to the original, raw segments of CxCHP files which have not had
modifications, Calls, Interpretations, or Inheritance made. CxCHP files which
have had segments modified or had Calls, Interpretations or Inheritance made
will have had their smoothing and joining parameters fixed and will not adopt
changes made to the array type's Segment Data smoothing and joining settings.

Figure 123 User Configuration window, Segment Data tab

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Segment data tab options and descriptions

Option Description

Use default segment data rules configuration For the CytoScan 750K and HD Arrays, the default smoothing and
joining rules are:
– Smooth Gain or Loss CNState runs to the most common
marker value, then generate segments.
– Join any "split" CNState runs separated by no more than 50
normal-state markers.
– Join Gain or Loss CNState runs interrupted by normal state
data which are separated from each other by no more than
200 kbp
– Skip segments from the smoothing operation for all arrays
that have a CN < 1.
For SNP 6 arrays, the default smoothing rule:
– Smooth Gain or Loss CNState runs to the most common
marker value, then generate segments.

Smooth Gain or Loss CNState runs to the most Smoothing to the most common marker state value is only applied to
common marker value contiguous CNState runs of the same type (gain or loss).

Limit smoothing of CNState data to not smooth If this option is chosen, CNState runs which are farther apart than the
aberrant segments more distant than this number “smoothing maximum jump limit” will not be smoothed. For example,
of CNStates if the smoothing maximum jump limit is set at 1, then adjacent
segments with CNState 3 and 5 will not be smoothed.

Join Gain or Loss CNState runs separated by no If this option is chosen, only Gain or Loss CNState Runs which are
more than this number of markers of normal state separated by less than a threshold number of markers of normal state
data data will be joined. For example, if the marker threshold is set at 50,
then CNState runs separated by more than 50 markers of normal
state data will not be joined.

Join Gain or Loss CNState runs interrupted by For the CytoScan 750K and HD Arrays, the default smoothing and
normal state data which are separated from each joining rules are:
other by no more than this distance measured in – Smooth Gain or Loss CNState runs to the most common
kbp marker value, then generate segments.
– Join any "split" CNState runs separated by no more than 50
normal-state markers.
– Join Gain or Loss CNState runs interrupted by normal state
data which are separated from each other by no more than
200 kbp
For SNP 6 arrays, the default smoothing rule:
– Smooth Gain or Loss CNState runs to the most common
marker value, then generate segments.

Limit the joining of CNState data (which flanks Smoothing to the most common marker state value is only applied to
normal state data) to not join aberrant segments contiguous CNState runs of the same type (gain or loss).
more distant than this number of CNStates

IMPORTANT! If multiple smoothing and/or joining check boxes are selected, all criteria must
be met to smooth and/or join the segments.

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After smoothing and joining, the marker count, mean marker distance and confidence
values get recalculated. For more information:
• See "About smoothing" on page 130.
• See "About joining" on page 131.

About smoothing Note: The examples shown below are for a case where the expected copy number is
2. Similar calculations take place for the X and Y chromosomes where the expected
copy number may be 0, 1 or 2, depending on gender and whether the segment is
located within or outside of the PAR region.
If you have a contiguous set of segments with gain values (for instance, of CN State
values of three and four), with no markers of copy number 2 or lower, without
smoothing they will be treated as a series of individual gain segments. The same rules
apply to a set of segments with loss values of 0 or 1.
If you have a contiguous set of markers with gain values of three and four, with no
intervening markers of copy number 2 or lower, with smoothing they will be
consolidated into a single gain segment. (Figure 124)

Figure 124 Simplified schematic representation of smoothing

If you have a contiguous set of markers with loss values of zero and one, with no
intervening markers of copy number 2 or higher, after smoothing, they will be
consolidated into a single loss segment.

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The smoothing process is the same as the process automatically performed by the
Segment Reporting Tool in GTC. Different methods are used to assign the CN state
value and perform the confidence calculations, as described below. See the GTC User
Manual for more information.

Copy Number State for Smoothed Segments

The median CNState of all the markers in the Segment is assigned as the Copy
Number State value for the new smoothed segment. The median will thus always be
either an integer or a half integer (like 3.5).
For all the half-integer cases:
 Gains are rounded up to the next full integer (3.5 goes to 4)
 Losses are rounded down to the next full integer (0.5 goes to 0, 1.5 goes to 1).

About joining The joining options enable you to join segments with the same type (gain or loss)
aberrant CNState that are separated by no more than a specified number of normal-
state markers or by no more than a specified distance of normal-state data
(Figure 125).

Figure 125 Simplified schematic representation of joining

The equivalence of CNState of the segments to be joined could have happened as a

result of smoothing, or been from “raw” unsmoothed segments with the same
CNState.

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XON segment merging

Note: Implementation of the new Whole Genome Copy Number segmentation
algorithm may make XON merging no longer necessary in your workflow.
XON Merging is on by default. XON Merging combines consecutive XON segment
calls of the same Type (XON Region Gains or XON Region Loss) into a larger segment.
Once an XON segment of a different Type (normal state or gain/loss) is encountered,
the XON Merge is terminated. A Merged XON segment is represented as the larger
segment in the Segments Table.
Note: The individual XON segments can still be viewed within the rectangle, provided
the appropriate Levels are selected in the Filter Settings. In addition, the breakpoints
of the Merged XON Segment will stop with an XON segment and may not line up
exactly with the probe level data.
Note: A merged XON segment is assigned to the lowest XON annotation number
within that merged segment. For example, if a merged XON segment overlaps XON
Regions annotations of Level 1 and Level 3, the whole merged XON segment will be
considered Level 1.
The Merged XON segment is represented by the transparent rectangle. (Figure 126) If
you want to turn off this feature see "Turning off XON merging".

Figure 126 Merged XON segment example

Turning off XON 1. To turn off XON Merging, go to Preferences → User Configuration.
merging The User Configuration window appears. (Figure 127)

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Figure 127 User Configuration window, Segment Data tab

2. Click the Segment Data tab, then select CytoScan XON from the array drop-
down.
3. Uncheck the Use default segment data rules configuration check box
4. Uncheck the XON Merging check box.
5. Close the ChAS browser, then reopen it.
XON Merging is now off/disabled.

Setting QC parameters in the ChAS browser

ChAS checks the analysis results files for certain QC values. The software notifies you
if the QC parameters do not meet the thresholds.
Note: Custom QC metrics can be viewed in both the Analysis Workflow and the
Browser. However, any custom settings you wish to use, have to be entered
separately in both the Analysis Workflow and the Browser. To create custom QC
settings in the Browser see below. To create custom QC settings in the Analysis
Workflow, see "Creating your own custom QC setting" on page 57.
You can adjust the QC threshold values or select different QC metrics.

IMPORTANT! Selecting different QC thresholds is not recommended.

Note: When using custom QC thresholds for CytoScan HTCMA in RHAS, these
custom thresholds will also need to be updated in ChAS to reflect the desired QC
thresholds.

Viewing QC 1. Click Preferences → Edit User Configuration.

thresholds The User Configuration window appears.
2. Click the QC Thresholds tab. (Figure 128)
3. Select an array type from the drop-down list.
Note: QC parameters are specified per array type.

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Figure 128 CytoScan HD array QC Thresholds default settings.

QC Thresholds tab options and descriptions

Option Description

Property Name SNPQC is a QC metric for SNP probes that is derived from polymorphic (SNP) probes
MAPD is a QC metric for all probes used to determine copy number that is derived from both polymorphic
(SNP) and non-polymorphic (CN) probes
Waviness SD is a global measure of variation of microarray probes that is insensitive to short-range
variation and focuses on long-range variation.
nd SNP QC is a QC metric for SNP probes that is derived from polymorphic SNP probes in normal diploid
regions.
nd Waviness SD is the same measure as Waviness SD, but only calculates in those regions that are
identified as normal diploid.
Cel Pair Check is a test that inspects each pair of intensity (*.cel) files to determine whether the files have
been properly paired and assigned to the correct channel. (OSCHP only)
DQC (DishQC) measures the amount of overlap between two homozygous peaks created by non-
polymorphic probes. DQC of 1 is no overlap, which is good. DQC of 0 is complete overlap, which is bad.
QC Call Rate is the percentage of autosomal SNPs with a call other than NoCall (measured at the Sample
QC step).
SMN MAPD is a QC metric for all probes used to determine copy number that is derived from both
polymorphic (SNP) and non-polymorphic (CN) probes calculated during SMN analysis.
SMN WavinessSD is a global measure of variation of microarray probes that is insensitive to short-range
variation and focuses on long-range variation calculated during SMN analysis.
Note: The property names are from the header information of the xxCHP file. QC thresholds are not
established for Reproseq Aneuploidy files, but QC metrics are displayed in the QC and Sample Info tab.

Type Value or algorithm used for that type of QC.

Operator The type of comparison performed.

Value Value assigned to the threshold.

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Table 10 Default Copy Number QC Thresholds

Array Type QC Parameter

MAPD snpQC Waviness SD ndsnpQC ndWavinessSD

CytoScan 750K and HD Arrays < 0.25 >15.0 < 0.12 - -

CytoScan XON Arrays < 0.20 >10.0 < 0.08 - -

CytoScan (Normal Diploid Analysis) < 0.25 > 15.0 < 0.12 > 15.0 < 0.12

CytoScan HTCMA =< 0.28 >= 10 = 0.07 =- =-

CytoScan Optima Array MAPD < 0.29 > 8.5 < 0.12 - -

Genome-Wide Human Array SNP 6.0 < 0.35 - - - -

Table 11 Default Genotyping QC Thresholds

Array Type QC Parameter

DQC QC Call Rate

CytoScan HTCMA > = 0.88 98.5%

Arrays

Table 12 Default SMN QC Thresholds

Array Type QC Parameter

SMN MAPD SMN WavinessSD

CytoScan HTCMA = < 0.35 = < 0.1

Arrays

Table 13 Default QC metrics for OncoScan Arrays

Array Type QC Parameter

MAPD ndSNPQC CelPairCheckStatus

OncoScan Arrays < 0.3 > 26 Pass

Note: The waviness SD metric is applicable to blood and cell line data. The waviness SD
metric is not intended for alternative sample types such as solid tumor or FFPE samples
in which the results may vary as a result of the biological complexity. For these sample
types, it is recommended using nd Waviness SD.
Effect of SNPQC value (for a Single Sample Analysis) on the Allele Difference Track.
(Figure 129)

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Figure 129 SNPQC Metric vs. Track Quality

SNPQC is one of the CytoScan within-array QC metrics which provides insight into
the overall level of data quality from a SNP perspective. When evaluating the SNPQC
values, the key consideration is to ensure that the threshold is exceeded. The quality
of the SNP allele data is compromised, from an interpretation perspective, when the
SNPQC values are below the recommended acceptance threshold as illustrated by
the two left most graphs representing the two and three copy allelic state.
For the CytoScan HD array, when the SNPQC value is below 15, (as illustrated by the
data in the two graphs above), the noise within the array is higher than expected. This
in turn, compromises the overall data quality and clarity of the results. However, when
the SNPQC value is above 15, the consideration is whether the SNPQC value is above
or below the threshold value and not the absolute magnitude.
As long as the SNPQC value exceeds the threshold, there is a retention in the data
quality as illustrated by the graphs which demonstrate clear allelic data across a broad
range of SNPQC values that exceed the recommended threshold. The threshold was
determined from thousands of arrays processed across multiple reagent lots,
operators, and sample aberration types. SNPQC is one of the metrics used to assess
array quality and should be helpful in determining which experimental data sets are of
satisfactory quality to continue with subsequent interpretation.

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Adding a QC 1. Click Preferences → Edit User Configuration.
property The User Configuration window appears.
2. Click the QC Thresholds tab. (Figure 130)

Figure 130 Adding a new row to the QC Thresholds table

New Row

3. Select an array type from the drop-down list.

4. In the QC Thresholds tab, uncheck the Use default QC configuration check
box.
5. Click the Add button .
A new row appears in the table.
To delete a property row, select the row, then click the Remove button.
6. Click the Property Name field, then enter a new QC property name.
7. Click the Type field to select Decimal Number or Whole Number.
8. Click the Operator field to select an operator from the drop-down list.
9. Double-click the Value field to enter the threshold value for the newly added QC
property.
10. To add another QC property, repeat steps 5-9.
11. Click OK to apply the newly added QC threshold(s).

Editing an 1. Click on an existing Property Name, then edit its QC property name.
existing QC 2. Click the Type field to edit its Decimal Number or Whole Number.
threshold
3. Click the Operator field to choose a different operator from the drop-down list.
4. Double-click the Value field to edit the current threshold value.
5. To edit another existing QC property, repeat steps 1-4.
6. Click OK to apply the newly edited QC threshold(s).

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Histogram data

Loading
histogram data
IMPORTANT! You must be logged into the ChASDB to view Histogram data.

The histograms load by default. If they are not currently displayed, click ChAS DB →
Refresh ChAS DB data to view them in the ChAS Browser.
Note: The histograms are only available for NetAffx Genomic annotation files for
genome build Hg19. The Browser produces an error message, if you try to load Hg19-
based histograms while a hg18 or hg38 based NetAffxGenomeAnnotation is currently
displayed.

Changing the 1. From the File tree (upper left column), locate the Default Histogram entry.
default histogram 2. Right click on Default Histogram.
filters
A menu appears.
3. Click View/Edit Properties.
The File Properties window appears. (Figure 131)

Figure 131 File Properties window and Default Histogram Filters tab

4. Click the Histogram Filters window tab, then use its check box(es), selections,
and radio buttons to modify the default Histogram’s factory settings.
5. Click on the Change Filter Parameters button to select new filter settings.

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6. Optional: To change filter parameters, click Change Filter Parameters.
The Set Filter Parameters window appears. (Figure 132)

Figure 132 Set Filter parameters window

7. Use this window’s check boxes, pre-populated entries, and/or the provided text
fields (to enter the filter parameters you want).
8. Click OK to save your changes.
Note: If using the aDGV containing segments from both HD and XON arrays, use the
Categories filters to limit the histogram data to only HD (check Gain and Loss) or only
XON (Gain XON Region and Loss XON region)

Changing the 1. From the File tree (upper left column), locate the Default Histogram entry.
default histogram 2. Right click on Default Histogram.
colors
A menu appears.
3. Click View/Edit Properties.
The File Properties window appears.
4. Click on the Histogram Colors tab. (Figure 133)

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Figure 133 File Properties window and Histogram Colors tab

5. Click on the color square representing the histogram track you want to change.
A change color window appears.
6. Select a new color, then click OK.
7. Repeat steps 5-6 as needed.
8. Click OK to save your color changes or click Reset to Defaults to return to the
default color settings.

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Adding filtered You can add additional histograms filtered on certain properties for viewing in the
histogram data Detail View.
1. Go to ChASDB → Add Histogram
The Add a Histogram window appears. (Figure 134)

Figure 134 Add a Histogram window

2. In the Label text box, enter a name for the histogram.

3. In the Graph Style pane, click the appropriate check box(es) and/or radio
button(s) to define your filtered Histogram’s graphic style.
4. Use this window's check boxes and radio buttons to create the desired graph
style. Click on the Change Filter Parameters button to select filters to be
applied to your new histogram. Click on the Histogram Colors tab to select
colors for your new histogram tracks. See "Changing the default histogram
colors" on page 139 for details.
5. Click OK.
The histogram is added to the bottom of the File tree list. The histogram can be
moved to a different position in the Detail View by clicking on the name of the
histogram, then dragging it to the desired location within the File tree.
You can access what segments are in a particular bin of the histograms by right-
clicking on the histograms and selecting, Show Histograms items in bin. For more
details, see "Segment intersections" on page 393.
Note: When right clicking to Show Histograms in bin, the percentages for DB
Coverage Count and DB Overlap Count columns in the Segment Intersections window
represent the percentage intersection with the query region (the light blue vertical
bars) shown in the Segment Intersections window. For more details on this Segment
Intersection window, see Figure 431 on page 394.

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Removing a 1. Locate the Histogram you want to remove in the Files window pane. (Figure 135)
histogram 2. Right-click on it, then click Close.
Note: Closing a Histogram removes the Histogram from the Detail View. In order
to view this Histogram again, you must recreate it using the Add Histogram steps
listed above. See "Adding filtered histogram data" on page 141.

Figure 135 Right-click on a

Histogram to remove it.

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Displaying options of analysis results data

 Graphic Displays
See “Displaying data in graphic views” on page 152.
 Tables
See “Displaying data in table views” on page 327.
After the data is loaded, you can:
 Filter the segments by Segment Parameters to hide segments that do not meet
your requirements for significance. See “Filtering segments” on page 217.
 Select a region information file for use as a CytoRegion file and:
 Perform differential filtering for segments in CytoRegions and in the rest of the
genome.
 Display only segments that appear in CytoRegions using Restricted Mode. See
“Using CytoRegions” on page 267.
 Select a region information file for use as an Overlap Map and use the Overlap filter
to conceal segments that overlap with the Overlap Map items. This functionality
may be helpful for tracking or filtering out benign copy number change regions.
See “Using the overlap map and filter” on page 279.
 Add selected features of the genome to new or existing Region (AED) files, and edit
annotation data on existing annotations. See “Creating and editing AED files” on
page 287.
 Prepare reports on your findings by exporting graphics and table data in PDF and
other formats. See “Exporting results” on page 415.
 Save setups of ChAS for different tasks in user profiles and named settings.See
“User profiles and named settings” on page 438.

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Overview of ChAS window components

Figure 136 ChAS window

Menu Bar
Tool Bar

Karyoview in
Upper Display Area

Files List

Selected
Chromosome

Named
Setting
drop
down list

Detail View in
Lower Display Area

Data Types
List

Status Bar

The ChAS window components (Figure 136) include:

 Menu Bar: Access to the functions of the software.
 Tool Bar: Quick access to commonly used functions.
 Files List: Displays data and annotation files that can be displayed. (page 145)
 Data Types List: Displays the type of data available in the files. (page 147)
 Named Settings: Displays a list of the previously saved display settings for ChAS.
(page 148)
 Status Bar (page 148): Displays:
 Software status
 ChAS Browser’s NetAffx Genomic Annotation file version.
 hg version
 The annotation or probe that your mouse pointer is nearest (in the Detail View).

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 Display Area (page 149): Displays the following data in graphical and table
formats:
 Analysis results graph data.
 Detected Segments
 Histograms
 Regions
 Reference Annotations

Files list
The Files list (Figure 137) displays the different sources of data and annotations that
are loaded in the Chromosome Analysis Suite. Files are grouped by type in the Files
list.

Figure 137 Files list

Sample data

AED/BED regions file and VCF files

Reference annotations* and Histogram

information

Markers and Cytobands

*Reference annotations displayed may be different than shown above depending on the NetAffx Genomic
Annotation file loaded.

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Displayed files grouped by type:
 Sample Data
Colored nibs display the color used for the data lanes for that sample in the
Karyoview, Selected Chromosome View, and Detail View. The appropriate
gender symbol is displayed to the right of the colored nib.
If a loaded file has a QC parameter that is out of range, an alert symbol
appears next to the file name. (Figure 138)

Figure 138 QC alert for Sample Data files

 Region Information Files

 Icons indicate the file type (AED or BED) and whether the loaded files have been
selected as a CytoRegion file or Overlap Map file.
 Reference Annotations (loaded during software start-up). Note: Icons indicate the
annotation type.
 Histogram information (loaded during software start up if connected to ChAS DB).
 Cytobands (Separated from other reference annotations because cytobands
cannot be moved in the displays)
See “Selecting data for display” on page 190. for information on using the Files list to
select loaded data and region information files, and reference annotation for display.
You can export the feature information in these files to a new AED region information
file. See “Exporting information in AED or BED format” on page 318..

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Data types list

The Data Types list (Figure 139) shows the types of data available for display in the
Karyoview, Selected Chromosome View, and Detail View. The available data types may
vary, depending upon the type of sample data available. See “Introduction to loading data”
on page 118.

Figure 139 Data Types list

The Data Types list enables you to select from Segments data and Graph data.
The Segments data is displayed graphically in:
 Karyoview
 Selected Chromosome View
 Detail View
If filtering is applied to a segment type, a funnel icon appears next to the segment
symbol in the list.
Graph data, indicated by the icon, is displayed only in the Detail View. See "Detail view"
on page 170 for more information.
Unselected data is also concealed from the different tables and graphs.
See “Selecting data types for display” on page 192. for information on using the Data
Types list to select different data types for display.

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Named settings
The Named Settings drop-down list (Figure 140) enables you to apply a previously
created setting for ChAS. The settings may include things like:
 Segment Filter and Overlap Map Filter settings
 Types of data to be displayed
 Restricted Mode ON/OFF status. See “Using restricted mode” on page 275.

Figure 140 Named Settings

Note: Default Named Settings (indicated by the icon) should not be deleted from
the system because they are shared by all user profiles.
See Chapter 20, "User profiles and named settings" on page 438 for information on
creating and using Named Settings.
Note: The OncoScan Default Named Setting has no filters applied so all segments
called by the TuScan algorithm can be viewed. Users can create their own appropriate
custom filter Named Setting for their data, see "User profiles and named settings" on
page 438.

Status bar
The status bar (Figure 141) (very bottom of browser) displays information on:
 NetAffx Genomic Annotation database and its hg version
 Restricted Mode status (See “Using restricted mode” on page 275.)
 Edit Mode status (See “Using edit mode” on page 224.)
 Cursor (Mouse Over) Position
 User Profile ID

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Figure 141 Status Bar

NetAffx Genomic Annotation Restricted Mode Cursor Position information User Profile
database and its hg version Indicator ID
currently loaded in the ChAS
Browser (the database is not
array-specific)

Display area
The Display Area (Figure 142) is divided into three panes:
 "Upper panes" on page 150
 "Selected chromosome view" on page 150
 "Lower panes" on page 150

Figure 142 Display Area showing Segments Table and Detail View

Selected
Chromosome

Karyoview pane

Details View
pane

Chromosome
Selection List

The tabs in the upper and lower panes display different types of data, in both graphical
and table formats. Data from the same sample files is displayed in all three panes.
You can display a pane in a separate window by clicking the icon on the tab.
To close the window and return the information to the tab panel, click the icon in
the window.

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Upper panes The Upper pane displays the following data in graphics and table formats:
 "Karyoview" on page 153: Displays selected segment types for selected sample
files for all chromosomes.
 "Segments table" on page 337: Displays a list of the detected segments in the
selected sample files.
 "CytoRegions table" on page 272: Displays a list of the Regions in the AED/BED
file selected as the CytoRegion file. Includes information on detected segments
which lie in CytoRegions.
 "Viewing the overlap map table" on page 283: Displays a list of the Regions in the
AED/BED/Reference Annotation file selected as the Overlap Map. Includes
information on detected segments that are overlapped by Overlap Map Items.
 "Graphs table" on page 345: Displays marker data for the loaded and selected
xxCHP files.
 "Variants table" on page 351: Displays somatic mutation data from OncoScan CNV
Plus and Carrier Variant data from CytoScan HTCMA arrays.
 Query Samples Table: Displays sample level results from searches performed on
the ChAS DB.
 Query Segments Table: Displays segment level results from searches performed
on the ChAS DB.

Selected The Chromosome View displays detected segments in selected sample files for the
chromosome chromosome selected in the Karyoview, while the Chromosome Selection List (far
view right column) displays its number.
See "Selected chromosome view" on page 168 for more information.

Lower panes The Lower Pane displays:

 "Detail view" on page 170: Displays the selected section of the chromosome
displayed in Selected Chromosome View and includes:
 Detected segments, variants, and graph data in selected xxCHP files.
 Histograms, AED/BED file regions and annotations.
 Reference annotation files
 "QC and sample info tab" on page 355: Displays QC metric information as well as
information about the loaded Sample and Region (AED) files.
 "Chromosome summary data" on page 362:
 Summarizes particular data across each chromosome in the loaded sample
data files (for example, proportion of each chromosome found to be in the state
of LOH).
 Calculated Properties: Calculates the Percent Autosome LOH in the sample
based on the LOH filter setting.

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Changing the NetAffx genomic annotation file version 7

Changing the NetAffx genomic annotation file version

1. At the top menu bar, click File → ChAS browser NetAffx Genomic Annotation
file version.
2. From the Select NetAffx Database drop-down menu (Figure 143), click to select
the NetAffx Build version you want, then click OK.
Note: If there are loaded xxCHP files with hg version different from the selected
NetAffx database, a message appears stating that these data files will be closed
(in both the ChAS browser and the MSV) before the NetAffx annotations are
loaded.
Note: More current NetAffx Genome Annotation files have the date the file was
generated imbedded into the file name. To load the most current file from your
library folder, select the file with the most recent date.

Figure 143 Select a NetAffx Genomics Annotation file

version

For more information on what types of data is in the database files and how this
information varies in different versions, see "ChAS browser NetAffx Genomic
Annotations" on page 487.

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ChAS provides multiple graphic views for detected segments and other data.
Use these graphic views to:
 Get an overview of the detected segments.
 Get an overview of segments stored in the ChAS DB.
 Compare segments between samples.
 View sample data for the whole genome.
 Drill down to examine areas of interest in more detail.
 View the graph and marker information used to generate the detected segments.
 Take advantage of reference annotations and external web sites.
 Create your own Affymetrix Extensible Data (AED) files with regions of interest and
annotations.

Graphic views
Data can be displayed in a Karyoview, Whole Genome View, Selected Chromosome
View, and a Detailed View, as shown in Figure 144.

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Figure 144 Graphic display views

Karyoview

Selected
Chromosome
View

Detail View

Data from the same sample files is displayed in all the views at different scales.
If an item in any of the views is selected, the icon for that item is enlarged or
highlighted in the views.

Karyoview The Karyoview (Figure 145) displays a genome-wide view of the detected segments
and other data.
In the Karyoview:
 Click a chromosome in the Karyoview to select it.
 Press Ctrl + Left/Right Arrow keys to move between chromosomes.
 To jump to chromosome 1, press Ctrl+Home
 To jump to chromosome Y (last chromosome in the Karyoview), press the
Ctrl+End.

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Figure 145 Karyoview Controls

Vertical
Stretch Scroll
Slider Bar

Selected Chromosome

Using the mouse, click and drag on a selected chromosome to select an area for
display in the Detail View. This area is highlighted in the Selected Chromosome View.
(Figure 146)

Figure 146 Karyoview, Selected Chromosome View, and Detail View

Selected
Chromosome

Detail View

Note: To easily remove the blue highlight surrounding the selected chromosome for
image captures, go to View → Hide Karyoview Highlights.

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Use the Stretch Slider and Vertical Scroll Bar to zoom in on a section of the Karyoview.
You can also use the mouse wheel as detailed below:
 Alt + mouse wheel stretches the display.
 Mouse wheel scrolls up and down.
The following information is displayed for each chromosome: (Figure 147)
 Chromosome number
 Cytobands
 Segment Data - Uses separate lanes for each sample file and each displayed
segment type. Each sample is assigned a unique color in the display that is used
for the lane. You can:
 Change the grouping of samples and segment types. See "Changing the
grouping of samples and data types" on page 193.
 Change the position of samples. See "When the lanes are grouped by sample,
the different segment types for each sample are kept together in the Karyoview
and Selected Chromosome View (Figure 189) and in the Detail View." on page
194 and "Lanes grouped by sample" on page 194.
 Variant Data (only available for OSCHP and RHCHP)
 CytoRegions in selected CytoRegion File.
 Items in selected Overlap Map file.

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Figure 147 Detail of a highlighted chromosome

Cytobands Segment Data lanes for the different samples

Section selected for display in

Chromosome View and displayed in
Detail View

Items in CytoRegions displayed as gray bands

Overlap Map that stretch across the entire
chromosome cell

Chromosome
Number

Click on a chromosome in the Karyoview to select it for display in the Selected

Chromosome View and the Detail View. The selected Chromosome is highlighted in
the Karyoview.
The Stretch Slider and the vertical scroll bar controls the vertical stretch of the Display
area.
At higher magnifications, more details of the Cytobands are displayed in the
Karyoview. You can see Cytoband labels if the display has room.
The portion of the chromosome selected in the Selected Chromosome View and
displayed in the Detail View is highlighted in the Karyoview.

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If you have selected a CytoRegions file, the CytoRegions are displayed as gray bands that
stretch across the entire chromosome cell, from right to left of the Cytobands.
If you assigned an Overlap Map file, the overlap map items are displayed as small
rectangles to the left of the cytobands. Its color is the same color used in the Details View.
Note: You can mouse over a feature in the Karyoview, Selected Chromosome View, or
Detail View to display a pop-up with information about the feature. Also, you can right-click
on a feature in the Karyoview or Selected Chromosome View to open a shortcut menu of
options, as shown in Figure 148.

Figure 148 Karyoview shortcut menu

Whole genome view

The Whole Genome View (Figure 149) displays the following data in a single display from
Chromosome 1 to Y for:
 CYCHP: Log2 Ratio, Weighted Log2 Ratio, Copy Number State, Smooth Signal, LOH
Allele Difference, and B-allele Frequency.
 XNCHP: Log2 Ratio, Weighted Log2 Ratio, Smooth Signal, LOH, Allele Difference, and
B-allele Frequency.
 CNCHP: Log2 Ratio, Copy Number State, Smooth Signal, Allele Difference
 RHCHP: Log2Ratio, Smooth Signal, Copy Number State, LOH, Allele Difference, and
B-allele Frequency.
 OSCHP: Log2 Ratio, Weighted Log2 Ratio, Copy Number State, Smoothed Signal,
Allele Difference, and B-allele Frequency.
 ReproSeq Aneuploidy .zip: Copy number state data provides the sequencing tile
data.

Note: When opening ReproSeq for the first in the Whole Genome View, the graphs may
appear empty. Use Choose Data to select the Copy Number Graph type to view the data.

Note: The Y axis on the left represents the data points in that graph (Log2/Weighted Log2
Ratio). The Y axis on the right represents the line graph data (Smooth Signal/Copy
Number).

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Displaying the 1. Right-click on the Sample name in the File Tree (Figure 149), then select Show
Whole Genome WGV.
View for a
sample(s) Figure 149 Right-click menu - File Tree

2. The Whole Genome View for the selected file(s) opens. (Figure 150)

Figure 150 Whole Genome View

3. To select a different sample(s) to display:

 Select File → Choose File.
 Click on a different file name, then click OK.

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Changing graph 1. Click on View → Choose Data.
types The Choose Data window appears. (Figure 151)

Figure 151 Choose Data window

 Up to three rows of data can be viewed simultaneously for each sample.

 Use the Row Data and/or Row Line to assign which data tracks to view.
 Select <no Dots> or < no Line> to disable the display (of any data) in the row.
Figure 152 is an example of no data being assigned to the Bottom Row, therefore
only two rows of data are displayed in the Whole Genome View.

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Figure 152 Choose Data window

Note: The Y axis settings for the Whole Genome View are initially determined from the
Y axis settings set in the Detail View Graph Settings. The Y axis on the left of the WGV
pertains to the Row Data. The Y axis on the right of the WGV pertains to the Line data.
Also, not all graphs are available for a given xxCHP file. If a graph type is selected in
which data is not available, the graph will appear with no data points.

Changing colors Graphs can be viewed in a single color or alternating colors every three chromosomes.
of the data points 1. Click View → Choose Data. (Figure 153)
or line data
Figure 153 Choose Colors pane

2. Select the radio button to change to either 1 color data points or alternating 3
color data points.

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3. Click on the colored square(s) to open a Color Selection palette. Select new colors
for the Whole Genome View.
4. Click OK to return to the Whole Genome View with your new selection
.

Note: Changing Data display and/or Colors affects the current sample only. To save these
settings as default setting (whenever a file is opened), save these settings as the Default
WGV State. (See "Setting a default WGV state display and colors".)

Setting a default 1. Select the Data and Colors to be displayed as your Default settings when opening
WGV state files in the WGV, as described in "Changing colors of the data points or line data" on
display and colors page 160.
2. Select View → Save as default WGV State. (Figure 154)

Figure 154 Save as default WGV State

A confirmation message appears.

3. Acknowledge the message, then click OK to save these settings as the Default WGV
display.

Note: If changes have been made to colors, data or Y axis values, you can return to this
WGV Default State by clicking View → Apply default WGV State or click Load a WGV
State → Default.

Creating WGV Multiple WGV States can be created, then saved for a quick selection of different graph/
states color settings.
1. Select the Data and Colors to be displayed as your Default settings when opening
files in the WGV.
2. To save these selections as a WGV State, click on View → Save WGV State.
3. Enter a name in the dialog box, then click OK to save this new WGV State.

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Applying a saved 1. Select View → Load a WGV State.
WGV state(s) 2. Choose a saved WGV state from the drop-down list.
3. Click OK to apply the WGV State (or click Cancel to keep the current display).

Deleting a saved 1. Click on View → Delete a WGV State.

WGV state 2. Select the saved WGV state you want to delete from the drop-down list, then
click OK.
A message appears asking if you are sure you want to delete it.
3. Click OK or click Cancel to keep the WGV State.

Using the WGV zoom feature

1. Click on the chromosome number that appears along the bottom row, as shown
in Figure 155.

Figure 155 Zoom in

2. The following “zoomed in” WGV window appears. (Figure 156)

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Figure 156 Zoomed in WGV window

3. Click Previous or Next to view adjacent chromosomes in this window.

4. To return to the Whole Genome View (Figure 155), click on the chromosome
number again or click View→ Show all chromosomes.

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Adding a reference line to the WGV

1. Click on the + (above the panel) to add a reference line to that panel.
Note: When a row of data has both Dots and Line data, click the + sign next to
the data type to which you would like to add the Reference Line.

Figure 157 Add a reference line

2. Click on the Line color button to select a color for the Reference Line.
3. In the Coordinate text field, enter an approximate coordinate (based on the Y
axis) where you want the Reference Line placed.
Note: The Reference Line can be dragged and dropped to a different location
once placed onto the graph.
4. Click OK.
5. Repeat steps 2-4 to place additional Reference Lines onto the graph.
Note: Additional Reference Lines can also be added by right-clicking in the
graph and selecting Add Reference Line for... (Figure 158)
6. Delete a single Reference Line by right-clicking on the Line and selecting Delete
Selected Line. Remove all Reference lines by right-clicking in the graph and
selecting Delete All Lines. (Figure 158)
7. To change the color or coordinate of a Reference Line, right-click on the selected
Reference Line, then select Edit Selected Line. (Figure 158)

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Figure 158 Add a reference line - right-click menu

Adding a Use this feature to view two samples in the same WGV window.
comparison file Note: Before using this feature, both analysis files MUST BE loaded and available in
the ChAS Browser.
1. Open the first file in the Whole Genome View, as you normally would.
2. Click File → Add Comparison File.
A Comparison File window opens with available analysis results files loaded into
ChAS Browser.
3. Click to highlight the file to be viewed with the first file (already open in the WGV),
then click OK.
The data for the files are loaded in the same window (Figure 159) displaying the
following alternating tracks:
 Track 1: Weighted Log 2 and Smooth Signal for File 1
 Track 2: Weighted Log 2 and Smooth Signal for File 2
 Track 3: Allele Difference for File 1
 Track 4: Allele Difference for File 2
 Track 5: B-allele Frequency for File 1
 Track 6: B-allele Frequency for File 2

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Figure 159 Example of the displayed alternating tracks

Note: To remove a comparison file, click File → Remove Comparison File.

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Selecting a new 1. Click on the second of the filenames to open the file selection window
comparison file 2. Highlight a new file from the Choose a comparison file window (Figure 160),
then click OK.

Figure 160 Selecting a new comparison file

The newly selected file and its data is displayed.

Exporting a WGV 1. Click File → Export window PNG.

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Selected chromosome view

The Selected Chromosome View (Figure 161) is similar to the Karyoview, but it
displays a single selected chromosome at higher magnification. Click, then drag in the
Chromosome View to select an area for display in the Detail View.

Figure 161 Selected Chromosome View

Markers Segment Data lanes for the different samples
Cytobands

Shaded areas are not displayed in

the Detail View
Vertical
Stretch Slider Regions in CytoRegions file
(shown in darker gray)

Items in Overlap Area selected in Chromosome View that

Map is displayed in the Detail View

Position Indicator

Vertical Scroll Bar

Shaded areas are not displayed in

the Detail View

Regions in CytoRegions file

(shown in darker gray)

hromosome
umber

Use the Stretch Slider and Vertical Scroll Bar (Figure 161) or press the Alt key and turn
the mouse wheel to zoom in on a section of the Selected Chromosome View.
If you have selected a CytoRegions file, the CytoRegions are displayed as gray bands
that stretch across the entire chromosome cell (from right to left of the Cytobands).

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If you have selected an Overlap Map file, the overlap map items are displayed as small
rectangles (Figure 161) to the left of the Cytobands. Its color is the same color used
in the Details View.
The Position Indicator is a dashed horizontal blue line. Click in the Selected
Chromosome View to set the position of the indicator. The position is highlighted in
the graphs table and used as the center point when zooming.
The marker positions are displayed to the right of the Cytobands. When zoomed out,
they appear as green ribbons. When zoomed in, the markers and their positions can
be seen, as shown in Figure 162.

Figure 162 Selected Chromosome View, markers in zoomed-out view (left)

and zoomed-in view (right)

Position
Indicator

Markers

 SNP markers are displayed in the light green band nearest the cytobands. The SNP
marker/probe names in the CytoScan start with the letter ‘S’.
 There is one marker track for every distinct array type that is loaded.
 Copy Number markers are displayed in the dark green band nearest the detected
segments. The non-polymorphic copy number probe names on the CytoScan start
with the letter ‘C’.
 You can mouse over a marker to learn more about it.
 Segments selected in any view are highlighted in the Selected Chromosome View.
 For information on the other features of the Selected Chromosome View, see
"Selected chromosome view" on page 168.

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Detail view
The Detail View (Figure 163) enables you to look in detail at the detected segments,
marker data, regions, and reference annotations for the loaded files.

Figure 163 Detail View

Position Indicator

Data

Region
Files

Histograms

Reference
Annotations

Chromosome Info
Details
(see below)

Chromosome Number

Chromosome Info Details

Markers

Data

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Viewing CytoScan CytoScan XON generates both whole genome segments and XON region segments.
XON region Whole genome segments capture the larger copy number events while XON region
segments in detail segments capture copy number aberrations at the exon level.
view CytoScan XON regions segments and probe level data are categorized into four
different levels. Note: The four levels do not apply to Whole Genome segmentation for
CytoScan XON.
 Level 1: Includes genes with the highest level of evidence: developmental delay,
epilepsy, ASD, XLID, Metabolic disorders, hereditary cancer OMIM™ Morbid
genes.
 Level 2: ClinVar genes not covered in Level 1.
 Level 3: Other OMIM genes.
 Level 4: Other Ref Seq, UCSC, Ensembl genes, LOVD.

In the Filters tab, when only Level 1 is selected and Levels 2-4 remain unchecked (as
shown in Figure 164 on page 172) then:
XON Region segments that overlap regions of the genome designated as Level 1 is
visible in the XON Region Segment Track and in the Segments Table. All remaining
data (log2 ratio, weighted log2 ratio, smooth signal, allele difference, B-allele
Frequency) contained within Level 1 regions is colored the same color as the color nib
of the sample. XON Region segments that overlap regions of the genome designated
as Levels 2-4 are not visible on the XON Region segment track or in the Segments
Track. All remaining data (log2 ratio, weighted log2 ratio, smooth signal, allele
difference, B-allele Frequency) contained within Level 2-4 regions is colored gray.
In the Filters tab, when Levels 1 and 2 are selected and Levels 3 and 4 remain
unchecked (as shown in Figure 165 on page 172) then:
XON Region segments that overlap regions of the genome designated as Level 1 or
Level 2 will be visible in the XON Region Segment Track and in the Segments Table.
All remaining data (log2 ratio, weighted log2 ratio, smooth signal, allele difference, B-
allele Frequency) contained within Levels 1 or 2 regions will be colored the same color
as the color nib of the sample. XON Region segments that overlap regions of the
genome designated as Levels 3 or 4 will not be visible on the XON Region segment
track or in the Segments Table. All remaining data (log2 ratio, weighted log2 ratio,
smooth signal, allele difference, B-allele Frequency) contained within Level 3 and 4
regions are colored gray.
If selected Level 3, then XON Region Segment calls are displayed on the XON Region
Segment track and the marker level data are colored the same color as the color of
the color nib of the sample.
When all four Levels are selected in the Filters Tab, all XON Region segment calls for
the sample are displayed and all marker level data is colored the same color as the
color of the color nib of the sample.

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Figure 164 Example: Level 1 check only

Whole Genome Copy Number Segments

XON Region Segments

Figure 165 Example: Level 1-4 checked

Whole Genome Copy Number Segments

XON Region Segments

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Viewing CytoScan The CytoScan XON array offers whole genome segmentation for larger duplications
XON whole and deletions. These segments appear on the Copy Number State Gain and Loss
genome track. The track can be turned on/off using the Copy Number State Gain/Loss check
boxes in the Data Types File tree.
segments in the
detail view Viewing CytoScan XON whole genome segments and xon region segments
simultaneously in the Detail View.
Whole genome segments and xon region segments maybe be viewed at the same
time in the Detail View by turning on both the Copy Number State and XON Regions
tracks. When both tracks are turned on, any xon region segment that overlaps a larger
whole genome segment will appear grayed out and will not be displayed in the
Segments Table or published to the ChAS Db. Using the whole genome segment to
represent the copy number event eliminates redundant segment calls in the Segment
Table. To view only the xon region segment calls, turn off the Copy Number State
Gain/Loss track.
XON merging can still be used on the XON region segments but is no longer necessary
due to the more robust whole genome segmentation algorithm. Any merged XON
regions that overlap the whole genome segments in the Copy Number State track will
appear grayed out and will not appear in the Segment Table. To enable grayed out
XON region segments, turn off the Copy Number Gain/Loss Segment Track.
XON regions that overlap a larger Whole Genome Copy Number segment that is below
the filter thresholds will be enabled and will appear in the Segment table.
Grayed out segments will not appear in the Segments Table as the loss is already
represented by the larger loss in the Copy Number State Track, as shown in
Figure 166.

Figure 166 Grayed out segments example

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Annotation color In the Detail View, DGV annotations are color-coded to indicate association with gain
codes or loss.

 Purple – Gain and loss are associated with the region

 Red – Only loss is associated with the region
 Blue – Only gain is associated with the region
 Gray – Copy number variation is associated with the region, but information
regarding the number of times gains or losses were observed is not present in the
annotation record in the DGV database

Annotation OMIM In Browser annotation files version NA32.3 and higher, the following OMIM colored
color codes gene entries were generated by genome.ucsc.edu and are based on the associated
OMIM phenotype map key. For more information on OMIM display conventions, go
to: www.genome.ucsc.edu
 Lighter Green for phenotype map key 1 OMIM records - the disorder has been
placed on the map based on its association with a gene, but the underlying defect
is not known.
 Light Green for phenotype map key 2 OMIM records - the disorder has been
placed on the map by linkage; no mutation has been found.
 Dark Green for phenotype map key 3 OMIM records - the molecular basis for the
disorder is known; a mutation has been found in the gene.
 Purple for phenotype map key 4 OMIM records - a contiguous gene deletion or
duplication syndrome; multiple genes are deleted or duplicated causing the
phenotype.
 Light Gray for Others - no associated OMIM phenotype map key info available.

Changing an annotation color

1. Right-click an annotation type in the Files window pane and select Set Custom
Color on the shortcut menu, as shown in Figure 167.

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Figure 167 Open the color palette

Current Color of BACs

annotations in the Detail
View

2. Specify a color for the selected annotation type using the color controls in the color
palette (Figure 167), then click OK.
The new color is applied to the annotations in the Details View.
3. To return to the default annotation color, right-click the annotation in the Files
windowpane, and select Clear Custom Color on the shortcut menu.

Data in the detail view

The Detail View displays the following types of data for CytoScan (CYCHP):

Table 14 Data for CytoScan array

Data Types Definition

Detected Segment Types

GainMosaic Non-integer amplifications or duplications

LossMosaic Non-integer hemizygous or homozygous deletions

Gain Amplifications or duplications

Loss Hemizygous or homozygous deletions

LOH Loss of Heterozygosity (CN <2 LOH = light purple, CN 2 (or higher) LOH = dark purple)
Note: In Dark Scheme (page 195), CN <2 LOH = dark purple, CN 2 (or higher) LOH = light purple.

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Table 14 Data for CytoScan array

Data Types Definition

Probe array data (displayed as graph data)

Copy Number HMM-derived integer Copy Number State

State

Log2 Ratio Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction for
sample specific variation.

Weighted Log2 Contains the Log2 Ratios processed through a Bayes wavelet shrinkage estimator. These processed
Ratio values are input to the CNState algorithm HMM.

LOH Loss of Heterozygosity

Allele Difference Filtered and smoothed values for individual markers. Nonparametric estimation is used to understand
possible regional peak structure towards which the data is smoothed. The amount of filtration and
smoothing is dynamically adapted based on sample quality. Allele difference is computed based on
differencing A signal and B signal, then standardizing based on reference file information.

Genotype Calls SNP genotype calls (single sample, BRLMM-P-plus algorithm)

Smooth Signal Gaussian Smoothed Calibrated Copy Number Estimate

B-allele Frequency Number of B alleles/number of A+B alleles used to show allelic imbalances.

The Detail View displays the following types of data for a CytoScan HTCMA array:

Table 15 Data for CytoScan HTCMA array

Data Types Definition

Detected Segment Types

Gain Amplifications or duplications

Loss Hemizygous or homozygous deletions

LOH Loss of Heterozygosity (CN <2 LOH = light purple, CN 2 (or higher) LOH = dark purple)
Note: In Dark Scheme (page 195), CN <2 LOH = dark purple, CN 2 (or higher) LOH = light purple.

Probe array data (displayed as graph data)

Copy Number State HMM-derived integer Copy Number State

Log2 Ratio Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction
for sample specific variation.

LOH Loss of Heterozygosity

Allele Difference Filtered and smoothed values for individual markers. Nonparametric estimation is used to
understand possible regional peak structure towards which the data is smoothed. The amount
of filtration and smoothing is dynamically adapted based on sample quality. Allele difference is
computed based on differencing A signal and B signal, then standardizing based on reference
file information.

Genotype Calls SNP genotype calls (single sample, BRLMM-P-plus algorithm)

Smooth Signal Gaussian Smoothed Calibrated Copy Number Estimate

B-allele Frequency Number of B alleles/number of A+B alleles used to show allelic imbalances.

Variants Location and detection of variants.

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Note: There is a subset of ~55,000 SNP probes which are used for allelic information
analysis but which are not used for Copy Number analysis (on the CytoScan HD
Array).
For these SNP probes, LOH and Allele Peaks data will be displayed, but these SNP
probes will not have Log2 Ratio, Weighted Log2 Ratio, SmoothSignal, or Copy
Number State data displayed, nor will they be used for ascertainment of Mosaicism.
The calculation of Segment data for all the various Segment types takes this into
account. All non-polymorphic (copy number) and the vast majority of SNP probes are
NOT affected by this change, and will continue to display all graphs and their data
points from the CytoScan HD Array CYCHP files.

Table 16 Data for CytoScan XON Array

Data Types Definition

Detected Segment Types

XON Region Gain Amplifications in XON regions.

XON Region Loss Hemizygous or homozygous deletions in XON regions.

Gain Amplifications or duplications.

Loss Hemizygous or homozygous deletions.

LOH Loss of Heterozygosity (CN <2 LOH = light purple, CN 2 (or higher) LOH = dark purple)
Note: In Dark Scheme (page 195), CN <2 LOH = dark purple, CN 2 (or higher) LOH = light purple.

Probe array data (displayed as graph data)

Log2 Ratio Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction for
sample specific variation.

Weighted Log2 Contains the Log2 Ratios processed through a Bayes wavelet shrinkage estimator. These processed
Ratio values are input to the CNState algorithm HMM.

LOH Loss of Heterozygosity

Allele Difference Filtered and smoothed values for individual markers. Nonparametric estimation is used to understand
possible regional peak structure towards which the data is smoothed. The amount of filtration and
smoothing is dynamically adapted based on sample quality. Allele difference is computed based on
differencing A signal and B signal, then standardizing based on reference file information.

Genotype Calls SNP genotype calls (single sample, BRLMM-P-plus algorithm)

Smooth Signal Gaussian Smoothed Calibrated Copy Number Estimate

B-allele Frequency Number of B alleles/number of A+B alleles used to show allelic imbalances.

The Detail View displays the following kind of data for Genome-Wide SNP Array 6.0
Array data (CNCHP):

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Table 17 Data for Genome-Wide SNP Array 6.0 (CNCHP)

Data Types Definition

Detected Segment Types

Gain Amplifications or duplication

Loss Hemizygous or homozygous deletions

LOH Loss of Heterozygosity (CN <2 LOH = light purple, CN 2 (or higher) LOH = dark purple)
Note: In Dark Scheme (page 195), CN <2 LOH = dark purple, CN 2 (or higher) LOH = light purple.

Probe array data (displayed as graph data)

Copy Number State HMM-derived integer Copy Number State

Log2 Ratio Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction
for sample specific variation.

LOH Loss of Heterozygosity

Allele Difference Difference of A signal and B signal, each standardized with respect to their median values in the
reference.

Smooth Signal Smoothed Calibrated Copy Number Estimate

Table 18 Data for OncoScan Array (OSCHP)

Data Types Definition

Detected Segment Types

Gain Amplifications or duplication

Loss Hemizygous or homozygous deletions

LOH Loss of Heterozygosity

Probe array data (displayed as graph data)

Copy Number State TuScan derived Copy Number State.

Log2 Ratio Per marker Log2 Ratio of normalized intensity with respect to a reference, with further correction
for sample specific variation.

Weighted Log2 Ratio Contains the Log2 Ratios processed through a Bayes wavelet shrinkage estimator. These
processed values are input to the CNState algorithm HMM.

LOH Loss of Heterozygosity.

Allele Difference Difference of A signal and B signal, each standardized with respect to their median values in the
reference.

Smooth Signal Smoothed Calibrated Copy Number Estimate.

Variants Location and detection of Somatic Mutation. (OncoScan FFPE Assay only)

B-allele Frequency Number of B alleles/ number of A+B alleles, used to show allelic imbalances.

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Table 19 ReproSeq Aneuploidy data

Data Types Definition

Detected Segment Types

Gain Amplifications

Loss Hemizygous or Homozygous deletions

Graph Data

Copy Number State The copy number state of sequence tiles

See "Changing graph appearance" on page 196 for more information about
controlling the display of graph data.
In addition, the Detail View displays:
 Regions: Features in the various region files loaded into ChAS, including
CytoRegions and Overlap Map items.
 Annotations: Indicate the known or suspected locations of features, such as
mRNAs, exons, structural variants, and so forth.
You can expand or contract the annotations. See "Expanding and contracting
annotations" on page 195.
 Database Display
 Default Histograms: displays all segments in the database.
 Filtered Histograms: displays all segments meeting the filter criteria set by the
user. For information on how to create a filtered histogram, see "Adding filtered
histogram data" on page 141.
 Chromosome info, with:
 Coordinate scale
 Marker position information
 Chromosome number
 Cytoband information

Selected segments are displayed with enlarged icons; selected regions or annotations
are outlined and highlighted. (Figure 168)

Figure 168 Selected Segment

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Navigation
controls in detail
view

Figure 169 Detail View navigation controls

Zoom Slider

Stretch
Slider
Vertical
scroll bar
Position Indicator

Chromosome Coordinates Scale

Horizontal scroll bar

Control Function

Chromosome Shows the position along the genome.

Coordinates scale

Zoom Slider Controls the horizontal zoom and the area of the chromosome displayed.

3x Zoom In Press Ctrl + Plus to view up to three preset Zoom In settings.

3x Zoom Out Press Ctrl + Minus to view up to three preset Zoom Out settings.

Zoom in Using Place your mouse cursor over a point of interest. Press Shift while holding down the left mouse button.
Click and Drag Drag the mouse cursor to frame/zoom in on your point of interest.

Stretch Slider Controls the vertical stretch of the Display area.

Scroll bars Used to select the area displayed after zooming or stretching the vertical or horizontal scale.

Position Indicator Dashed vertical blue line. Click in the view to set the position of the indicator
The position that is highlighted in the graphs table.
The position that is used as the center point when zooming.

Use Stretch Slider and Vertical Scroll Bar to zoom in on a section of the Detail. You
can also use the mouse wheel as shown below:
 Alt + mouse wheel stretches the display
 Ctrl + mouse wheel zooms in on the horizontal scale
 Mouse wheel scrolls up and down

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Obtaining You can obtain summary metrics from the data tracks displayed in the Detail View
summary metrics once you have zoomed in to a region of interest.
for a zoomed in 1. In the Detail View, zoom in to a region of interest using any of the techniques
region described above.
2. Hover the mouse over a data point on the data track for which you would like
summary metrics. For example, log 2 ratio, weighted log 2 ratio, Allele Difference,
etc.
A pop-up appears and displays the following metrics for markers currently
displayed in the Detail View:
 Region Size
 Number of Markers
 Min Marker Value
 Max Marker Value
 Mean Value
 Standard Deviation
 Median Value

Selecting a Data from the same sample files is displayed in all 3 views, at different scales.
chromosome You can select a particular chromosome, or a section of the chromosome, for detailed
section for study using:
display  "Karyoview and selected chromosome view"
 "Coordinate range box" on page 182
 "Zooming to a selected item" on page 183
 "Navigation controls in detail view" on page 180
You can also double-click on an item in a table to zoom to the region of the
chromosome where that item is located.

Karyoview and Selecting a chromosome for detailed examination

selected 1. Click a chromosome in the Karyoview.
chromosome
view The chromosome is displayed in the Selected Chromosome View and the Detail
view.

Examining a section of the chromosome

1. Click and drag on the section in the Karyoview or the Selected Chromosome
View.
The selected section is displayed in the Detail View. (Figure 170)

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Figure 170 Areas displayed in Karyoview, Selected Chromosome View, and Detail View

Coordinate Range Box

Karyoview: X Chromosome selected

with a section of the chromosome
highlighted

Detail View shows highlighted section

of the X chromosome

Coordinate range The Coordinate Range box (Figure 171) is located in the ChAS main tool bar. It shows
box the selected chromosome and the start and stop positions displayed in the Detail
View. You can enter coordinates in the box to update the Detail View.

Figure 171 Coordinate Range Box in Main tool bar

Coordinate Range Box

Going to a specific coordinate or coordinate range

 Enter the desired location in any one of these formats then press the <Enter> key:
 “chromosome number: start - end”: sets the view to the given start and end
coordinates on the given chromosome.

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 “start: end” or “start - end”: sets the view to the given start and end coordinates
of the current chromosome.

Returning to a previous location

 To return to previous genomic coordinates, click on the <>
buttons above the
chromosome number field (far right), as shown in Figure 172.

Figure 172 Previous coordinate buttons

Zooming to a selected item

There are several ways to zoom in on a feature.
 Click a segment in the Segment table, CytoRegions table, or Overlap Map. Clicking
on items auto-zooms to your configured zoom buffer (15% of item size is default),
To edit the zoom buffer, see "Zoom buffer" on page 186.
 Double-click a feature in the Details View, Karyoview or Selected Chromosome
View.
 Press Ctrl+Space to zoom - all the way in - to the selected item's start and end
coordinates, with no buffer.
 In the Karyoview, Selected Chromosome View, or Details View, you can use the
Zoom to selection option in the feature right-click menu (Figure 173) to go to the
start and stop coordinates of the selected feature.

Figure 173 Right-click menu options

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Setting a vertical highlight
Use this feature to set a vertical highlight on a selected segment(s) or annotation(s) to
view its breakpoints across other data types and/or annotations. This highlighting
option can be useful when aligning a segment/annotation of interest with other
samples or annotations.
 Right-click on a selected segment(s) or annotation(s), then click Set highlight
region from selection to apply a vertical yellow highlight through the Detail View,
as shown in Figure 174.

Figure 174 Vertical highlight example

Edit configurations in the misc tab

The Misc tab contains:
 Autosave
 Coordinate Box Format
 Zoom Buffer
 Chromosome Sorting Order
 CHP File Colors
 Remapping Segment patterns
 Microarray Nomenclature configuration

Accessing the 1. Click Preferences → Edit User Configurations or click on the upper tool
Misc tab bar.
The User Configuration window appears.
2. Click the Misc tab. (Figure 175)

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Figure 175 User Configuration window - Misc tab window

Autosave  Click to check the Autosave check box to automatically save your files as they are
edited. Uncheck to disable auto-save. (Figure 176).

Figure 176 Autosave

Coordinated box  Click the appropriate radio button to choose the format of your displayed data.
format (Figure 177)

Figure 177 Coordinate Box Format

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Chromosome  Click the appropriate radio button to sort the segments in the Segment Table.
sorting order (Figure 178)

Figure 178 Chromosome

Sorting Order

Zoom buffer By default, the zoom percentage is set to 15% in new user profiles.
The Zoom Buffer feature offers 3 settings:
 No Buffer: Click this radio button to turn off the Zoom Buffer feature.
 Number of bases: Click this radio button, then manually enter the number of
bases you want.
 Percent of segment length: Click, then drag the slider bar (Figure 179) to the
zoom percentage you want.

Figure 179 Zoom Buffer

CHP file colors

Figure 180 CHP File Colors

There are five preset CHP file colors assigned to your CHP data (Figure 180), but each
default color, can be changed to a different color.

Changing a CHP file color

1. Click on the colored icon you want to change.

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A color wheel appears. (Figure 181)

Figure 181 Pick a Color

window

2. Use the color wheel to locate the specific color you want or click on one of the
several coloring options (including a website-safe color
pallet).

3. Click OK.
4. Repeat steps 1-3 to change additional default colors.
At anytime, click Reset to Default to return the 5 CHP file colors back to their
default colors. (Figure 182)

Figure 182 CHP File Colors

To return a single CHP file color back to its default color, click on the CHP file
color, then click the Color Wheel’s Reset button.
5. Click the User Configuration window’s OK button to save your changes and exit.
Note: Samples that are currently loaded while a color change is made, may not reflect
your new color scheme. To remedy this, close, then re-open ChAS to ensure your new
color choices are reflected throughout all your samples.

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Remapped Choose how segments (remapped from an hg19 ChAS db to an hg38 ChAS db) are
segment patterns represented. See "Additional segment intersection information" on page 397 for
information on default patterns.
1. Click the With no added/removed markers: drop-down to select a pattern to
represent segments in an hg38 ChAS db that were mapped from an hg19 ChAS
DB, in which all the markers in the original segment mapped to the new genome
version.
2. Click the With added/removed markers: drop-down to select a pattern to
represent segments in an hg38 ChAS db that were mapped from an hg19 ChAS
DB, in which one or more markers in the original segment no longer map to the
new genome version.

Microarray Define how the ISCN Microarray nomenclature will be represented in the segments
nomenclature table and exports. Any format from ISCN 2013, 2016 and 2020 can be configured
configuration  Coordinates: choose the radio button to display genomic coordinates with or
without commas.
 Genome names: choose the radio button to display genome versions using either
GRCh or hg.
 Range separator: choose the radio button to display either a dash (-) or an
underscore (_) between genomic positions.
 Mosaic separator: choose the radio button to display either a dash (-) or a tilde (~)
between copy number values on mosaic segments.
 (Optional) Select the check box to automatically have information in the Inheritance
field appended to the Microarray nomenclature field.

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Controlling the display of data

ChAS (Figure 183) provides controls for:
 "Selecting data for display" on page 190
 "Selecting data types for display" on page 192
 "Changing the grouping of samples and data types" on page 193
 "Selecting display schemes" on page 195
 "Expanding and contracting annotations" on page 195
 "Changing graph appearance" on page 196
Later chapters explain other options for filtering data, how to specify certain regions
for extra attention or ignoring, and how to create Region files with region information
and annotations.

Figure 183 ChAS with data loaded

Menu Bar Display Area

Tool Bar

Files List
Upper Pane

Named
Setting
Drop-down
list Selected
Chromosome
View

Lower Pane
Data Types List

Status Bar

NetAffx annotation database Restricted Mode Cursor Position Information

and hg version currently indicator
loaded in the ChAS Browser

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Selecting data for The Files list (Figure 184) enables you to select sample data, region files, histograms,
display and reference annotations for display in the graphic view.

Figure 184 Files list

Sample Data

AED and BED annotation and region files

Indicates the file is selected as a CytoRegions file
Indicates the file is selected as an Overlap Map file

Reference Annotations

Histogram Data from the ChAS Database

Cytobands

The Files list displays the files grouped by:

 Sample Data
 Colored nibs display the color used for the data lanes for that sample in the
Karyoview, Selected Chromosome View, and Detail View.
 The appropriate gender symbol is displayed to the right of the colored
nib. GenomeWide SNP 6.0 CNCHP file data may also contain a “?” if the gender
was determined to be “unknown”.
 If a loaded file has a QC parameter that is out of range, an alert symbol
appears next to the file name.
 Region Data Files
Icons indicate the file type ( AED or BED) and whether the loaded files have
been selected as a CytoRegions file or Overlap Map file . VCF files are also
loaded here.
 Histograms: Displays Gains, Loss, and LOH segments stored in ChAS DB. The
display is loaded in the Detail View upon software start up or by selecting ChAS
DB → Load Histograms (when connected to the ChAS DB).
 Reference Annotations: Loaded during software installation and startup. Only
displayed in Detail View.
 Cytobands: Separated from other reference annotations because they cannot be
moved in the displays, and because they are also displayed in the Karyoview and
Selected Chromosome View.

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Selecting and deselecting files for display
1. Click in the check box next to the file name.
The order in the Files list determines the order of display of the lanes in the
Karyoview, Chromosome view, and Detail View.

Changing the order of the Sample lanes or reference annotations

1. In the Files list, click a file name and drag it to a new position.

Viewing data properties

1. Right-click a file and select View/Edit Properties on the shortcut menu.
The Properties window appears.
(Optional) Use the Filter “Property Name” search text field (Figure 185) to quickly
locate a property of interest.

Figure 185 View data properties - Filter “Property Name” field

Closing a file
1. Right-click on the file you want to close.
2. Select Close from the menu. (Figure 186)

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Figure 186 Closing a file

The file is removed from the Files list and the data is no longer displayed.

Selecting data The Data Types list (Figure 187) shows the data types that can be displayed in ChAS.
types for display
Figure 187 Data Types list

Detected Segments
and Graph Data

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Figure 187 displays a list of data that can be displayed in the Karyoview, Selected
Chromosome View, Detail View, and tables. The available data types may vary,
depending upon the type of sample data available.
It enables you to select from Segments data and CN/LOH discrete graph data.
The Segments data is displayed in:
 Karyoview
 Selected Chromosome View
 Detail View
If segment parameter filters have been applied to a segment type, a funnel symbol
appears next to the segment type name, as shown in Figure 188.

Figure 188 The funnel graphic denotes filters

have been applied.

The Graph data is displayed only in the Detail View.

Selecting and deselecting data types for display

 Click in the check box next to the Data Type name.

Changing the order of the data types:

 In the Data Types list, click a file name and drag it to a new position.
Note: The selections made here can be saved with a Named Setting (see "Named
settings" on page 439).

Turning the symbols used for segments on or off:

 From the View menu, select or de-select Segment Symbols.

Changing the A unique color is assigned to each sample and used for the lanes in the Karyoview,
grouping of Selected Chromosome View, and Detail View.
samples and data Each segment type is assigned to its own lane and has its own symbol.
types
Changing the grouping
1. From the View menu, select Group by Sample or Group by Type or in the tool
bar, click the Group by Sample or Group by Type button.

This enables you to perform different types of comparisons between samples

and segment types.

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Lanes grouped by sample
When the lanes are grouped by sample, the different segment types for each sample
are kept together in the Karyoview and Selected Chromosome View (Figure 189) and
in the Detail View.

Figure 189 Lanes grouped by sample in Karyoview

When the lanes are grouped by data type, the lanes for different samples are kept
together for each segment or graph type in the Karyoview and Selected Chromosome
View and in the Detail View.
Note: You can change the order of samples and Data types in the views by clicking
and dragging in the Files and Data Types list.

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Selecting display You can choose to display the graphics using a light background or a dark
schemes background (called Dark Scheme).

Selecting a dark scheme display

1. From the View menu, select Use Dark Scheme; or
2. Click the Dark Scheme button in the main tool bar.
The Dark/Light scheme is used (Figure 190).

Figure 190 ChAS with Dark Scheme selected

Expanding and For tracks containing multiple rows of annotations, collapsing tracks consolidates all
contracting rows within a track into two rows. Any annotations after the first one will be placed in
annotations the second row (Figure 191).
When there are multiple annotations of one type at the same coordinate, the separate
annotations will be shown on separate rows.
Collapsing tracks is useful if you don’t need to see all the details. However, be aware
that in collapsed tracks larger annotations may obscure smaller ones; annotations
with introns may be obscured by annotations that don’t show the intron.
To expand or collapse just a single annotation track, right-click on the track name in
the Files tree and choose Expand (or Collapse) Annotation track. The Annotation track
check box must be checked in order to see this option in the right-click menu.
Note: The maximum number of tracks that can be displayed for any reference
annotation is 25.

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Figure 191 DGV annotations view examples: Expanded

(top) Collapsed (bottom)

Toggling between collapsed and expanded display of annotations:

 From the View menu, select Expand/Collapse Annotations
OR
 Click the Expand/Collapse button on the main tool bar.

Changing graph You can modify many properties of the graphs in the Detail View. ChAS provides
appearance options for:
 "Selecting different graph styles" on page 197
 "Changing graph attributes" on page 201
 "Changing scale" on page 202
Settings and adjustments that are specific for graphs can be made using the Graph
Settings window.

Opening the Graph Settings window

1. From the View Menu, select Graph Settings or click on the Graph Settings
button in the Graphs Tab tool bar.
The Graph Settings window opens. (Figure 192)

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Figure 192 Graph Settings window

The Types box displays the graph data types being displayed in the Detail View.

Changing the settings for a graph type

1. Click on a data type to change the settings for that type.
2. Make changes to the graph settings by typing in new values or by operating
sliders in the Graph Adjuster panel. For details, see:
 "Selecting different graph styles" on page 197
 "Changing graph attributes" on page 201
 "Changing scale" on page 202
Note: Any changes you make to the values in the Graph Settings window will apply to
all currently selected graph types.

Selecting different graph styles

Graphs can be shown in various representational styles. The type of graph that is most
appropriate depends on the type of question being asked about the data. For
example, when comparing trends and patterns, it is very useful to use the line graph
display method. The user is encouraged to experiment with the different display types
to find out which method works best for specific purposes and at specific zoom in
magnifications.

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Changing the graph style
1. In the Style section choose one of the options. (Figure 193)

Figure 193 Graph Settings window

Note: Line, Min/Max/Avg, and Stairstep are not available for CytoScan XON arrays
due to the differential coloring based on Level assignment.
 Bar – Individual values are shown as vertical bars that are one base wide for
position graphs. (Figure 194)

Figure 194 Bar

 Line – Subsequent values are linked with a line. Even if the input file was not sorted,
the values will be connected in order along the genomic coordinate axis.
(Figure 195)

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Figure 195 Line

 Points – Shows a single dot for each data value. (Figure 196)

Figure 196 Points

 Big dots – Shows a single big dot for each data value. (Figure 197)

Figure 197 Big Dots

 Min/Max/Avg – This style is especially useful for showing very densely populated
graphs with data points for large numbers of positions. (Figure 198) Note: This
data style is not available for CytoScan XON arrays due to regions annotated by
Levels.

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Figure 198 Min/Max Average

When Detail View is zoomed all the way in, the display is equivalent to the Line
style. When zooming out, ChAS starts to summarize values. When the scale of
the display reaches the point where individual x-values are associated with
multiple score values, ChAS picks the maximum and minimum values and draws
a vertical bar between them. In addition, ChAS draws lines through the average
of all the data points represented at each x value.
 Stairstep – Similar to the bar graph style, except that bar widths along the
horizontal axis are stair-stepped. (Figure 199) Note: This data style is not available
for CytoScan XON arrays due to regions annotated by Levels.

Figure 199 Stairstep

For example, if position 100 has a value of 50 and position 200 has a value of 75
and there are no values in between, then ChAS will draw a bar of height 50 that
starts at position 100 and stops at position 200. Then, at position 200, ChAS will
draw a new bar of height 75 that terminates at the next location with a value.
 Auto-Size Dots - Transition from Points to Big Dots when zooming in the Detail
View. You can select the window size (in base pairs) in which the transition occurs.
(Figure 200)

Figure 200 Auto-Size dots

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 Heat map – Instead of showing relative intensity via the height of the line at each
pixel or coordinate as in most other graph styles, a heat map shows expression
levels via color or brightness of the line at each pixel or coordinate (Figure 201).
This graph style is useful if you want areas of unusual values to jump out at you. If
a graph does not render or is hard to see, adjust the visible bounds of the graph
until features are readily visible. Several heat map color schemes are available to
choose from.

Figure 201 Heat Map

There are now two Red/Gray/Blue heat maps.

One is designed to look good for copy number data scaled from 0 to 4 (or 1 to 3), with
2 = normal, and the other is designed to look good for copy number data scaled from
0 to 5 with 2 = normal.
The user must be careful to test that the heat map scaling is appropriate for the data.

Changing graph attributes

You can display graphs with:
 Value scale
 Zero Line
 Grid

Changing graph attributes

 Select the attributes you want to display in the Detail View. (Figure 202)

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Figure 202 Graph Settings window

Changing scale
Changing the visible bounds involves changing the scale of the graph by setting the
maximum and minimum values to be displayed.
To set these visible bounds, use the Range section of the Graph Properties dialog.

Setting specific minimum and maximum values

 Use the sliders, or type in values to the boxes.
These values will be applied to each selected graph. You are free to set maximum
and minimum values that cover a range smaller or larger than the actual range of
your data.
 Click the Automatic Dynamic Range check box to auto-set the Y-axis min/
max range.
 Click the Always include Zero check box to include a 0 point of reference on
the Y axis.

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Note: The algorithm detects CN state up to 4 for Genome-Wide Human SNP
Array 6.0 CNCHP files and CytoScan Array CYCHP files. The TuScan algorithm
detects CN State > 50 for OncoScan FFPE Assay OSCHP files. In the Graphs
Settings, the Copy Number State range can be set to what is appropriate to the
data.

Changing the vertical height of a graph

 Use the Height Slider to stretch all the graph type in the vertical direction.

The graph height slider is used to increase or decrease the size of a given graph type.
The size is specified in a relative manner. The final graph size will depend on the
number of other graphs and annotations being displayed.

Learning more about features

You can use the following tools to learn more about features in the different views:
 "Pop-ups"
 "Right-click menu options" on page 206
 "Selection details table" on page 208
 "Linking to external websites" on page 213

Pop-ups You can mouse over a feature in any of the views to display a popup box with
information on the feature. The information provided depends on the type of data that
the mouse arrow is on.
Pop-ups are available for:
 Cytobands
 Detected segments
 Graph data
 Marker position indicators
 Histograms
 Reference annotations
Note: You should expand the reference annotations before selecting one to avoid
selecting multiple annotations. See "Expanding and contracting annotations" on page
195.

 Displayed Region files, including

 Overlap Map Regions
 CytoRegions
The information displayed differs depending upon the type of feature selected, as

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shown in the samples below.
For all segments, the segment start coordinates are always lower by one bp from the
coordinate for the starting probe of the segment as reported in the graphs table while
the end coordinate matches the coordinate for the ending probe as reported in the
graphs table (see Appendix E, "Genomic position coordinates" on page 488).
You can learn more about the terms used in the pop ups in "Selection details table"
on page 208.

Turning pop-ups on or off

1. From the View menu, select Mouse-over Pop-ups.
The information (Figure 203, Figure 204, Figure 206, and Figure 207) can include
custom properties created by a user (see "Viewing and editing annotations" on
page 297 for more information).

Figure 203 Pop-up for CN State

Graph

Figure 204 Pop-up for a Gain Segment

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Figure 205 Pop-up for a XON Region Gain

Segment

Figure 206 Pop-up for a Gene

Figure 207 Pop-up for a Histogram

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Right-click menu You can right-click on any of the following types of features to open a menu with
options options for learning more about the feature:
 Detected segments (Figure 208)
 Histograms (Figure 209)
 Reference annotations, including cytobands (Figure 210)
Note: You should expand the reference annotations before selecting one to avoid
selecting multiple annotations. See "Expanding and contracting annotations" on page
195.

 Displayed Region files, including (Figure 211):

 Overlap Regions
 CytoRegions
Note: Not all options are available for the different feature types. Also, In the Detail
View you can select multiple items of different types. The available options will differ,
depending upon the number and types you have selected.

Some menu options are common to the different types of features:

 Number of items selected (if more than one item is selected, the options available
may differ, depending upon the type and number of items).
 Zoom to selection: See "Zooming to a selected item" on page 183.
 Selection Details: Opens the Selection Details box with information about the
feature. See "Selection details table" on page 208.
 Add to a file: Add the selected segment, annotation, or region to a region file. See
"Adding regions to an existing AED file" on page 292.
 View/Edit Annotation Properties: Displays the Annotations Properties window
for the selected feature. You may or may not be able to edit the properties. See
"Viewing and editing annotations" on page 297.
 Query ChAS DB: Displays the segments in the database that match the user
defined Overlap and Coverage threshold settings. See "Setting up a ChAS DB
query" on page 390.

Figure 208 Segment right-click menu

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Figure 209 Histogram right-click menu

Special options for annotations include:

 Link to remote web site for more information. (Figure 210)

Figure 210 Annotation right-click menu

Custom functions for regions include (Figure 211):

 New User Annotation: Opens the New User Annotation window, which enables
you to add user annotation to a region. For more information, see "New user
annotations" on page 304.
 Increment Counter: Increments the counter in the annotation properties, allowing
you to track the number of times a feature has been seen. For more information
about the annotation properties, see "Viewing and editing annotations" on page
297.

Figure 211 Region right-click menu

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Selection details The Selection Details table (Figure 212) displays information available for items
table selected in the graphic display views (Karyoview, Chromosome View, and Detail
View). It is accessed by right-clicking on an item in one of the views and selecting
Selection Details.
The information is presented in two tables:
 Upper table shows one item per row – Provides summation feature and PDF or tab-
separated text file export capabilities.
 Lower table shows one item per column – Provides ability to export the table to a
tab-separated text file.
To reorder the columns in the upper table, drag a column header left or right. The
corresponding row in the lower table is automatically moved to the new location in the
table.

Figure 212 Example: Selection Details table

Upper table: One item per row

Lower table: One item per column

Click an arrow to hide or show
one of the tables. Your display
choice is retained the next time
ChAS is started.

The Selection Details table may include the following columns:

Column Description

Common

Label Identifier for the item.

Chromosome Chromosome on which the item is located.

Min Zero-based index position of the first base pair in the sequence.

Max Zero-based index position of the last base pair in the sequence, plus one. Adding one ensures
that the length of any (hypothetical) segment containing a single marker would be one, and
ensures that the coordinates match the coordinate system used in BED files.
For all segments, the segment start coordinates are always lower by one bp from the coordinate
for the starting probe of the segment as reported in the graphs table while the end coordinate
matches the coordinate for the ending probe as reported in the graphs table (see Appendix E,
"Genomic position coordinates" on page 488).

Size (kbp) Size of the item.

Type Type of segment (Gain, Loss, GainMosaic, LossMosaic LOH) or annotation.

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Column Description

Segments

File File the segment was detected in.

CN State Copy Number State (not displayed for LOH segment types).
The expected Copy Number State on the X chromosome in normal males is not constant over
its entire length. This is due to the structure of the sex chromosomes. See "LOH segments on X
and Y chromosomes" on page 49 for more information.

Mean Marker Distance Length of the segment in base pairs divided by the number of markers in the segment.

Interpretation User-editable field for free-text interpretation on the segment

Call User-editable field populated by a user-configurable drop list of Calls.

Inheritance User-editable field populated by a user-configurable drop list of Inheritance.

Curation By The current computer Operating System login ID and ChAS user profile name at the time that
the Call or Interpretation field was last edited.

Curation Time The time and date when the Call or Interpretation field was last edited.

Materially Modified Indication that segment was previously merged, deleted, or had its start or end boundary, type,
Segment or state altered by a ChAS user. (ChAS-based processes of Smoothing and Joining are not
“Modifications”, nor are making Calls or Interpretations, in this context).

Materially Modified By The current computer Operating System login ID and ChAS user profile name at the time that
the segment was last materially modified.

Materially Modified Time The time and date when the Segment was last materially modified.

Max % Overlap The highest percentage by which some item(s) in the Overlap Map overlaps the segment.
Segments completely overlapped by an Overlap Map item are 100% overlapped. This number
is used for Filtering Segments out by “Overlap”.

Overlap Map Items (% of Item(s) in the Overlap Map which overlap the segment, followed by the percentage by which the
Segment overlapped) segment is overlapped by that Item.

CytoRegions Names of the CytoRegions with which the segment shares coordinates.

Use in Report Allows manual selection of Segments for export to a Segments Table PDF, DOCX, or Text rather
than all segments in the table.

Marker Count Number of markers in the segment.

Cytoband Start Cytoband in which the segment begins.

Cytoband End Cytoband in which the segment ends.

Genes List of RefSeq genes from the Genes track that share coordinates with the segment. Identically
named gene isoforms are NOT repeated.

Gene Count A count of the gene names listed in the Genes column

DGV List of DGV variations that share coordinates with the segment.

sno/miRNA List of sno/miRNA features that share coordinates with the segment.

OMIM Genes List of OMIM Genes that share coordinates with the segment.

OMIM Gene Count A count of the OMIM Gene names listed in the OMIM Genes column.

OMIM Phenotype Loci List of OMIM Phenotype Loci that share coordinates with the segment.

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Column Description

OMIM Region List of OMIM Phenotype associated with a genomic region. The OMIM Morbidity information is
Phenotype Loci displayed when using all three OMIM tracks. (OMIM Genes, OMIM Phenotype Loci and OMIM
Region Phenotype Loci)

Segmental Duplications List of Segmental Duplications that share coordinates with the segment.

Smoothed/Joined Indication that segment was created by smoothing or joining two or more segments in the initial
segment detection.

Segment Label A label comprised of the segment's Type, State, and Filename.

Segment Name/ID File-specific identifier assigned to the detected segment.

Start Marker The array marker name which marks the beginning of the segment.

End Marker The array marker name which marks the end of the segment.

Preceding Marker The array marker just above the segment in the data track used as input for the segment. Note:
This column is only applicable to CNState Gain and Loss segments.

Preceding Marker The coordinate location of the array marker just above the segment in the data track used as
Location input for the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Following Marker The array marker just below the segment in the data track used as input for the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Following Marker The coordinate location of the array marker just below the segment in the data track used as
Location input for the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Mean Log2 Ratio The mean of all the Log2 Ratio values contained in the segment.

Mean Weighted Log2 The mean of all the Weighted Log2 Ratio values contained in the segment.
Ratio

Microarray An ISCN-based description of the segment.

Nomenclature

Sample UUID Unique identifier for the CHP file.

Max % Coverage The highest percentage by which a segment covers some item(s) in the Overlap Map.

Number of Overlap Map Number of Overlap Map items which share genomic coordinates with the segment.
Items

% of Overlaps Map Item Overlap Map Item and the percentage by which it is covered by the segment.
covered by Segment

Full Location Chromosome Start and Stop in a user-friendly format for use in external databases.

Median log2 The median of all the Log2 Ratio values contained in the segment.

DB Count Both Number of segments in the database meeting both the user defined thresholds of minimum
Percent Overlap Count and Coverage Count.

DB Coverage Count Number of segments in the database meeting the minimum Percent Coverage Count.

DB Overlap Count Number of segments in the database meeting the minimum Percent Overlap Count.

XON Region Level The annotation Level assigned to this region of the genome.

Summarized Log 2 Ratio The median of the LR, after transformation to adjust for individual marker responsiveness.

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Column Description

Genes

Chromosome Chromosome on which the item is located.

Min Zero-based index position of the first base pair in the sequence.

Max Zero-based index position of the last base pair in the sequence, plus one. Adding one ensures
that the length of any (hypothetical) segment containing a single marker would be one, and
ensures that the coordinates match the coordinate system used in BED files.
For all segments, the segment start coordinates are always lower by one bp from the coordinate
for the starting probe of the segment as reported in the graphs table while the end coordinate
matches the coordinate for the ending probe as reported in the graphs table (see Appendix E,
"Genomic position coordinates" on page 488).

Size (kbp) Size of the item.

Type Type of segment (Gain, Loss, GainMosaic, LossMosaic LOH) or annotation.

Accession Number Unique identifier assigned to the sequence in GenBank.

CDS Min Minimum position of the coding sequence (BED-style coordinates).

CDS Max Maximum position of the coding sequence (BED-style coordinates).

Strand The sequence strand of the item.

%Hi Dosage sensitivity indicator derived from DECIPHER (https://decipher.sanger.ac.uk/). The lower
the percentage, the more likely the gene is to be dosage sensitive.

pLI Probability of loss intolerance. Genes with higher numbers are more likely to be dosage
sensitive. Derived from gnomAD (https://gnomad.broadinstitute.org/).

CI Dosage sensitivity indicator derived from gnomAD

(https://gnomad.broadinstitute.org/) for hg38 only. Not yet implemented by gnomAD.

pHaplo Probability of Haploinsufficiency): The higher the value (0-1), the more likely to be dosage
sensitive. Collins et al. A cross-disorder dosage sensitivity map of the human genome. 2022.
PMID: 35917817

pTriplo Probability of Triplosensitivity): The higher the value (0-1), the more likely to be dosage sensitive.
Collins et al. A cross-disorder dosage sensitivity map of the human genome. 2022. PMID:
35917817

Ensembl Genes

CDS Min Minimum position of the coding sequence (BED-style coordinates).

CDS Max Maximum position of the coding sequence (BED-style coordinates).

Strand The sequence strand of the item.

OMIM

OMIM Gene Title The title of the gene associated with the OMIM entry.

OMIM Gene Symbol List A list of genes associated with the OMIM entry.

OMIM Disorder Disorder associated with the OMIM entry.

OMIM Phenotype Key Indicates how this phenotype was placed on the map.

OMIM Gene Symbol Symbol of the gene based on gene title.

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Column Description

OMIM Phenotype Loci

OMIM Phenotype ID Unique identifier to an OMIM phenotype.

OMIM Phenotype Map Indicates how this phenotype was placed on the map.
Key

OMIM Phenotype Locus Describes the phenotype or disorder associated at the OMIM Phenotype Loci.
Description

OMIM Region Phenotype Loci

OMIM ID Unique identifier to an OMIM phenotype.

Cytoband Location of the region.

Min Start location of Genome.

Max End location of Genome.

Gene Symbol Symbol of the gene (based on gene title).

Gene Title The title of the region associated with the OMIM entry.

Comment Additional information for the entry from OMIM.

Gene-Phenotype Loci Information of Gene-Phenotype relationships for the region.

Data

Sentimental Duplications

Score Score based on the raw BLAST alignment score. The score for segmental duplications is set to
zero in NetAffx annotation 31 and higher.

FracMatch The fraction of matching bases.

FracMatchIndel The fraction of matching bases with Indels.

Strand The sequence strand of the item.

Note: Thermo Fisher Scientific does not generate or verify the information for genes,
FISH clones, Segmental Duplications, sno/miRNAs, DGV annotations, or OMIM data.
Segmental Duplication and sno/miRNA annotations do not have any unique terms; but
sno/miRNA annotations use the “type” field to indicate subtypes like “cdBOX” and
“HAcaBOX”.
Some information may not be displayed, depending upon the feature type. The
information can include custom properties created by a user (see "Viewing and editing
annotations" on page 297).
You can export data from the table using the standard table export tools (see
"Exporting table data" on page 422).
You can perform multi-column sorts. See "Sorting by columns" on page 328.

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Linking to external websites

You can view a selected area within the Detail View at one of the following public sites:

 UCSC

 Ensembl

 Toronto DGV

 ClinVAR

 ClinGen

 DECIPHER

 Load TaqMan Assays Track

Viewing a 1. In the Detail View, zoom and scroll to the area of interest. (Figure 213)
selected area at a
public site
Figure 213 Selected area in Detail View

2. From the View menu, select View Region at [site name] or click the appropriate
site’s tool bar button.
A browser opens, displaying the selected area of the chromosome.

Linking to TaqMan copy number and genotyping assays

Viewing and TaqMan assays can easily be accessed from within ChAS. These assays can be
ordering TaqMan used for confirmation of copy number aberrations. TaqMan assays can only be
assays for CN ordered based on hg38 genome coordinates.
Do the following for the region(s) you would like to view and order TaqMan assays
for Copy Number:
1. Locate the region containing the aberration in the Detail View.

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2. Select the TaqMan shortcut in the tool bar (Figure 214) to view which TaqMan
assays are available within the genomic coordinates populated in the text box at
the top center of the browser.
The TaqMan assays load in a track in the Detail view.
Note: This track is only available for the genomic coordinates for the current
query. To view TaqMan assays in another region of the genome, repeat steps 1
and 2.

Figure 214 TaqMan Shortcut icon and the genomic coordinate

3. Right-click on the TaqMan assays you want to order, then click Order TaqMan
assay to link out to the website, as shown in Figure 215.

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Figure 215 Link to selected TaqMan ID

Viewing and TaqMan assays for genotyping can be ordered from VCF files that contain dbSNP IDs.
Ordering TaqMan Note: The VCF file must contain an rsID for the SNP to directly access the TaqMan
assays for website for that SNP. Also, TaqMan assays can only be ordered based on hg38
genotyping genome coordinates.
1. Load a VCF file clicking File → Open.
2. Right-click on an SNP for which you would like to view and order a TaqMan
assay.
A menu appears. (Figure 216)

Figure 216 Right-click menu for TaqMan ordering

3. Click on the provided “Link to” link.

You will be directed to the TaqMan website for details about the assay.

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Figure 217 Assay details example

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9
ChAS enables you to filter the detected segments using different segment
parameters, concealing segments that do not meet requirements for significance for:

 Marker Count
 Length
 XON Level Assignment (XNCHP only)

You can apply these filters to different segment types, using different parameters for
each type. The filtering is done on the fly, with changes to the parameters reflected in
the different views as they are made.
A segment must pass all filter requirements for the segment type to be displayed.
You can apply different filter values for areas inside CytoRegions and areas outside
the CytoRegions (genomewide). See “Using filters with CytoRegions” on page 275.
The Overlap Map filter is described in "Using the overlap map and filter" on page 279.
Filter settings are saved when a Named Setting is created and can be reapplied. See
“User profiles and named settings” on page 438.

IMPORTANT! The Filters set in the browser are NOT linked to the filters for the MSV. The same
filter settings should be set in both the ChAS browser and the MSV separately. The MSV does have
a flag to indicate when filter settings do not match. For more information, see the RHAS User
Guide.

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Applying segment parameter filters

Opening the 1. Select View → Segment Filters on the menu bar

Segment Filters 2. Click the Segment Filters tool bar button
window
3. Right-click on a segment type in the Data Types list, then select Filters… from the
right-click menu. (Figure 218)

Figure 218 Right-click menu

Note: If you use the right-click menu option, only the filter settings for the selected
segment type are displayed.

The Segments Filters window opens. (Figure 219)

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Figure 219 Segment Filters window

Genome and CytoRegions tabs are displayed only when a cytoregions file
is selected.

Different
Segment
Types

Note: The Overlap Map filtering parameter is set using the same window. The Overlap
Map function is described in "Using the overlap map and filter" on page 279.
 For XON, check the Level check box(es) (Figure 220) to reveal any XON region
segment calls in regions assigned to the Level(s) you selected.

Figure 220 Level selections

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Segment Filter Function

Option

Hide All Segments Hides all the segments. This is particularly useful when using a CytoRegions file for CytoScan XON
in this Region arrays. Check the Hide All Segments in this Region check box on the Genome Tab so that ONLY
segments overlapping CytoRegions will be shown. Note: This option is only available with a
CytoRegions file is assigned.

Hide LOH where Selecting this option will hide LOH segments that are assigned a median copy number less than 2.
median CN < 2 LOH with median copy number of 2 or higher will still be displayed.

Marker Count The number of markers the segment encompasses from start to finish. A segment must have at least
as many markers as you specify to be displayed. Each marker represents a probe which represents a
sequence along the genome at a particular spot. Markers are probe sequences of DNA, each sized
from 12-50 base pairs long, depending on the type of array data. The 12-50 bp sequence is unique to
that one spot on the genome it represents.

Size Based on the start and end markers of a segment. Because each segment represents a single place
in the genome, you can measure from start to end, in DNA base pairs, and by filtering, demand a
segment be at least that long to be visualized.

XON Segment Based on the Level Assignment to the region in the genome.
Level Level 1: Medical Research exome and cancer
Level 2: ClinVar genes not covered in Level 1
Level 3: Other OMIM genes
Level 4: Opportunistic regions from Refseq/UCSC/Enseble/LOVD.

The XON Segment Filters can be used to narrow down the number of XON segments to review based
on their annotation level assignment. Those regions assigned as Level 1 contain genes/regions that
have been identified as part of the Medical Research Exome along with regions associated with
cancer. By selecting only Level 1 in the filter settings, only XON segment calls in regions assigned as
Level 1 will be displayed. XON segments for all other Levels will be hidden from view as well as hidden
in the Segments Table. To expose XON segment calls in other regions simply check the box for those
Levels in the Filters Windows. For more details on CytoScan XON analysis workflow
recommendations, Appendix H, "Recommended CytoScan XON array workflows" on page 511.

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Using segment 1. Click the check box next to the parameters you want to use as filters. (Figure 221)
parameter filters
Figure 221 Gain Segment filter
settings

2. Use the slider to set the value for the parameter or enter a value in the provided
text field. (Figure 221) Note: As you move the slider from left to right, more
segments are removed.
Your filtered results are displayed instantly in all tables and graphs, as shown in
Figure 222.

Figure 222 Filtering results

No Filters Applied Segment parameter filters

applied

For information about using the Overlap setting, see "Using the overlap map and filter"
on page 279. For information on using different filtering settings in CytoRegions, see
"Using filters with CytoRegions" on page 275.

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Bypassing segment filters

A specific segment can be assigned to ignore the current filter settings. The segment
will still displays even though its marker or size thresholds are not met. To use this
feature:
1. From any graphical view (Karyoview, Selected Chromosome View, or Details
View), right-click on the segment you want to bypass the segments filters with.
A menu appears.
2. Click View/Edit Annotation Properties.
The Annotation Properties window appears. (Figure 223)

Figure 223 Annotation Properties window

3. Click the Curation tab.

4. Click the Ignore Filters check box.
5. Click OK.
The segment you wanted to bypass your filter settings with is now displayed.

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Editing segment data overview
 ChAS enables you to edit data segments; merge, delete, draw de novo, adjust
boundaries, and change the Copy Number State of CHP data segments, or undo
your changes.
 The instant a file is modified by editing of one or more segments, having a segment
interpreted, or called, ChAS auto-generates a “sidecar” or CHP Change Archive
(CHPCAR) file which saves these modifications. ChAS then uses this CHPCAR file
for further user-defined edits and modifications, while your original (native) xxCHP
file (CYCHP, CNCHP, or OSCHP) is safeguarded (remains un-touched).
 The smoothing, joining and XON merging settings for each CHP file are locked at
the time of CHPCAR file creation, while unmodified CHP files without CHPCAR
files will still respond to array type-specific changes in smoothing and joining
settings.
 In order for the changes stored in the CHPCAR file to show up in the CHP file data
displayed in the ChAS Browser, the CHP file and CHPCAR file must be stored in
the same directory/folder (the xxCHP file is still the only file that is required to be
“loaded” into the browser, the CHPCAR file's edits, calls and interpretations will
load when the CHP file is loaded).
 CHPCAR files are named using the entire CHP file's name, and contain the
extension: *.chpcar
 Changing the name of either file and not the other to match will disrupt the ability
for the files to be recognized as associated with each other in the ChAS Browser.
 CHP files which have associated CHPCAR files detected (and in use), display as a
special “CHP” icon in the File → Open dialog window, and in the Files tree of
the Browser.
 Please move the CHP and CHPCAR files together when moving or archiving data.
 Two people using CHAS on different systems should NOT attempt to edit a CHP
file at the same time.
 Modification made to segments in the ChAS browser will also be updated in the
MSV.
 Files downloaded from ChAS DB can only use the delete segment option for
editing segments.
Note: Segment modification does not apply to ReproSeq Aneuploidy data.

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Using edit mode

IMPORTANT! Make sure the Edit Mode feature is turned on BEFORE you start editing
segments. Segments can not be published to ChAS DB while in Edit Mode. Edit Mode must be
turned off to enable the Publish function.

Edit Mode is accessible in three places:

1. The Browser’s icon row (top).

2. The Detail View’s icon row (top right)

3. Click View → Edit Mode

By default, Edit Mode is OFF. Click (located on the Browser’s top icon row or
above the Detail View) to turn Edit Mode ON.

 Click to turn Edit Mode OFF and remove all visual indications of your segment
changes.
 When Edit Mode is ON, deleted segments are visible, and edited segments
appear distinct from non-edited segments.
 When Edit Mode is ON, a track on a dotted axis line will appear showing the
original calls made by the software for comparison with the manual
modifications on the segment track.
 When Edit Mode is OFF, deleted segments are invisible, and edited segments
look identical to non-edited segments.

IMPORTANT! Turn Edit Mode OFF, before exporting a report of your data. Also, Edit Mode
must be OFF, before publishing to the database.

Figure 224 Edit Mode ON/OFF Deleted Segment example

Edit Mode ON

Edit Mode OFF

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Types of segment editing

 "Tracking original calls" on page 226
 "Merging all segments types" on page 226
 "Deleting all segments types" on page 232
 "Editing the start/end Coordinates of all segment types" on page 235
 "De Novo segment drawing" on page 237
 "Changing all copy number segment types" on page 241
 "Promoting mosaic segments" on page 243
 "Editing the Microarray Nomenclature (ISCN 2013) and Microarray Nomenclature
fields" on page 246
Note: Before you start any segment editing, make sure the Detail View tab is
selected, as shown in Figure 225.

Figure 225 Detail tab (bottom left)

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Tracking original calls

Original calls can be tracked to view original segment calls made by the software.
 This track is only visible when Edit Mode is ON.
 This track is only for visualization in the Detail View and is not populated elsewhere
in the software.
 The Original Calls track will disappear when the Edit Mode is OFF.

Figure 226 Original Call Track in Edit Mode example

Merging all segments types

There are two ways to merge segments:
 "Merging segment groups"
 "Segment to segment merge" on page 229

Merging segment Note: Merging segment groups together, cancels out any previously assigned Calls.
groups However, un-doing the group of merged segments (page 232) reinstates their original
Calls.
1. Click File → Open.
Your Sample File data folder window appears.
2. Click to select the file you want to edit, then click Open.
The file appears in the ChAS browser’s Detail view.
3. Left-click, hold, then move the mouse to frame the segments you want to merge
together. (Figure 227)

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Figure 227 Framing your segments

4. Release the mouse button.

Your selected segments, including their Loss symbols are now highlighted in
blue, as shown in the example below. (Figure 228)

Figure 228 Framed segments now highlighted

5. Right-click on a highlighted segment.

The following menu appears. (Figure 229)

Figure 229 Right-click menu

6. Click Merge together selected segments.

A message regarding your planned merge may appear. (Figure 230)

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Figure 230 Merge All? message

7. Click OK to acknowledge it.

The Pick a state window appears. (Figure 231)

Figure 231 Pick a state window

8. In the State field, enter a Copy Number, then use the drop-down menu to select
a Type (Gain/Loss) for the new segment. (Figure 231)
Note: For CytoScan XON arrays (XNCHP files), it is not required to enter a copy
number state value.
9. Click OK.
In cases where the segment to be merged into a group contains a Call or
Interpretation, the following message appears: (Figure 232)

Figure 232 Merge Warning message

10. Acknowledge the message, then click OK.

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11. Your selected segments are now merged together and appear as shown.
(Figure 240)

Figure 233 Merged segments

Segment to
segment merge
IMPORTANT! When merging segments during the editing of the start or end of one particular
segment, only the segment whose start or end you are editing has the option of having its Call
or Interpretation saved (or not).

Segments which are being engulfed by the edit start/end procedure being performed will not
have the option of having their Call or Interpretations placed on the resulting segment.
However, un-doing the edit resulting in this type of merging (page 232) will reinstate previous
Call and Interpretation information for all the original segments involved.

1. Click File → Open.

Your Sample File data folder window appears.
2. Click to select the file you want to edit, then click Open.
The file appears in the ChAS browser’s Detail view.
3. Click to select the segment you want to merge with another. (Figure 234)

Figure 234 Selected segment to merge with another

4. Click the Start Editing button.

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5. A shaded area over your selected segment appears. (Figure 235)

Figure 235 Click Start Editing button

6. Click, then drag the shaded area over the segment you want to merge it with.
Make sure you overlap your target segment just slightly, as shown. (Figure 236)

Figure 236 Click Start Editing button

7. Click the Start/End button.

The following message appears: Figure 237

Figure 237 Click Start Editing button

8. Acknowledge the message, then click OK.

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If the segment whose Start or End you are editing contains Call or Interpretation
information, the following message appears: Figure 238

Figure 238 Keep Call or Interpretation message

9. Click the appropriate button.

Your two segments are now merged together. While Edit Mode is ON, the
segment appears in a distinct color. (Figure 239). (When Edit Mode is OFF, the
edited segments look identical to non-edited segments.)

Figure 239 Click Start Editing button

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Un-Merging

Figure 240 Merged segments

Merged
Segments 1. Right-click on the newly merged segments (Figure 240), then click Un-do
Merge.
The following message appears. (Figure 241)

Figure 241 Confirm deletion

2. Acknowledge the message, then click OK.

Your previously merged segments return to their original states, including any
Calls or Interpretations made on the original segments (prior to their merging).

Deleting all segments types

1. Click File → Open.
Your Sample File data folder window appears.
2. Click to select the file you want to edit, then click Open.
The file appears in the ChAS browser.

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3. Left-click, hold, then move the mouse to frame the segments you want to delete.
(Figure 242)

Figure 242 Framing your segments for deletion

4. Release the mouse button.

Your selected segments, including their Loss symbols are now highlighted, as
shown in the example below. (Figure 243)

Figure 243 Framed segments now highlighted

5. Right-click on a highlighted segment.

The following menu appears. (Figure 244)

Figure 244 Right-click menu

6. Click Delete Segments.

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A message regarding your planned deletion appears. (Figure 245)

Figure 245 Confirm deletion

7. Click OK to acknowledge it.

Your selected segments are deleted and graphically represented as “ghosts”
while Edit mode is ON. (Figure 246). When Edit Mode is OFF, deleted segments
are invisible and NOT displayed in any view or table.

Figure 246 Deleted segments

Note: Even though your selected segments are deleted, ChAS preserves their data
for future reference. See "Right-click menu options" on page 206 for information on
how to view and edit segment properties and view segment details.

Un-deleting a 1. Right-click on the deleted segment(s), then click Un-do Delete.

deleted The following message appears. (Figure 247)
segment(s)
Figure 247 Confirm deletion

2. Acknowledge the message, then click OK.

Your previously deleted segment(s) return to their original states, including any
Calls or Interpretations made on the original segments (prior to their deletion).

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Editing the start/end Coordinates of all segment types

IMPORTANT! Only the boundaries of 1 segment, can be adjusted/modified at one time.

Note: Segment start or end boundaries can be moved left and/or right. The Adjusting/
Modifying Segment Boundaries example that follows, shows how to move a segment
end boundary farther to the right.
1. Using the zoom tools and scroll bars (if needed), identify the segment whose start
or end (or both) you want to modify
2. Single-click on the segment to highlight it. (Figure 248)

Figure 248 Selected segment

3. Click the Start editing... button.

The following appears: (Figure 249 on page 235)
4. Place the mouse cursor on the very-right edge of the current segment boundary.
(Figure 249)

Figure 249 Selected segment - Start editing

Edit Start or End button

5. Click, then drag the segment’s right-edge boundary to the right, then stop at an
appropriate point. (Figure 250) You will ONLY be allowed to set the Start or End
position to match the position of a marker probeset.

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Figure 250 Selected segment - Start editing

6. Click the Set start/end... button. (Figure 251)

The newly adjusted/modified segment boundary appears as shown. (Figure 251)

Figure 251 Selected segment - Start editing

Set Start/End button

7. ChAS auto-calculates various properties of the newly edited segment. Mouse

over the segment to view its new details. (Figure 252)

Figure 252 Selected segment - Start editing

Un-doing the 1. Right-click on the previously adjusted/modified segment, then click Un-do Edit.
edited start/end The segment returns to its previous state, including, previous boundaries, calls,
coordinates of a and interpretations.
segment

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De Novo segment drawing

1. Within an existing segment track, locate an empty space where you want to draw
in a brand new segment.
2. Right-click inside this empty space.
A Create a Copy Number State segment around XX,XXX,XXX ribbon appears
(Figure 253)

Figure 253 Selected segment - Change Copy Number - Pick a state window

3. Click on the ribbon, as shown in Figure 253.

The Pick a state window appears. (Figure 254)

Figure 254 Drawing a new segment

-- Pick a state window

4. Enter a Copy Number and Type for the new segment.

5. Click OK.

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Your newly drawn segment appears. (Figure 255)

Figure 255 Newly drawn segment limited in size by the Copy Number State track

Copy Number State Data Track

IMPORTANT! Newly drawn segments will stop when they encounter another segment,
whether or not that segment is currently drawn or whether it is currently filtered out; see
Figure 255 for an example in the CN State data track which is used to draw Copy Number
Segments of Gain and Loss.

New segments will also stop when they encounter the last appropriate marker on the
chromosome. Because of this, new segments drawn will vary in their initial size.

6. Move the mouse cursor over the newly drawn segment to reveal its properties.
(Figure 256)

Figure 256 Newly drawn segment - Mouse over to see its properties

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Un-doing a 1. Right-click on the newly drawn segment.
segment De Novo The following menu appears. (Figure 257)
drawing

Figure 257 Newly drawn segment - Un-do drawn segment

2. Click Un-do Create.

The previously drawn segment is removed, along with any Calls or Interpretations
it had been given. (Figure 258)

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Figure 258 Newly drawn segment - Drawn segment removed

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Changing all copy number segment types

Note: For CytoScan XON arrays only, you are not required to assign a copy number
to the segment.
1. Right-click on the segment that contains the copy number you want to change
2. Click Change copy number. (Figure 259)

Figure 259 Selected segment - Change copy number

The Pick a state window appears. (Figure 260)

Figure 260 Selected segment -

Change Copy Number - Pick a state
window

3. Enter a new Copy Number State value and Type (Gain/Loss).

Note: For CytoScan XON arrays (XNCHP files), it is not required to enter a copy
number state value.
4. Click OK.
The segment now reflects your revised Copy Number State and Type.

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Un-doing a copy 1. Right-click on the segment you performed a Copy Number State change on, then
number change click Un-do Edit.
2. The following message appears. (Figure 261)

Figure 261 Confirm deletion

3. Acknowledge the message, then click OK.

The segment’s original Copy State Number is reinstated.

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Promoting mosaic segments

IMPORTANT! Segments in the Mosaic Segment Track are NOT uploaded to the database.

To capture the information for a mosaic segment in the database, that segment must
be "promoted" to the Copy Number State track. This is done to reduce redundancy in
those regions in which segments were called by both the copy number algorithm and
the mosaic detection algorithm. (Figure 262)

Figure 262 Promoting Mosaic Segments - Example

Promoted mosaic segments maintain their non-integer copy number state, marker
count, median log2 ratio, genome coordinates and size when they are promoted to the
copy number state track. (Figure 263)
The mosaic gain segments will have the same blue/red used for integer copy number
Gains/Losses, however, they maintain their non-integer copy number state to indicate
they are a mosaic.

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Figure 263 Promoted Mosaic Segment to Copy Number State Track

Modified segments in the segments table

IMPORTANT! When exporting a Segments table to text (TXT), please note that deleted
segments will be part of the export when Edit Mode is On, and will NOT be part of the export
when Edit Mode is Off.

In PDF reports, deleted segments are never shown in graphical views, nor are they listed in the
Segments Table, as Edit Mode is required to be OFF to generate a PDF report.

Editing mode on When the Edit Mode is ON , the Modified segments appear differently within the
Segments table, as shown in Figure 264.

 Deleted Segments are represented with a red X and a strike-through line. Deleted
segments do NOT show up in PDF reports because PDF reports cannot be created
while Edit Mode is ON.
 Materially Modified Segments (including segments that have been merged,
boundaries edited, or had their Copy Number States changed) are represented
with italicized text.

Figure 264 Segments table with Edit mode ON

Strike-through text example

Italicized text example

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Editing mode off Turning the Edit Mode OFF, displays the Segments table as follows: (Figure 265)

Note: The three deleted segment rows which were in strike-through text are removed
from the table when Edit Mode is OFF. In addition to when Edit Mode is OFF, the rows
which indicated Modified segments are no longer italicized.

Figure 265 Segments table with Edit mode OFF

Removing all edits made to a sample

1. Right-click on the File name in the Files list, then select Discard Changes.
(Figure 266)

Figure 266 Discard Changes

The Discard Changes window appears and displays the following options:
 Purge All Edits: Reverts all edits to segments and removes all calls and
interpretations.
Note: The log of the edits that have been performed on the sample can still be
viewed.
 Clear Edit Log: Purges all edits and clear the log of any edits performed on the
sample.
 Discard all changes: Purges all edits, clears the edit log, and deletes the CHCAR
file.

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2. Check the appropriate box, then click Yes. (Figure 267)

Figure 267 Discard Changes Confirmation window

Editing the Microarray Nomenclature (ISCN 2013) and Microarray

Nomenclature fields
The View/Edit Annotation Properties Curation tab enables you to update the copy
number nomenclature in the Microarray Nomenclature (ISCN 2013) and Microarray
Nomenclature fields.
Example: For Mosaic segments, the default name will show a range of copy number
such as x2-3. If you have the percent mosaicism information, this part of the
Microarray Nomenclature can be updated to reflect the percent mosaicism by typing
x3[0.6]. The field will be updated as follows:
Default name: arr[GRCh37] 5p15.33p13.2(113576_38205477)x2-3
Updated name: arr[GRCh37] 5p15.33p13.2(113576_38205477)x3[0.6]
1. Right-click on the Microarray Nomenclature cell for the segment you would like
to update, then click View/Edit Annotation Properties, as shown in Figure 268.

Figure 268 Discard Changes

The Annotation Properties window appears. (Figure 269)

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Figure 269 Discard Changes

2. Click the Curation tab.

3. At the ISCN Copy Number Text field (Figure 269), type in the copy number
nomenclature text you want, then click OK. Note: This field can be edited for
LOH segments to designate copy number in the Microarray Nomenclature field
for LOH segments as well.
4. Optional: To reset the text to the original default format, click the Reset ISCN
button.
Note: To automatically add the Inheritance field to the Microarray Nomenclature ISCN
2016 field, please see "Adding or removing inheritance calls" on page 259.

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11 annotations

Sample annotations
Sample file level annotations such as Sample-type, Phenotype, and Sample
Interpretation can be added to each sample.

Adding, 1. Click Preferences → Edit User Configurations or click on the upper tool
removing, and bar.
changing the The User Configuration window appears.
order of sample 2. Click the Vocabularies tab, then click the Sample Type tab. (Figure 270)
type text

Figure 270 Sample Type window tab

Adding a Sample Type

1. Click inside the Add Sample Type field, then enter your new Sample Type.
2. Click Add.

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Deleting a Sample Type
1. Click to highlight the Sample Type you want to delete.
2. Click Remove.

Re-arranging the order currently displayed Sample Types

1. Click to highlight the Sample Type you want to move.
2. Drag and drop it to its new location (order).
3. If needed, repeat steps 1-2 to re-arrange additional Sample Types.

Restoring the factory default Sample Types

1. Click Restore Defaults.
The factory default Sample Types are restored.

Adding, 1. Click Preferences → Edit User Configurations or click on the upper tool
removing, and bar.
changing the The User Configuration window appears.
order of 2. Click the Vocabularies tab, then click the Phenotype tab.
phenotype text
The following window tab appears: (Figure 271)

Figure 271 Phenotype window tab

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Adding a short Phenotype text
1. Click inside the Add Phenotype Type field, then enter your new Phenotype.
2. Click Add.

Deleting a short Phenotype text

1. Click to highlight the Phenotype you want to delete.
2. Click Remove.

Re-arranging the currently displayed Phenotypes order

1. Click to highlight the Phenotype you want to move.
2. Drag and drop it to its new location (order).
3. If needed, repeat steps 1-2 to re-arrange additional Phenotypes.

Restoring the factory default Phenotypes

1. Click Restore Defaults.
The factory default Phenotypes are now restored.

Adding 1. Right-click on a File name you want to add a Sample level annotation to.
annotations at the A menu appears.
sample (xxCHP)
2. Click View/Edit Properties.
file level
The File Properties window appears. (Figure 272)

Figure 272 File Properties window

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3. Click on the Sample Properties tab. (Figure 273)

Figure 273 Sample Properties window

4. Use this window to Add/Enter Sample ID(s), choose a Sample Type(s), enter
Phenotype(s), and Sample Interpretation(s). Note: The Sample ID defaults to the
File Name, but you can edit/change the Sample ID name if you want.
5. Click OK.

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Segment annotations
Segment level annotations such as Call, Interpretation and Inheritance can be added
to segment data.

Setting up the Note: If you are using a user profile from a previous version of ChAS, your default set
calls feature of Calls will NOT appear in the Calls drop-down list. To restore them, click on Edit User
Configurations → Vocabularies → Calls, then click the Restore Defaults button, as
shown in Figure 274 on page 252.

Adding and removing calls

1. Click Preferences → Edit User Configurations or click on the upper tool
bar.
The User Configuration window appears.
2. Click the Vocabularies tab.
The Calls window tab appears. (Figure 274)

Figure 274 User Configuration window - Vocabularies tab window

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Adding, deleting, The Calls window enables you to Add, Delete and Re-arrange current Calls.
and re-arranging
calls Adding calls to the Call drop-down list
1. Click inside the Add Call field, then enter your new Call.
2. Click Add.
Your newly added Call now appears in the Call drop-down-list.

Deleting calls from the Call drop-down list

1. Click to highlight the Call you want to delete.
2. Click Remove Call.
Your newly deleted Call is removed from the Call drop-down-list.

Re-arranging the order of Calls in the Call drop-down list

1. Click to highlight the Call you want to move.
2. Drag and drop it to its new location (order).
Your Call is now in its revised position/order within the Call drop-down-list.
3. If needed, repeat steps 1-2 to re-arrange additional Calls.

Restoring the factory default Calls

1. Click Restore Defaults.
The factory default Call(s) are now populated in the Call drop-down-list.

Using the calls Method 1: At the segments table

feature 1. Click the Browser’s Segments tab.
2. Scroll the Segment table to the right until you see the Call column.
3. Locate the appropriate row.
4. Single-click inside the field.
A blue drop-down bar appears.
5. Click on the drop-down to reveal the list of available Calls, as shown in Figure
275

Figure 275 Calls drop-down menu bar

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6. Click to select the appropriate Call.

7. Click outside the field or press Enter on the keyboard.
8. Your Call is entered. Note that the Curation By column is populated with the user’s
Windows login ID (left) and ChAS User Profile ID (right). (Figure 276)

Figure 276 Call is entered and Curation By field is populated

A Call can be assigned to multiple segments at the same time. To do this:

1. Shift-click or Ctrl-click on the Calls fields for the segments you want to assign to the
same call to.
2. Right-click on the highlighted area, then click Set Value.
3. Select the Call from the drop-down, then click OK to assign that call to all the
selected segments.

Method 2: At the View/Edit Annotation Properties Window

1. From any graphical view (Karyoview, Selected Chromosome View, or Details View),
right-click on the segment you want to add an interpretation to, then click the menu
selection View/Edit Annotation Properties.
The Annotation Properties window appears.
2. Click the Curation tab.
The Interpretation window tab appears: (Figure 277)

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Figure 277 Annotation Properties window - Interpretation window

3. Click the Call drop-down menu, then select your appropriate interpretation Call.
(Figure 278)

Figure 278 Call drop-down

menu

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Adding or The Snippets feature can be used in conjunction with the free-typing Interpretation
removing field (below the Calls drop-down). It allows for a convenient “shortcut” when common
interpretation words or phrases are used often in an interpretation.
snippets 1. Click Preferences → Edit User Configurations or click on the upper tool
bar.
The User Configuration window appears.
2. Click the Vocabularies tab, then click the Interpretation tab.
The Interpretations window tab appears. (Figure 279)

Figure 279 User Configuration window - Interpretation tab window

3. At the Interpretation window, click inside the field shown (Figure 279), then enter
the snippet you want to use with your interpretation(s).
4. Click Add.
The snippet now appears and is saved in the Interpretations List pane.
5. Repeat steps 3 and 4 to add additional snippets.
6. Click OK.

Removing a saved snippet

1. Click to highlight the snippet you want to remove.
2. Click Remove.

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Removing multiple saved snippets
1. Shift click or Ctrl click to highlight each snippet you want to remove.
2. Click Remove All.

Using the Method 1: At the segments table

interpretation 1. Click the Browser’s Segments tab.
snippets feature
2. Scroll the Segment table to the right until you see the Interpretation column.
3. Locate the appropriate row.
4. Click inside the field.
5. Right-click on the flashing cursor. If the field has existing text, place the flashing
cursor to the point where you want to add a snippet, then right-click.
A floating drop-down menu bar appears. (Figure 280)

Figure 280 Floating Snippets drop-down menu bar

6. Click the snippet bar’s drop-down to display the available snippets, then click on
the appropriate snippet. (Figure 280)

Figure 281 Snippets drop-down menu

The snippet appears in the appropriate Segment Interpretation row, as shown in

Figure 282.

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Figure 282 Snippet appears in field

7. Click outside the field.

Your snippet is entered. Note: The Curation By column is populated with the
user’s Windows login ID (left) and ChAS User Profile ID (right), as shown in
Figure 282.

Method 2: At the View/Edit annotation properties window

1. From any graphical view (Karyoview, Selected Chromosome View, or Details
View), right-click on the segment you want to add an interpretation to, then click
the menu selection View/Edit Annotation Properties.
The Annotation Properties window appears.
2. Click the Curation tab.
3. Type in your interpretation. If at any point you want to insert your preset
snippet(s), right-click inside the interpretation window.
A drop-down bar graphic appears. (Figure 283)

Figure 283 Drop-down menu bar

4. Click to select the appropriate snippet or click Close to exit. (Figure 284)

Figure 284 Snippet drop-down

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Your snippet (preset word, sentence, or phrase) now appears “in line” with your
typed text. (Figure 285)

Figure 285 Snippet in the Interpretation field pane

Adding or 1. Click Preferences →→ Edit User Configurations or click on the upper

removing tool bar.
inheritance calls The User Configuration window appears.
2. Click the Vocabularies tab, then click then Inheritance tab.
The Inheritance window tab appears. (Figure 286) The Inheritance window
enables you to Add, Delete and Re-arrange current Inheritance calls.

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Figure 286 User Configuration window - Inheritance window tab

3. Check the Include Inheritance in Microarray Nomenclature check box to have

Inheritance column entries automatically appended to the Microarray
Nomenclature field.
Example: If the dn is selected in the Inheritance column then the Microarray
Nomenclature field would be updated to read: arr[GRCh37]
22q13.31(44582928_44851090)x3 dn

Adding an Inheritance call to the Inheritance drop-down list

1. Click inside the Add Inheritance Call text field (Figure 286), then enter your new
call.
2. Click Add.

Deleting a call from the Inheritance drop-down list

1. Click to highlight the call you want to delete.
2. Click Remove.

Re-arranging the order of calls displayed in the Inheritance drop-down list

1. Click to highlight the Inheritance you want to move.

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2. Drag and drop it to its new location (order).
Your call is now in its revised position/order within the Inheritance drop-down-
list.
3. If needed, repeat steps 1-2 to re-arrange additional Inheritance.

Using the Method 1

inheritance 1. Click the Browser’s Segments tab.
feature
2. Scroll the Segment table to the right until you see the Inheritance column.
3. Single-click inside the field.
A blue drop-down bar appears.
4. Click on the drop-down to reveal the list of available Inheritance Calls.
(Figure 287)

Figure 287 Calls drop-down menu bar

5. Click to select the appropriate Inheritance.

6. Click outside the field or press Enter on the keyboard.
Your Inheritance is entered.

Method 2: From the View/Edit annotation properties window

1. From any graphical view (Karyoview, Selected Chromosome View, or Details
View), right-click on the segment you want to add an interpretation to, then click
the menu selection View/Edit Annotation Properties.
The Annotation Properties window appears.
2. Click the Curation tab.
3. Select the Inheritance call from the drop down.

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Adding Oncomine Reporter annotations

You may add annotations based on approved Oncomine Reporter search terms. Once
your segments have been annotated with Oncomine Reporter term(s), the Segments
Table can be exported as a txt file and directly uploaded to Oncomine Reporter for
literature searches based on the assigned annotation.
The annotation options for use with Oncomine Reporter are a controlled vocabulary.
Note: The options available in the drop-down list for the Oncomine Reporter column
are compatible nomenclature with Oncomine Reporter application.
1. Select to view the Oncomine Reporter column in the Segments Table. See
"Selecting columns to display or hide" on page 329.
2. Click in the Oncomine Reporter column for a given segment to assign the
appropriate annotation for that segment. Segments on a given chromosome will
only see relevant Oncomine Reporter terms for that chromosome. For example,
if there is a gain of Chromosome 8q, you will only see Oncomine Reporter terms
for Chromosome 8. All other terms for other chromosomes are hidden for that
segment.

Figure 288 Oncomine Reporter column example

For information on Oncomine Reporter Table State, "Saved table states" on page 332
on Table States.

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Tracking and reviewing the log file 11

Tracking and reviewing the log file

1. Right-click on the file, then click View Process Pipeline. (Figure 289)

Figure 289 Right-click menu

The Process Pipeline window appears. (Figure 290)

Figure 290 Process Pipeline - Smooth and Join

2. Click Smooth and Join for its description and summary. (Figure 290)
3. Click Edits for its description and summary of the file’s past user edits.
(Figure 291)

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Figure 291 Process Pipeline -Edits

4. Click Details.
A Edit Details window appears featuring an Edit and Log tab. (Figure 292)

Figure 292 Process Pipeline - Edit tab

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The Edit tab lists only recent edits that were NOT reverted. Use the horizontal
scroll bar to reveal additional edit information. For a complete historic account of
all edits made (including reversions of some edits), click on the Log tab.
5. Click OK to return to the Process Pipeline window or click the Log tab.
The Log tab displays an extensive summary of the file’s edited history to date.
Use the horizontal scroll bar to reveal additional log information. (Figure 293)

Figure 293 Log tab

6. Click OK to return to the Process Pipeline window. (Figure 294)

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Figure 294 Process Pipeline - Calculated properties

7. Click Calculated Properties for its description and summary.

8. Click OK to return to the ChAS browser.

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CytoRegions overview
The CytoRegions feature enables you to define parts of the genome that are of special
interest to you.
Note: The CytoRegions feature is designed for use with up to a few thousand regions.
Larger numbers of regions can be used, but will impact performance. A reference
annotation file, such as Genes, is not recommended for use as a CytoRegions file due
to the large number of reference annotations.
To use CytoRegions, you need to select a file(s) with position information for regions
of the genome as the CytoRegions file.
 Select Region information files in AED or BED format.
 Use existing Region file(s), or create a new one in AED format in ChAS, then add
regions to it by selecting segments, annotations, or regions in other loaded files.
 Add annotations to regions to help you track the information. See "Creating and
editing AED files" on page 287.

After selecting a CytoRegions file, you can:

 Use the Restricted Mode to display only Segments and graph data that appear in
those regions. While in this mode, annotations are not hidden by CytoRegions or
by the application of Restricted Mode.
 Use differential filtering options for these regions and for the rest of the genome.
 Protect a CytoRegions file. See "Protecting an AED file" on page 308.

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Selecting a CytoRegions information file

Select the CytoRegions file from the available region information files. See "Loading
files" on page 121. The software automatically checks the hg version of an AED or
BED file before loading. See Figure 295 for an example BED file. The file will not be
loaded if the hg version does not match what is loaded in the ChAS Browser. If an hg
version is not found for the AED or BED file, a warning message appears.

Figure 295 Example BED file

hg version

Do either of the following to select a CytoRegions file:

 In the files list, right-click a file and select Include as CytoRegion on the shortcut
menu, as shown in Figure 296.
 Multiple files can be selected to be included in the CytoRegions. To do this, right-
click on each AED/BED file to be included, then select Include in CytoRegions.
Note: All files (included in CytoRegions) are treated as they are one file.

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Figure 296 Select a CytoRegions file from the file list

Or
 From the menu bar, click View → Select as CytoRegions file(s).
Alternatively, in the CytoRegions Tab of the Upper display, click the Select to
include in CytoRegions button.

The Select CytoRegions File(s) window opens. (Figure 297)

Figure 297 Select CytoRegions File(s) window

 Select a regions information file(s) to use for CytoRegions, then click OK.
Note: You may select more than one Region file (AED/BED) to include as
CytoRegions. ChAS handles multiple selected files as single (larger) CytoRegion
file.
The Create New feature is described in "Creating an AED file of annotations" on
page 287.

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Note: If a region file was selected for the CytoRegion file before shutting off the
software, that file is automatically loaded as the CytoRegion file after the software
is opened the next time with the same user profile. To clear a CytoRegions file
map from ChAS, click Select None (Figure 297). Alternatively, right-click the file
in the Files list, then deselect Include in CytoRegions on the shortcut menu to
toggle the check mark off.

Viewing CytoRegions
After selecting a CytoRegions file, it can be displayed in either a graphic view or table.
• ʺCytoRegions in the graphic viewsʺ on page 270
• ʺCytoRegions tableʺ on page 272
Note: CytoRegions that share genomic coordinates with a detected segment are
listed in the “CytoRegions” column of the Segments table. See "Segments table" on
page 338.

CytoRegions in Regions specified in the CytoRegions file are displayed as dark gray stripes in the
the graphic views Karyoview and Chromosome Display (Figure 298) and Detail View (Figure 299).

Figure 298 Karyoview and Selected Chromosome View with CytoRegions Displayed

Karyoview Chromosome Display

Area displayed in
Detail View

Areas not displayed

in Detail View are
Cytoregions shaded in gray
displayed as gray
stripes

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Figure 299 Detail View with CytoRegions displayed

Cytoregions

You can turn off highlights by un-checking the View menu’s Hide CytoRegion
Background Highlights check box. (Figure 300) This action keeps the CytoRegions in the
Table View, however they are no longer highlighted in the Graph Views.

Figure 300 View menu - Hide CytoRegion check box

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CytoRegions The CytoRegions table (Figure 301) shows the intersections between regions in the
table designated CytoRegions file and the segments in the Segments table. Every region in
the CytoRegions file will be listed on at least one line of the CytoRegions table, even
if it does not intersect any segments. For those regions which intersect one or more
segments, there will be one table row for each intersection. Depending on the
columns which have been used to sort the CytoRegions table, these rows may or may
not be near each other. A segment that intersects more than one region in the
CytoRegions file appears multiple times in the CytoRegions table, one row for each
intersection.
In the CytoRegions table, the “CN State” value corresponds to the state of copy-
number and mosaicism segments that intersect the CytoRegion. There is no CN State
value for other types of segments that do not correspond to a copy-number call.

Figure 301 CytoRegions Table

Tool bar

Two different files within the rows of the

CytoRegions File column can be displayed.

Table Filtering field

Highlighting regions in the CytoRegions table and details view

If the Details View displays the CytoRegions file (the CytoRegions file is check marked
in the Files list), you can conveniently find and view items.
 Click a row in the CytoRegions table to select the corresponding annotation from
the CytoRegions file. All of the lines for that region are highlighted in the table. The
Details View zooms to the currently selected region. Note: If the Details View does
not automatically zoom to the selected region, confirm that the Auto-zoom option
is selected (click View → Auto-zoom to table selection from the menu bar.)

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 In the Detail View, click a region or select multiple regions of the CytoRegion file to
highlight all of the corresponding rows in the CytoRegions table. The CytoRegions
table automatically scrolls to show at least one of the highlighted rows.
 To quickly find a particular Segment in the CytoRegions table, first double-click
that segment in any of the views or in the Segments table (the current region will
be set to that segment), then press the tool bar button in the CytoRegions table
to show only the cytoregions in the current region.

CytoRegions tool bar

The tool bar (Figure 302) provides quick access to table functions. The standard
functions are described in "Standard tool bar controls" on page 328.

Figure 302 CytoRegions table tool bar

The tool bar has one specialized button.

Select CytoRegions file (See "Selecting a CytoRegions information file" on page 268 )

CytoRegion Table Description

Column

CytoRegion File Name of the AED/BED file that contains the region.

CytoRegion Type Type of file or element from which the CytoRegion is derived. Default User Annotations are annotations
derived from AED or BED file.

CytoRegion Identifier for region.

Chromosome Chromosome in which the region is located.

Min Starting position of the region.

Max Ending position of the region.

Size (kbp) Size of the region.

Segment Label Label assigned to the detected segment by ChAS.

Segment Name/ID Name/ID of the Segment.

Segment File Sample File that the segment was detected in.

Segment Type Type of segment:

– CN loss or gain
– XON loss or gain
– Mosaic loss or gain
– LOH

Segment Min Starting position of segment.

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CytoRegion Table Description

Column

Segment Max Ending position of segment.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic
position coordinates" on page 488).

Segment Size (kbp) Size of the segment.

CN State Copy Number State (Displayed for Gain, Loss, and Mosaicism segment types).

Shared Size Size of the contact between segment and cytoregion.

% of CytoRegion How much of the CytoRegion is contacted by the Segment.

touching Segment

% of Segment How much of the detected segment is contacted by the CytoRegion.

touching
CytoRegion

You can:
 Use the common table functions to control the display of data in the table. See
“Common table operations” on page 327.
 Export data in various formats. See “Exporting table data” on page 422..
 Search CytoRegions to display only regions of interest (see below).

Searching CytoRegions
The Search CytoRegions feature enables you to search the “CytoRegion” column for
text strings that match a search string.
1. Enter the search string in the Search CytoRegions box at the bottom of the
CytoRegions table.
2. Press Enter.
The table displays only annotations that match the search string.
3. To restore the table, click Clear Search Field.

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Using filters with CytoRegions

If you have CytoRegions information loaded into ChAS, you have the option to apply
different segment filtering parameters to the parts of the genome that are defined as
CytoRegions and the parts of the genome that are not within these regions (Genome).
For segment filtering to function as described below, the CytoRegion segment filters
should always be set identical to or less stringent than the counterpart Genome
segment filter settings.
The filter settings for CytoRegions and for the rest of the genome interact in different
ways, depending upon whether:
 A cytoregion information file is selected
 Restricted Mode is selected
If a cytoregion information file is selected, but Restricted Mode is not selected:
 Segments wholly within a cytoregion are filtered using the CytoRegions filter
settings.
 Segments that don’t touch a cytoregion are filtered using the Whole Genome
settings.
 A segment that touches both Genome and CytoRegions must pass both the
CytoRegions filter thresholds and Whole Genome filter thresholds, otherwise it will
not be shown.
If Restricted Mode is selected:
 Segments in or straddling cytoregion boundaries are filtered using the
CytoRegions filter settings.
These rules also apply when a region information file has been selected as an Overlap
Map and the Overlap filters are used.

Using restricted mode

The Restricted mode enables you to view detected segments and graph data only in
regions you have defined in advanced in the CytoRegions file.
Note: Restricted mode is not available unless a region information file or one of the
Reference Annotations is selected for the CytoRegions function.

Selecting/De-selecting Restricted Mode

 From the View menu, select Restrict to CytoRegion.
Or
 Click the Restricted Mode button from the main tool bar.
Note: Segments and graph data that are not in the defined CytoRegions are
concealed in the display. Segments in or straddling CytoRegions boundaries are
filtered using the CytoRegions filter settings. (Figure 303, Figure 304)

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Figure 303 Karyoview example shown in

unrestricted and restricted mode

Unrestricted Mode Restricted Mode

Figure 304 Detail View example in Restricted Mode

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When you deselect Restricted Mode, an Exit Restricted Mode window appears.
(Figure 305)

Figure 305 Exit Restricted Mode window

Click Yes to exit Restricted Mode.

Assigning a CytoRegion for targeted XON analysis

This option is designed for use with CytoScan XON array data. Assigning a
CytoRegion for a Targeted XON analysis combines these two steps:
1. Assigns the file as the CytoRegion.
2. Automatically sets the appropriate filters for Targeted XON analysis.
 Hides all segments in the Genome region and colors all the data gray.
 Turns on all levels in CytoRegions to reveal any XON Region segment call and
colors the data the assigned sample color.

Creating an AED File from a gene list

To create an AED file from a Gene List for use with the CytoRegion for Targeted XON
analysis or other region file (CytoRegion or Overlap Map) do the following:
1. Create a text tab delimited file containing your list of Genes for which you would
like to generate an AED file. The gene coordinates will be pulled from a selected
NetAffx Genomic Annotation file. The Gene List should just be a list of gene
names with no header and saved as a text tab delimited file.
2. Click Exports → Create and Export an AED file from a Gene List.
The following window appears: (Figure 306)

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Figure 306 Create Panel (AED) File from Gene List window

3. Select the NetAffx Genomic Annotation file from the drop down list. The
annotation database files visible are available files from the Library file folder. If
you do not see a NetAffx Genomic Annotation file that you want to use, please
copy the file into C:\Affymetrix\ChAS\Library and restart the ChAS browser.
4. Select an Input Gene List File: Click on Select File button and browse to the
location of your TXT tab-delimited Gene List file.
5. Select an Output AED File: Click on the Select File button, select the location to
save the output file, name the AED file, click Save.
6. Click OK to generate the AED file. (Figure 307)

Figure 307 Export Panel File confirmation window

Note: If entries in the Gene List are not found in the NetAffx Genomic Annotation file,
they will be listed in a message box. Any skipped entries can be added to the AED file.
See "Creating and editing AED files" on page 287 and "Adding annotations to an AED
file" on page 289.

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Overlap map and filter overview
 The Overlap Map enables you to show or hide segments in areas of the genome
that you are not interested in. For example, in regions of Benign Copy Number
Polymorphism, you can:
 Specify regions of the genome in an Overlap Map File.
 Optionally filter out detected segments that are overlapped by these regions.
You can also specify the percentage of the segment (between 1 and 100%) that
must be overlapped by the Overlap Map items before being filtered from
display.
 The Overlap Map filter operates separately from the CytoRegions features, but you
can apply different overlap map filtering parameters to CytoRegions and to areas
outside of CytoRegions.
 Protect an Overlap Map file. See “Protecting an AED file” on page 308..

Using the overlap filter

1. Select a region information file for the Overlap Map. For supported file types, see
"Selecting the overlap map file" (below).
2. Set Percent Overlap value for each segment type you want to filter in the
Segment Filters window. See "Using the overlap filter" on page 286.
3. Choose how you want to view the Overlap Map regions.
 "Viewing overlap map regions in the graphic displays" on page 282
 "Viewing the overlap map table" on page 283

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Selecting the overlap map file

Use the following file types for the Overlap Map:
 Region information files in AED and BED format.
 Position information from Reference annotation files.
The software automatically checks the hg version of an AED or BED file before loading
(see Figure 308 for an example BED file). The file will not be loaded if the hg version
does not match what is loaded in the ChAS Browser. If an hg version is not found for
the AED or BED file, a warning message appears.

Figure 308 Example BED file

hg version

Do either of the following to select an Overlap Map:

1. In the files list, right-click the file and select Set File as Overlap Map on the
shortcut menu. (Figure 309)

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Figure 309 Select an Overlap Map from the files

list

OR
1. On the menu bar, click Select View → Overlap Map.
Alternatively, in the Overlap Map tab in the upper display, click the Select Overlap
Map tool bar button.
The Select Overlap Map window appears. (Figure 310)

Figure 310 Select Overlap Map window

The window displays a list of the region and annotation files you can select for an
overlap map.
2. Select the file you want to use, then click OK.
The region file loads and its regions are displayed with overlap information in the
Overlap Map tab.

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The Overlap Map icon appears next to your selected file within the File List,
as shown below.

Note: To clear an Overlap map, click Select None. (Figure 310) Alternatively, right-
click the file in the files list, then select Set File as Overlap Map from the shortcut
menu.

Viewing overlap regions

You can view the Overlap Map regions:
 In the graphic display views. See “Viewing overlap map regions in the graphic
displays” on page 282.
 In the Overlap Map window tab. See “Viewing the overlap map table” on page 283.
Note: Overlap Map items that are covered by a detected segment are listed in a
column of the Segments table. "Segments table" on page 338.

Viewing overlap In the Karyoview and Selected Chromosome View, regions specified in the Overlap
map regions in Map file are displayed as short rectangles to the immediate left of the Cytobands.
the graphic (Figure 311)
displays
Figure 311 Karyoview and Selected Chromosome View with
Overlap Map Regions Displayed
Overlap Map regions Overlap Map regions in
in Karyoview Selected Chromosome View

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In the Detail View, the overlap map regions are displayed as rectangles below the
Cytobands (Figure 312). The default color is yellow, but you may select different colors
for displaying regions in a region information file.
You can change the colors used to display items by using:
 Specifying color when adding the item to an AED file. See “Entering general
information” on page 299.
 Using the Color Rules. See “AED/BED color rules” on page 310.

Figure 312 Detail View with Overlap Regions displayed

Overlap Map regions

Viewing the The Overlap Map table (Figure 313 on page 284) displays a list of overlapping items
overlap map table from the overlap map file and the Segments table. Each region in the Overlap Map file
will be listed on at least one row of the table, even if it does not overlap any segments.
For those regions which overlap one or more segments, there will be one for each
overlap. Depending on the columns which have been used to sort the Overlap Map
table, these rows may or may not be near each other. A segment that overlaps more
than one region in the Overlap Map file will appear multiple times in the Overlap Map
table, one row for each overlap.

Highlighting overlap regions in the overlap map table and details view
If the Details View displays the Overlap Map file (the Overlap Map file is check marked
in the Files list), you can conveniently find and view items.
 Click a row in the Overlap Map table to select the corresponding annotation from
the Overlap Map file. All of the rows for that region are highlighted in the table. The
Details View zooms to the currently selected region.
Note: If the Details View does not automatically zoom to the selected region, confirm
that the Auto-zoom option is selected (click View → Auto-zoom to table selection
from the menu bar.)

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 In the Detail View, click a region or select multiple regions from the Overlap Map
file to highlight all of the corresponding rows in the Overlap Map table. The Overlap
Map table automatically scrolls to show at least one of the highlighted rows.
 To quickly find a particular Segment in the Overlap Map table, first double-click
that segment in any of the views or in the Segments table (the current region will
be set to that segment), then press the tool bar button in the Overlap Map table
to show only the overlaps in the current region.

Figure 313 Overlap Map Table

Overlap map tool bar

The tool bar provides quick access to table functions. The standard functions are
described in "Standard tool bar controls" on page 328.

Select Overlap Map file (see "Selecting the overlap map file" on page 280).

Overlap Map Table Description

Column

Map Item Type Source of the position information (CN Gain or Loss segment, reference annotation, etc.)

Overlap Map Item Identifier for the item.

Chromosome Chromosome in which the item is located.

Min Starting position of the item.

Max Ending position of the item.

Size (kbp) Size of the item.

Segment Label Label assigned to the detected segment by ChAS.

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Overlap Map Table Description

Column

Segment Name/ID Name/ID of the Segment.

Segment File Sample File that the segment was detected in.

Segment Type Type of segment:

CN loss or gain
Mosaicism
LOH

Segment Min Starting position of segment.

Segment Max Ending position of segment.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic
position coordinates" on page 488).

Segment Size Size of the segment.

CN State Copy Number State (Not displayed for other segment types).

% Overlap How much of the detected segment is covered by the Overlap Map item. A Segment which has 20%
of its length somehow encompassed within the boundaries of an Overlap Map item has an Overlap
value of 20%.
This percentage value is used to filter segments out of the displays and tables when filtering segments
by “Overlap” in the filter slider dialogs.

% Coverage How much of the Overlap Map item is covered by the Segment.

Shared Size Size of the overlap between segment and Overlap Map item. Coverage values are not presently used
in filtration of Segments from the displays or tables.

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Using the overlap filter

After selecting an Overlap Map Region file, you have the option to set Overlap filters
for the different segment types.
1. Select a region information or Reference Annotation file for the Overlap Map.
2. Click the button to open the Segment Filters window. (Figure 314)

Figure 314 LOH filter settings, Overlap

selected

3. Select the Overlap check box(es) for the segment types you want to filter.
4. Use the slider to set the parameter’s value or enter a value in the adjacent text
box.
 As you move the slider farther to the right (or enter smaller values in the box)
more and more of the Overlapped segments are removed from the display.
 The detected segments must share at least the specified percentage of their
length with the Overlap Map region to be filtered out and hidden from display.
A Segment which has 20% of its length somehow encompassed within the
boundaries of an Overlap Map item has an Overlap value of 20%.
 The minimum value of a setting is 1%.
 The results of filtering are seen instantly in all tables and graphs.
 See “Using filters with CytoRegions” on page 275. for information about the
interactions of the Overlap Map filter with the CytoRegions.

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Creating an AED file of annotations
You can create AED files to include:
 User-selected annotations. The annotations in an AED annotation file can be
edited in ChAS.
 Position information on regions of the chromosome, as well as additional
annotation information on the regions. Note: AED region information files can be
used for CytoRegions or Overlap Map functions.
 Third party reference annotations converted to AED file format.
 User-generated AED region information files can be used for CytoRegions or
Overlap Map functions. Note: You can add a region to a new or previously created
AED file by selecting these feature types:
 Detected Segments
 Reference Annotations
 Regions in previously loaded files
1. In the Detail View, select the non-AED annotation(s) for the AED file using one of
the following methods:
 Right-click an annotation and select Add to a File on the shortcut menu.
(Figure 315)
Or
 Draw a box around multiple annotations, right-click the selection, and select
Add to a File on the shortcut menu.
2. In the window that appears (Figure 315), click Create New.

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Figure 315 Detail View, create a new AED annotation file

3. In the Create window (Figure 316), click to select a folder, then enter a file name.

Figure 316 Create window

4. Click Create.
The Select Destination File window appears and displays the name of your new
AED file. (Figure 317)

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Figure 317 Select Destination File window

5. Click OK.
The Details View shows the new annotation (AED).
Note: The AED file is automatically assigned the same genome assembly version
(i.e., “hg18”, “hg19”, etc.) as the currently loaded NetAffx annotations.

Adding 1. In the Detail View, use one of the following methods to select the annotation(s)
annotations to an you want to add to an AED file:
AED file  Right-click an annotation and select Add to a File on the shortcut menu
OR
 Draw a box around multiple annotations, right-click the selection, and select
Add to a File on the shortcut menu.
2. In the Select Destination File window, select an AED file, then click OK.
Note: Adding annotations to an AED file does not modify the genome assembly
version. If the AED file does not specify a genome assembly version, none is
automatically assigned to the AED file when annotations are added.

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Creating an AED file of regions

Note: You may want to incorporate new segments of features from a set of samples
in a new Regions file. You can also use the Export feature to export data in existing
files to an AED file. See "Exporting information in AED or BED format" on page 318.

Creating a new 1. From the View menu, choose Select CytoRegions file or Select Overlap Map.
CytoRegions file The appropriate Select File window appears. (Figure 318)
in AED file format

Figure 318 Select CytoRegions file window

Note: You can also create a new AED file when adding a region to an AED file.

Figure 319 Select Destination File window

2. Click Create New in the Select File window.

The Create window appears. (Figure 320)

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Figure 320 Create window

3. Use the window controls to browse to a folder for the AED file.
4. Enter a file name.
5. Click Create in the Create window.
The Select File window appears with the new file selected. (Figure 321)
Note: The AED file is automatically assigned the same genome assembly version
(i.e. “hg18”, “hg19”, etc.) as the currently loaded NetAffx annotations.

Figure 321 Select Destination File

You can select the new file or add regions to it, depending upon what function
you were performing initially.
Note: To open an AED file, click the button or select File → Open on the
menu bar.

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Adding regions to You can add a new region to an existing region information file in AED format by
an existing AED selecting the following features in the ChAS graphic views:
file  Detected Segments
 Reference Annotations
 Regions in previously loaded files.
Note: You can edit the color of DGV annotations that have been added to an AED file
by creating a color rule (see "Creating a color rule" on page 312). Alternatively, you can
edit the color of a particular DGV annotation added to an AED file, in the Detail View
(see "Entering general information" on page 299).

Adding a section to a new region (AED) file

1. Right-click on any of the following feature types in the graphic displays and
select Add to a File from the right-click menu (Figure 322):
 Segment
 Reference Annotation (including Cytobands) Note: You should expand the
reference annotations before selecting one to add to an AED file to avoid
selecting multiple annotations (see E"Expanding and contracting annotations"
on page 195).
 Region

Figure 322 Right-click menu

The Select Destination File window appears. (Figure 323)

Note: Some options may not be available, depending upon the number of type
of items you have selected.

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Figure 323 Select Destination File window

The Select Destination File window displays a list of the currently existing AED
files to which you may add the segment.
2. Select the region file you want to use, then click OK.
Note: The Annotation Properties window opens if you have selected a single
item (Figure 324). If you have selected multiple items, the Annotation Properties
window does not open.

Figure 324 Annotation Properties window

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See "Viewing and editing annotations" on page 297 for information on editing the
annotations.
3. After editing the annotation properties, click OK.
The section is saved in the Region file.

Deleting regions 1. Right-click on a region in a region file and select Delete Annotations(s)
from an AED file (Figure 325).

Figure 325 Right-click menu for region

The region is deleted from the Region (AED) file.

Viewing or Editing AED File Properties

In ChAS, you can:
 View AED or BED file properties
 Edit AED file properties (modify, add, or delete properties)
Note: BED files cannot be edited in ChAS. For more information on editing BED files,
see "Editing BED files" on page 490.

Viewing file 1. Right-click on a file, then click to select View/Edit Properties.

properties The File Properties window appears.
2. Click on the Extended tab.
A table with the file properties appears. (Figure 326 on page 295)

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Figure 326 View AED or BED file properties

Viewing the The assigned genome assembly version of a loaded file can be viewed in the
genome Properties box (Figure 326). The property, if it has been set for the file, is shown as
assembly version “ucscGenomeVersion(Affx)”. An AED file that is created within ChAS is automatically
assigned the same genome assembly version as the loaded NetAffx annotations (for
example, “hg19”). If you add annotations to an existing AED file, its genome assembly
version will not be modified; and if no version is specified for the AED file, no version
will be assigned to it.
Note: When you save a file as AED or BED, the current value of the genome assembly
version property, if present, will be saved in the file. If two or more files are merged
into an AED or BED file, the current value of the genome assembly version, if present
in at least one of the files, will be saved in the merged file.
If an AED file does not include a genome assembly version, you can manually set it.
To do this, in the Properties window:
1. Click + to add a new property row, as shown in Figure 327 on page 296.
2. Select the Property Name ucscGenomeVersion(Affx) from the drop-down list.
3. Select Text under the Type drop-down list.
4. In the Value column, enter the genome assembly version (for example,
“Constitutional”).
Note: You can manually set the genome version of an AED file by editing the
“ucscGenomeVersion(Affx)” property. For more details on editing a property
value, see "Editing a property value" on page 297.

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Adding a property 1. In the Properties window, click the symbol to create a blank row (Figure 327).
2. In the Property Name field, enter a property name or make a selection from the
Property Name drop-down list. (Figure 327)

Figure 327 Specify a property name and type

Click here to add a blank row or remove a selected row

3. Click Type, then make a selection from the drop-down list.

4. Click Value
A cursor appears inside the Value field. (Figure 328)

Figure 328 Value field

5. Enter a value, then click OK. For significantly longer values, click
(Figure 328) to open a Value editing window. Enter your (longer) value in this
window, then click OK.
The new value is entered in the File Properties table.
6. Click OK.

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Removing a 1. In the Properties window, select the row that you want to delete.
property 2. Click the icon.

Editing a property 1. Right-click the file and select View/Edit Properties on the shortcut menu.
value The File Properties window appears. (Figure 329)
2. Click on a row to select it.

Figure 329 Select a property to edit

For example, click the Value field. (Figure 330).

Figure 330 Set a new property value

3. Enter a value, then click OK. For significantly longer values, click to open
a Value editing window. Enter your (longer) value in this window, then click OK.
The new value is entered in the File Properties table.
4. Click OK.

Viewing and editing annotations

The Annotation Properties window opens:
 When adding a region to a Region (AED) file
 When you select View/Edit Annotation Properties from the right-click menu
(Figure 331) for the following types of features:
 Detected Segments

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 Reference Annotations (view annotations only)
 AED Annotations (view and edit annotations)

Figure 331 Right-click menu for View/Edit Annotation

Properties in the Detail View

Note: The View/Edit Annotation Properties menu option is not available if you have
more than one feature selected in the Detail View.
The Annotation Properties window has three tabs:
 General (See "Entering general information" on page 299)
 Additional (See "Adding Properties" on page 300)
 Curation (See "Adding a curation (Optional)" on page 303)
You can also create new user annotations if you select an element. This feature
enables you to create a region that is not based on a segment or reference annotation.
See "New user annotations" on page 304.

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Entering general
information
Figure 332 Annotation properties window of CHP Segment exported to AED

Editing the General tab properties in AED annotations

1. In the General window tab (Figure 332), enter, edit, or select:

Annotation Description
Label Label given to the AED, CHP, or other annotation. For annotations originating from CHP
segments, can be the Type, State, and Filename of the CHP file. The Label is not editable.
Name/ID Name/ID assigned to the annotation in the AED, CHP or other file.
Category Information on the source of the region. If the region was added by selecting a CHP segment,
the segment type is saved.
Strand The Sequence Strand of the item.
Chromosome Cannot be edited in Annotation Properties box. See "New user annotations" on page 304.
Min The smallest of the annotation's chromosomal coordinates.
Max The largest of the annotation's chromosomal coordinates.
Materially Modified Time Time stamp of when the start or end coordinate, type, or state of the segment or BED/AED
annotation was last altered.
Materially Modified By The Operating System user and ChAS User IDs of the Modifier who last changed a Material
property (start or end coordinate, type, or state) of the segment or annotation.
Note Information and comments about the region.
Note: Always use alphanumeric characters and underscores. Avoid the use of odd characters.
(Examples: & + ( ) [ ] { } ~ ^ and commas.)

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Annotation Description
Reference URL/web address associated with the annotation.

Click to link directly to the Reference from the Annotation Properties window. Internet
connection is required.
Modified The time stamp of the last modification of the annotation.
Modified By The Operating System user and ChAS User IDs of the Modifier who last changed the
annotation.
Counter enables you to track the number of times something has been seen.
Color Allows assignment of a hard-coded color to the Annotation in ChAS's graphical views.

Customizing Adding Properties

properties In the Additional tab you can enter new annotation information for an AED annotation.
The information will be displayed in the:
 Tool tip when you position the mouse arrow over an annotation in the Details
View
 Selection Details window

Adding custom properties

1. In the Annotation Properties window, click the Additional tab. (Figure 333 on
page 300)
:

Figure 333 Additional Annotation Properties tab

Additional Annotations Description

Annotation Property Name Name assigned to the property.

Type Type assigned to the property.

Value Value assigned to the property.

Note: Different default properties may already be assigned to the annotations

added from reference annotations.

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2. Click the button at the top of the table.
A new row appears in the table. (Figure 334)
If needed, click on a column’s edge, then drag it (right) to make it wider.
You can delete a property by selecting a row, then clicking the button.

Figure 334 New property row added

3. Click in the row under the Property Name column and enter a name for the
property. Note that your new entry is followed by the text “(custom)”. (Figure 335)
For more details, see "ChAS properties and types" on page 482.

Figure 335 Entering a custom property name and selecting its

Type

4. Click in the row under Type and select a property type from the drop-down list
(Figure 336). For more details, see "ChAS properties and types" on page 482.

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Choose from:
 Text
 Whole Number
 Decimal Number
 Date Time
 Boolean

5. Click in the row under Value and enter the value (Figure 336).

Figure 336 Enter a value for the property type

Alternatively, click the Browse button (Figure 336), then in the Value window
(Figure 337) that appears, enter the property value, then click OK.

Figure 337 Value window

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The property entry is completed. (Figure 338)

Figure 338 Property entry completed

6. Click OK in the Annotation Properties window.

Adding a curation (Optional)

1. Click the Curation tab. (Figure 339)

Figure 339 Curation tab

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2. Click the Call drop-down to select a Call. (Figure 340)

Figure 340 Call drop-down

menu

3. Click to select an appropriate Call.

4. If needed, (in the Interpretation field) type in your interpretation or right-click to add a
pre-configured snippet.
5. Click the Inheritance drop-down menu to select an Inheritance mode.
6. Click on the OKR drop-down menu to select an OKR annotation.
7. Click OK.

New user You can create a new annotation from an AED annotation.
annotations 1. In the Details view, right-click an AED annotation and select New User Annotation on
the shortcut menu. (Figure 341)

Figure 341 Detail View

2. In the window that appears, enter the annotation information (Figure 342). For more
details, see "Entering general information" on page 299 and "Customizing
properties" on page 300.

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Figure 342 Enter information for the new annotation

3. Click OK.
The new user annotation is created and saved in the AED file.
Note: The default New User Annotation information includes only the chromosome
number. It does not include any information or properties associated with the AED
annotation.

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Viewing and batch editing AED file contents

The AED Editor enables you to view multiple AED annotations and their properties in
a table format and edit the values of properties easily - for single annotations or to edit
a property for multiple annotations in a batch - to a new value.
1. At the Files pane (top left), right-click on the AED file you want to view/edit.
A pop-up menu appears. (Figure 343)

Figure 343 AED file - Right-click menu

2. Click View and Edit annotations in this file.

The AED File Editor table window appears. (Figure 344)

Figure 344 AED File Editor table

Note: Each row in this table represents a specific Annotation, while each
column in this table represents a specific Property.

Note: The AED File Editor table displays ALL properties and tabs of every
annotation contained in an AED file.

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Use the scroll bar to move the table to the right to see more column entries and/
or click, then drag the AED File Editor table window to make it wider.
To locate your table data faster, click on any appropriate column header to sort
in a descending or ascending order. Also, the number of columns displayed in the
Select Columns window, varies with each AED file.
3. Locate the group of editable annotations (rows) from a column (property) you
want to batch edit (combine together) as a single annotation.
4. Shift click or Ctrl click to select (highlight) each annotation (row) entry.
(Figure 345).

Figure 345 Selection of multiple annotations

Property (Column)

Annotations (Rows)

5. Right-click on a newly selected annotation.

The following menu appears: (Figure 346)

Figure 346 AED table field (right-click

menu)

IMPORTANT! Only editable fields can be edited. If a field is non-editable, the Annotations
Property Window pops-up. This window displays which fields are not editable (grayed out)
versus those that are editable. Also, not all user-editable AED file fields may currently be edited
from within the AED Editor. Some basic values (start, stop, type) cannot be edited in the AED
Editor table directly. You MUST use “View/Edit Annotation Properties...” for editing the
particular field in the annotation of interest.

6. Click Edit single property.

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7. The following window appears: (Figure 347)

Figure 347 Edit Text Value

8. Enter an appropriate label to distinguish your new batch annotation entry, then click
OK.
9. Your batch (group) of annotations appear as follows: (Figure 348)

Figure 348 Batch edit results - Before and After

Before Batch Editing After Batch Editing

Protecting an AED file

Protecting an AED file provides a warning prior to adding an annotation to an AED file. This
is an optional field and is intended to double-check the intention of adding an annotation
to the selected AED file.
1. Right click on the AED file in the File Tree, select View/Edit Properties.
2. In the Basic tab window, click the Protect File check box, as shown in Figure 349.

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Figure 349 Basic window tab - Protect File option

When adding annotations to a Protected AED file, the following warning message
appears. (Figure 350)

Figure 350 Protected File message

3. Click Yes to acknowledge the message, then click OK to add the annotation to
the AED file.
Click No to return to the browser window without adding the annotation to the
AED file.
Note: Protected AED files are noted with an asterisk, as shown in Figure 351.

Figure 351 Protected AED file

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AED/BED color rules

The Color Rules feature enables you to set display colors for annotations in AED files
by various annotation properties, depending upon the original source of the region
(detected segment, reference annotation, etc.). You can color annotations using the
properties of the annotations, including:
 name
 category
 markerCount
 confidence
Using the color rules, you can assign a different color to annotations with different
properties, making it easier to track the different types of segment data stored in AED
files. For example, you could assign different colors to different categories:
 GainMosaic
 LossMosaic
 Gain
 Loss
 LOH
You can also perform comparisons for numerical values, coloring only values above
or below a certain level.
By default, ChAS displays the regions in an AED or BED file in a single color. Do one
of the following to edit annotation color:
 Select a new default color for all AED or BED files (page 310).
 Create a color rule that specifies a color for annotations which meet user-specified
requirements. See "Creating a color rule" on page 312.
 In the Detail View, choose a color for a particular annotation in the Annotation
Properties window. See "Changing an annotation color" on page 317.
Note: An AED annotation color set in the Annotation Properties window (accessed in
the Detail View) takes precedence over a color rule and the default AED/BED file color.
A color rule can overwrite the AED or BED file default color.

Selecting a new 1. Open the User Configuration window (click the button or select
default color for Preferences → Edit User Configuration on the menu bar).
loaded AED or 2. In the Color Rules tab (Figure 352), click the button.
BED files 3. In the window that appears, choose a color swatch or use the color controls to
specify a color.
4. Click OK in the AED/BED Annotation Color window.

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Figure 352 AED/BED Annotation Color window

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Creating a color 1. Click the button or select Preferences → Edit User Configuration on the
rule menu bar.
2. The User Configuration window appears. (Figure 353)
3. Click the Color Rules tab.

Figure 353 User Configuration window - Color Rules tab

The Color Rules tab has five columns:

Column Description

AED/BED Annotation Name assigned to the property.

Property Name

Type Type assigned to the property (for example, text).

Operator Type of comparison with value performed.

Value Value assigned to the property.

Color Color assigned to the region property and value.

4. Click the Add button at the top of the table (Figure 354).

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Figure 354 New row added to the Color Rules table

A new row appears in the table.

5. Click in the row under the Property Name column and enter a name for the
property or select a property from the drop-down list (Figure 355). For more
details, see Appendix C, "ChAS properties and types" on page 482.
To delete a property, select the appropriate row, then click the Remove
button.

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Figure 355 Enter or select a property name

6. Click in the row under Type, then select a property type from the drop-down list.
7. Click in the row under Operator, then select an appropriate operator from the
drop-down list. (Figure 356)

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Figure 356 Selecting property type and operator for the comparison

8. Click in the row under Value, then enter a value for the property.
9. Click in the row under Color.
The Pick a Color window appears. (Figure 357)
10. Select a color, then click OK.

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Figure 357 Property entry completed

Your property entry is completed.

11. Click OK to close the Color Rules window.
Regions that satisfy the property comparison are displayed in your selected color
(for all views), as shown in Figure 358 on page 316.

Figure 358 Regions displayed in color

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Changing an 1. Click Choose Color.
annotation color The Pick a Color window appears. (Figure 359)

Figure 359 Pick a Color

window

2. Choose a color in the Swatches tab, or click the HSB or RGB tab to define a
color.
3. Click OK.
Note: The color set in the Annotation Property window overrides the colors
specified by a Color Rule created in the User Configuration window. For more
details, see "AED/BED color rules" on page 310.

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Exporting information in AED or BED format

You can export position data for the different features to AED or BED file format. The
exported BED file contains only the names and locations of the detected segments.
The exported AED file contains additional information, such as header information,
feature ID, and hg version (which is the same as the NetAffx Genomic Annotations
Database file loaded in the Browser at export).
For more information on the AED file format, see page 473.
Note: AED or BED files created in ChAS 1.0, 1.0.1, or 1.1 do not automatically include
the hg version.

Position Data Export to AED File Export to BED File

Detected Segments for xxCHP files Regions, names, and properties Regions and names

Annotation Features in Reference Regions, names, and properties Regions and names
Annotation files

Exporting 1. From the File menu, select Export as AED…

position data as Alternatively, right-click the file in the Files list and select Export File as AED on
an AED or BED the menu. (Figure 360)
file
Figure 360 Right-click menu

The Export window appears. (Figure 361)

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Figure 361 Export window, AED file format selected

2. Click the Filter Exported Segments check box to restrict the export to the
contents of the Segments table. If filters have been applied to the data, only the
retained segments will be exported. Graph data and Chromosome Summary
data will not be exported.
Note: If this option is not selected, all segments which were loaded with the
CxCHP file will be exported along with header information, regardless of whether
filters are applied. The export includes all segment data, regardless of check
mark status (ON or OFF) in the Files window pane.
3. Select a folder location for the file, as you normally would.
4. To export to AED file format, enter a name for the file.
To export to BED file format (Figure 362), enter a name for the file, then select
Browser Extensible Data (BED) from the Files of Type drop-down list.

Figure 362 Export window; BED file format selected

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5. Optional: Select the Filter Exported Segments window to export only segments
that meet filter criteria.
6. Click Export in the Export window.
The AED file is exported and can be loaded as a region information file or sent to
another user.
You can also merge feature position data from multiple different files.

Merging and exporting feature position information for multiple files

1. Select files in the File List by clicking on them while pressing the CTRL key.
2. Right-click the selected files, then click Merge Files to AED. (Figure 363)

Figure 363 Files selected for merging AED

outputs

The Export window appears. (Figure 364)

Figure 364 Export window

3. Use the navigation controls to select a folder for the merged AED file and enter
a file name for the file.
4. Click Export.
The file with the merged AED region information is created and can be used as a
region information file in ChAS.

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IMPORTANT! After two AED files are merged, the original metadata in the header is not
retained. Also, when two or more files are merged into AED/BED format, the current value of
the genome assembly version property, if present in at least one of the files, will be saved in
the merged file.

Expression AED files containing Gene Expression information and data can be created using
analysis AED file Thermo Fisher Scientific Human Gene Expression arrays analyzed in the Transcription
generation Analysis Console (TAC) 3.0 or higher.
For details on how to create an AED file containing Gene Expression/miRNA data,
please see the Gene Expression Copy Number Analysis Quick Reference Card.

Viewing a Gene Expression AED file in ChAS

1. Load the AED file exported from TAC using File → Open.
The AED is now visible in the Detail View. (Figure 365)

Figure 365 AED file in Detail View

You can simultaneously view fold change from your Gene Expression dataset with
copy number data from xxCHP files. Positive gene expression fold changes are
represented by blue transcript cluster IDs. Negative fold changes are represented by
red transcript cluster IDs. The deeper the color (blue or red) the larger the fold change.

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Loading VCF files
VCF files containing genotyping, copy number and structural variants can be
visualized in the Detail View in conjunction with CHP file data.
VCF files are a flexible format, therefore you must use the following guidelines when
formatting VCF files for use in ChAS.
 Each VCF file must contain a single sample only.
 The VCF file will display genotype/indel/copy number/LOH and Structural Variation
data.
 The VCF file must contain only 10 columns.
 The chromosome ID should use the format chr1, chr2 or 1, 2.
 Only chromosomes 1-22, X and Y are supported. Information from other
sequences or variant chromosome assemblies will be ignored.
 The DATA column (column 10) can not be left blank/empty.
 A binary compressed VCF is not supported.
 The vcf.gz format can also be viewed in the ChAS browser.
 VCF entries representing structural variations (CNV, DEL, DUP, etc.) do not require
GT values.
 Other VCF entries must contain GT in the FORMAT column, preferably in the first
position.
 The length of structural variation segments should be indicated with a SVLEN
value. If missing, the software auto-checks for LEN and END.

IMPORTANT! If your VCF file(s) do not strictly adhere to the above guidelines, the file(s) will not
be compatible with, nor load into ChAS.

1. From your software, export your VCF file (based on the above guidelines).
2. Click File → Open.
An Explorer window appears.
3. Navigate to your VCF file location, click to highlight it, then click Open.
A message appears indicating that the Genome Version could not be detected.
If you are certain that the genome build for the VCF file matches the Genome
Version loaded in the ChAS Browser, click OK to acknowledge the message.

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The VCF file loads, then appears inside the Detail View. Copy number and
structural variants are displayed in a upper track, while genotype calls are display
on the lower track, as shown in Figure 366.

Figure 366 VCF file displayed in Detail View

Upper track Displays the VCF’s CNV, LOH, and SV

Lower track Displays the VCF’s Genotypes

Genotype Data (Lower track)

Data Type Description Color
GT Heterozygous Genotype Cyan
GT Homozygous Alternate Genotype Magenta
GT Homozygous Reference Genotypes Gray
Segment Data (Upper track)
Data Type Description Color
CNV Alt allele = DUP Blue
CNV* Copy Number Value >2 (>1 on Y) Blue
CNV Alt allele = DEL Red
CNV* Copy Number Value < 2 (<1 on Y) Red
LOH Alt allele = LOH Purple
INS Insertion Gray
INV Inversion Gray
DUP:Tandem Tandem Duplication Gray

* CNV segments on the X and Y chromosomes may appear gray if the gender of the file cannot
be determined which in turn, prevents the gain/loss status from being determined.

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4. Optional: Mouse over a segment or a genotype in the VCF track to display more
detail, as shown in the genotype example. (Figure 367)

Figure 367 VCF file mouse over

details

Mouse-over table definitions

Type File Type
Location Genome location for the SNP (or Indel)
Reference Reference Base
Alternate Variant base
GT Genotype Call, 0 = Reference Base, 1 = Variant Base
Quality Quality Score assigned from the assay platform
Zygosity Homozygous or Heterozygous Call
GT DNA Call in genotyping format (applies to segment data too)

To link to TaqMan assays from the VCF file, see "Viewing and Ordering TaqMan
assays for genotyping" on page 215. Note: Linking feature applies to hg38 analyses
only.

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Exporting VCF files

IMPORTANT! Before you can export VCF files, you must install RHAS on the same workstation.

Exporting CN 1. Click Exports → Export CHP files to VCF. (Figure 368)

and/or variant
data as a VCF file
Figure 368 Exports menu
(for use in 3rd
party browsers)

The Export to VCF window appears. (Figure 369)

Figure 369 Export to VCF window

2. Select the files to be exported in VCF format by clicking on the check box next
to the file name.

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3. Review the Genome filters to make sure the correct data will be exported into the
VCF format. If not, click Cancel, update the filters accordingly, then repeat
Step 1.
4. Click the Path Browse button.
A Explorer window appears.
5. Navigate to the location where you want to save your exported VCF, then click
Save.
Your selected output directory appears.
6. Optional: Click the Include Genotyping check box to export the copy number
segments and genotype data together. For HTCMA arrays, check Best and
Recommended Probesets Only to export genotypes for those probesets the
algorithm selected as the best and recommended.
7. Click OK.

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Display overview
The data in the xxCHP files can be displayed and exported in tabular format, as well
as the graphic representation in the Karyoview, Selected Chromosome View, and
Detail View.
 "Selection details table"
 "CytoRegions table"
 "Viewing the overlap map table"

Common table operations

The controls that are common to all tables are described in this section and include:
 "Standard tool bar controls"
 "Sorting by columns"
 "Changing the order of table columns"
 "Selecting columns to display or hide"
 "Sum, mean, and median calculator"

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Standard tool bar The tool bar provides quick access to table options.
controls

Left side
Export as TXT file. See "Exporting tables as TXT file" on page 426.

Export as PDF Report. See "Exporting table data into a PDF" on page 422.

Export as MS Word DOCX file. See "Exporting as Word (DOCX) format" on page 420.

Copy selected cells to clipboard. See "Exporting a segments table with modified segments to a TXT
file" on page 428.
Calculate the sum, median, and mean of the selected values from a numeric column.

Display results for entire genome.

Display results for selected chromosome.

Display results for portion of chromosome displayed in Detail View.

Far Right
The number of rows in the table.

Opens the Select Columns window that enables you to choose the column headers to show or hide.

The Export functions are described in "Exporting table data" on page 422.

Sorting by You can sort a table by a single column’s values, or by the values in up to three columns.
columns Note: You may sort on any column except, for reasons of efficiency, the marker name
column in the graphs table.
Sorting on certain columns can cause a noticeable decrease in performance. For example,
it is recommended that you do not sort a table using the columns in the Segments table
that show the overlapping RefSeq, FISHClones, or other items. The data for these table
cells is calculated only on an as-needed basis when it needs to be displayed. Using such
a column for sorting would force the calculation of the data for all such cells. Since the
sorting would be alphabetical, it is unlikely to be useful. Similarly, for reasons of efficiency,
sorting based on the marker name column in the Graphs table is not allowed.

Sorting a table by a single column

1. Click in the header of the column to sort the table by that column’s values.
A triangle appears in the header.
 Up triangle = ascending order.
 Down triangle = descending order.
2. Click the header to toggle between Ascending, Descending, or no sort order.
Note: The Type column in the Segments table sorts segments based on the order that
they appear in the Data Types window pane, not in an ascending/descending alphabetical
order.

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Performing a multi-column sort
1. Click in the header of the first column you want to sort on.
2. Click in the header of the second column.
3. Click in the header of the third column, if desired.
The last selected column has sort priority.
Sort priority is indicated by the size of the triangle in the header (Figure 370).

Figure 370 Table sorted by descending order of Segment ID and ascending order of Size

Changing the 1. Click and drag in the column header to move the column to a new location.
order of table
columns

Selecting You can select columns using these two methods:

columns to  Select Columns window.
display or hide
 Right click on a column header, then choose Select columns.

1. Click the Select Columns tool bar button . The Select Columns window
opens. (Figure 371)
Note: Specific items may vary, as they are dependent upon the type of table and
data being displayed.

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Figure 371 Select Columns window

The columns in the left side pane are displayed in the table (in their default order).
 To hide columns within the table, move the column entry from the left (Chosen) pane
into the right (Available) pane.
 To view different columns in the table, click and drag entries from the right pane to the
left pane.
 Column order can be determined by clicking onto a column entry, then dragging it into
its desired location (inside the left pane).
 Use the Table Sorting drop-down menus to sort your columns.
Note: These choices are auto-saved between sessions.

Using the right- Right-click on a column header to perform the following:

click menu  Hide the selected column.
 Show all columns, including hidden ones.
 Expand selected column to display complete heading.
 Auto-size all columns.
 Restore the default selection of columns.
 Select other columns to hide or show.
 Create, select, save, and delete saved table states.

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Using a column header’s right-click menu
1. Right-click on the appropriate column header.
A menu appears. (Figure 372)
Note: Right-click menu items vary, as they are dependent upon the type of table
and data that is displayed.

Figure 372 Column heading right-click menu

2. Click to select the option you want.

Sum, mean, and median calculator

Use this calculator to calculate the sum, mean, and median of the selected or multiple
numeric fields.

Calculating 1. Ctrl click or Shift click to highlight multiple numeric fields (MUST BE in the same
multiple numeric column).
values in a 2. Click .
column Your multiple numeric values are calculated and summarized, as shown in.
Figure 373.
3. Click OK

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Figure 373 Calculator

Saved table states

Saving multiple customized tables is a very useful tool, as it enables you to use a large
number of columns in a table for interpreting the biology of a particular sample. On the
other hand, saving a table state with a smaller subset of columns in a different order -
may be more appropriate for including in a report.
In either case, having various Saved Table States enables you to switch back and forth
between multiple sets of tables/columns without having to painstakingly recreate
interpreting and reporting columns for each of your sample selections.
In the Segments Table, there are six pre-loaded Table States available for use in
ChAS:
 Cytogenetic
 Default
 Oncology
 Oncomine Reporter
 ReproSeq
 ClinVar
There are two pre-loaded Table States available for use in the Variants table. See
"Variants table" on page 351 for details.
 CytoScan HTCMA
 OncoScan
There are six pre-loaded Table States in the QC & Sample Info table based on relevant
metrics for the array type loaded.
 CytoScan QC View

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 Default
 CytoScan HTCMA QC View
 OncoScan QC View
 ReproSeq QC View
 SMN Sample Info View

IMPORTANT! You can restore your default settings at any time by right-clicking on a table
column header and selecting Restore Defaults from the menu or selecting the Default Table
State under Apply Table State.

Saving the current 1. Right-click on any column header.

segment table A menu appears.
state to its default
2. Click Save table state.
The following window appears: (Figure 374)

Figure 374 Save Table State

- Enter a name

3. Type Default.
4. Click OK.
The table is now saved (as Default) to your User Profile for future use and/or
reference.

Adding columns 1. Click the Select Columns icon. (Top right of Segments table)
to table states

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A list of available columns appears. (Figure 375)

Figure 375 Save Table State - Available Columns

2. Move the scroll bar downward to reveal more available columns.

3. Click and drag the column header inside the right pane into the desired location
inside the left pane.
4. Click OK.
The additional column(s) is now added to your the left pane location. If the
column is not in the position you want, click on the column, then drag and drop
it into its correct spot.

Removing (hiding) 1. Right-click on a column header you want to remove (hide) from the table.
columns in a table The following menu appears: (Figure 376)
(for report use)
Figure 376 Save Table State - Remove (Hide)
Column

2. Click to select Hide “Column Name”.

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The column is now removed (hidden) from your table.
3. Repeat steps 1-2 to remove (hide) additional columns that are not required for a
report.

Saving a newly 1. Right-click on any column header.

edited segment A menu appears.
table state
2. Click Save table state.
A pop-up window appears. (Figure 374)

Figure 377 Saved Table State - Example: Table used for reporting.

3. Type a name for your new table state. (Example: Reporting_brief)

The saved table state remembers the columns that you selected, their order, their
widths, and which ones were used for sorting.
4. Click OK.
The edited table is now saved to your User Profile for future use/reference.

Applying There are six Table States that are created automatically in ChAS.
previously saved  Default: Commonly used columns in any xxCHP file analysis
table states
 Oncomine Reporter: Simplified Table State for export and use with Oncomine
Reporter Software.
 Cytogenetic: Commonly used columns when analyzing constitutional samples.
 Oncology: Commonly used columns when analyzing cancer samples.
 ReproSeq: Standard columns for use with analyzing ReproSeq samples.
 ClinVar: All required columns for using the ClinVar export.

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1. Right-click on any column header.
A menu appears.
2. Click Apply table state.
A sub-menu appears displaying your saved tables, as shown in Figure 378.

Figure 378 Apply Table State - Saved tables list

3. Click on the table you want to display.

The table is now displayed.
4. (Optional) Repeat steps 1-3 to apply (open) other previously saved tables.

Deleting 1. Right-click on any column header.

previously saved A menu appears.
table states
2. Click Delete table state.
The following dialog window appears: (Figure 379)

Figure 379 Apply Table State - Deleting

saved tables

3. Click the drop-down button to reveal your saved tables.

4. Click to select the table you want to delete.

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5. Click OK
6. (Optional) Repeat steps 1-5 to delete other saved tables.

Segments table
The Segments table (Figure 380) displays a list of the detected segments in the loaded
sample data files.

Figure 380 Segments Table

Segment Table components:

 "Segments table tool bar" on page 338
 "Segments table" on page 338
There are certain columns in the Segments table which dynamically compute
intersections of reference annotations with the segments. The data in these columns
is computed on an as-needed basis for each cell. You may see text such as
“<Working…>” in these cells while the data is being calculated. The results for all cells
will be calculated when exporting to PDF or TXT, or copying to the clipboard. Hiding
columns that are not needed may improve performance, particularly during export
operations.
Note: Sorting the table based on the dynamically computed columns may be slow.
To highlight segments in the views or the table:
 Double-click in a row of the table to zoom to the segment in the Karyoview,
Selected Chromosome and Detail Views.
 Click on a segment in the Karyoview, Selected Chromosome or Detail View to
highlight the segment in the Segments table.

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Segments table The tool bar (Figure 381) provides quick access to table functions. The standard
tool bar functions are described in "Standard tool bar controls" on page 328.

Figure 381 Segments Table tool bar

Use the Use in Export check boxes to check/select all or uncheck/deselect

all segments displayed in the table.

Note: If the Use in Export column is hidden from the Segments table, then all rows
are exported.

Segments table In the Segments table, “N/A” can mean that the information (for example, FISH Clones
or sno/mRNA) is not available in the NetAffx database because the information has not
yet been mapped. For example, FISH Clones or sno/mRNA files will not appear in the
Files list for the NA31 (hg19) ChAS Browser NetAffx Genomic Annotation file. “N/A”
can also mean that a column which has been persisted to appear from a previous user
profile, no longer has data in the current NetAffx Genomic Annotation file that is
loaded.
Annotations which share genomic coordinates with a segment are listed in order of
start coordinate value, smallest values first (i.e. from left to right in the Details View).
For annotations with the same start coordinate (for example, isoforms of a single
gene), the one with the smallest end coordinate is listed before others with larger stop
coordinates.
If a column in the Segments table contains more than 10 items, “…” is displayed after
the 10th item to indicate that some data are not displayed in order to save calculation
time. For example, “…” will follow the 10th name in the Genes column. However, a
complete list of the genes will be included when the information is copied to the
system clipboard or exported to reports. For gene isoforms with identical names, only
one instance of the gene locus will be listed in the Segment table to reduce duplicate
gene names.
The table can display each segment with the following information (the default set of
columns in a new user profile may include only a subset of the total columns listed.
For instructions on how to switch quickly between table column sets for a particular
table, see "Saved table states" on page 332.
Materially Modified Segments (merged, created de novo, segments with edited start
or end coordinates) and deleted segment have a different appearance in the
Segments Table and export to TXT differently depending on the software settings. For
more information, see "Exporting a segments table with modified segments to a TXT
file" on page 428.

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Segment table
columns

Column Description

% of Overlaps Map Overlap Map Item and the percentage by which it is covered by the segment.
Item covered by
Segment

BACs List of BACs that share coordinates with the segment.

Call User-editable field populated by a user-configurable drop list of Calls

Call Approval Can be used as a bookmark for segments that have been reviewed.

Call From The Call term assigned based on Tier or Score Classification. For more information, see "Viewing
Prioritization segment prioritization in the segments table" on page 380.

Chromosome Chromosome on which the segment was found.

CN State Copy Number State (not displayed for LOH segment types).
The expected Copy Number State on the X chromosome in normal males is not constant over its entire
length. This is due to the structure of the sex chromosomes. See "LOH segments on X and Y
chromosomes" on page 49 for more information.

Confidence The log likelihood that the called copy number state is not normal ploidy, example 2 on autosomes
(ReproSeq) (reflects the likelihood of the region's ploidy number being different than the normal ploidy 2).

Curation By The current computer Operating System login ID and ChAS user profile name at the time that the
Curation field was last edited.

Curation Time The time and date when the Curation field was last edited.

Cytoband End Cytoband in which the segment ends.

Cytoband Start Cytoband in which the segment begins.

CytoRegions Names of the CytoRegions with which the segment shares coordinates.

DB Both The number of segments in the database meeting BOTH the Minimum Percent Overlap and the
Minimum Percent Coverage. This number can change depending on whether the "match only same
gain/loss type" box is checked. Right-click on the a row in the Segment Table. From the menu, click
DB Count Both. See "Querying a segment from the segment table" on page 392.

DB Coverage The number of segments in the database meeting the Minimum Percent Coverage. This number can
change depending on whether the "match only same gain/loss type" box is checked. Right-click on
the a row in the Segment Table. From the menu, click DB Coverage Count. See "Setting up a ChAS
DB query" on page 390.

DB Overlap The number of segments in the database meeting the Minimum Percent Overlap. This number can
change depending on whether the "match only same gain/loss type" box is checked. Right-click on
the a row in the Segment Table. From the menu, click DB Overlap Count. See "Setting up a ChAS DB
query" on page 390.

DGV List of DGV variations that share coordinates with the segment.

DGV-GS List of curated Database of Genomic Variants considered "Gold Standard" that share coordinates with
the segment.

End Marker The array marker name which marks the end of the segment.

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Column Description

Evidence Provides information on which annotations the segment overlapped. For more information, see
"Viewing segment prioritization in the segments table" on page 380.

File File the segment was detected in.

Filtered DB Both The number of segments in the database meeting the Minimum Percent Overlap and Minimum Percent
Coverage and the selected Filter Criteria.

Filtered DB The number of segments in the database meeting the Minimum Percent Coverage and the selected
Coverage Filter Criteria.

Filtered DB The number of segments in the database meeting the Minimum Percent Overlap and the selected Filter
Overlap Criteria.

FISH Clones List of FISH clones that share coordinates with the segment.

Following Marker The array marker just below the segment in the data track used as input for the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Following Marker The coordinate location of the array marker just below the segment in the data track used as input for
Location the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Full Location Chromosome Start and Stop in a user-friendly format for use in external databases.

Gene Count A count of the gene names listed in the Genes column

Genes List of RefSeq genes from the Genes track that share coordinates with the segment. Identically named
gene isoforms are NOT repeated.

Inheritance User-editable field populated by a user-configurable drop list of Inheritance.

Marker Count Number of markers in the segment.

Materially Modified The current computer Operating System login ID and ChAS user profile name at the time that the
By segment was last materially modified.

Materially Modified Indication that segment was previously merged, deleted, or had its start or end boundary, type, or
Segment state altered by a ChAS user. (ChAS-based processes of Smoothing and Joining are not
“Modifications”, nor are making Calls or Interpretations, in this context).

Materially Modified The time and date when the Segment was last materially modified.
Time

Max End position of segment.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic
position coordinates" on page 488).

Max % Coverage The highest percentage by which a segment covers some item(s) in the Overlap Map.

Max % Overlap The highest percentage by which some item(s) in the Overlap Map overlaps the segment. Segments
completely overlapped by an Overlap Map item are 100% overlapped. This number is used for Filtering
Segments out by “Overlap”.

Mean Log2 Ratio The mean of all the Log2 Ratio values contained in the segment.

Mean Marker Length of the segment in base pairs divided by the number of markers in the segment.
Distance

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Column Description

Mean Weighted The mean of all the Weighted Log2 Ratio values contained in the segment.
Log2 Ratio

Median Log2 Ratio The median of all the Log2 Ratio values contained in the segment.

Microarray An ISCN-based description of the segment.

Nomenclature

Microarray ISCN 2013 based description of the segment.

Nomenclature
ISCN 2013

Min Start position of segment.

Number of Overlap Number of Overlap Map items which share genomic coordinates with the segment.
Map Items

OMIM Gene Count A count of the OMIM Gene names listed in the OMIM Genes column.

OMIM Genes List of OMIM Genes that share coordinates with the segment.

OMIM Phenotype List of OMIM Phenotype Loci that share coordinates with the segment.
Loci

OMIM Region Lists the Gene Title of any region that overlaps with a copy number or LOH segment.
Phenotype

Oncomine Report A drop-down list of annotations compatible with the Oncomine Reporter Software. For details on this
application, go to: https://www.thermofisher.com/order/catalog/product/A34298

Overlap Map Items Item(s) in the Overlap Map which overlap the segment, followed by the percentage by which the
(% of Segment segment is overlapped by that Item.
overlapped)

Preceding Marker The array marker just above the segment in the data track used as input for the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Preceding Marker The coordinate location of the array marker just above the segment in the data track used as input for
Location the segment.
Note: This column is only applicable to CNState Gain and Loss segments.

Precision The log likelihood that the called copy number state is different than next closest copy number state
(ReproSeq) (reflects the likelihood that the precise ploidy number is correct).

Protein Coding List of protein coding RefSeq genes from the Genes track that share coordinates with the segment.
Genes Identically named gene isoforms are NOT repeated.

Protein Coding Number of Protein Coding RefSeq genes that shapre coordinates with the segment.
Genes Count

Protein Coding List of protein coding Ensembl Genes annotations that share coordinates with the segment. Identically
Ensembl Genes named gene isoforms are NOT repeated.

Protein Coding Number of Protein Coding Ensembl Genes that share coordinates with the segment.
Ensembl Genes
Count

Sample UUID Unique identifier for the CHP file.

Segment User-editable field for free-text interpretation on the segment

Interpretation

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Column Description

Segment Label A label comprised of the segment's Type, State, and Filename.

Segment Name/ID File-specific identifier assigned to the detected segment.

Segmental List of Segmental Duplications that share coordinates with the segment.
Duplications

Size (kbp) Size of the segment.

Smoothed/Joined/ Indication that the segment was created by smoothing, joining or merging two or more segments in
XON merged the initial segment detection.

sno/miRNA List of sno/miRNA features that share coordinates with the segment.

Start Marker The array marker name which marks the beginning of the segment.

Summarized Log 2 The median of the LR, after transformation to adjust for individual marker responsiveness.
Ratio

Tier or Score The assigned Tier or Score value based on the Segment Prioritization method selected. When using
Tier based, the column will display the assigned Tier. When using Score based, the column will display
the score value based on the annotations the segment overlaps.For more information, see "Viewing
segment prioritization in the segments table" on page 380.

Type Type of segment, for example, LOH. When sorting by this column, the segments of a particular sample
are listed in the same order that they appear in the Data Types window pane.

Use in Report Allows manual selection of Segments for export to a Segments Table PDF, DOCX, or Text rather than
all segments in the table.

XON Region Level The annotation Level assigned to this region of the genome.

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Obtaining all 1. Select a segment in the Segments table, Karyoview, Detail View, or Selected
annotations Chromosome View, then press Ctrl+Space or right-click on the segment to select
associated with a Zoom to selection from the menu.
segment The exact length of the selected segment fills the entire width of the Detail View
(Figure 382).

Figure 382 Detail View zoomed in on the segment selected in the Segments table

Detail View

2. Click the tool bar button to expand all annotation tracks.

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Figure 383 Detail View, annotations have been expanded and selected

Annotations that are associated with the

segment are selected (outlined in blue)

3. Using the mouse, draw a box around all of the genes and annotations of interest.
When you release the mouse button, a blue box outlines the selected items in the
Detail View. (Figure 383)
4. Click the tool bar button.
The Selection Details table appears (Figure 384). It includes all of the items
selected in the Detail View. For more details on the table, see "Selection details
table" on page 208.

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Figure 384 Selection Details table

Click a button
to export the
information

For details on exporting from the Segment table, see "Exporting table data" on page
422.

Graphs table
IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

The Graphs table displays the marker data used to create the graphs in the Detail
view. Markers that are not used for the graphs currently displayed do not appear in
this table. As in the Detail View, only markers from a single chromosome are displayed.
The column headings are colored according to the tracks used for the Karyoview,
Selected Chromosome View, and Details View.

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The Graphs table includes genotype SNP calls for CytoScan array results (Figure 385).

Figure 385 Example Graphs table with Genotype Calls for CytoScan HD results

The table displays each data point in the displayed graphs.

To highlight markers in the views or the table:
• Click in a row of the table to place the cursor on the marker in the Chromosome
and Detail Views.
• Click on a marker in the Selected Chromosome or Detail View to highlight the
marker in the Graphs table.

Graphs table The Graphs columns display:

properties

Column Description

In CytoRegion Whether marker is located in a CytoRegion or not:

In CytoRegion
Not in CytoRegion.
See "Using CytoRegions" on page 267 for more information.

Markers Marker ID. Right-click to link to NetAffx information about the marker.
Note: For efficiency reasons, it is not possible to sort the table on this column.

Genotype The SNP genotype call.

Graph Data types

The Column header displays:

Color Nib
Data Type
Name of sample file
The table cell displays the value for the marker.

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Graph Table Tool
bar

Figure 386 Graphs tool bar

The tool bar (Figure 386) enables you to:

 Export data in TXT format only. See "Exporting tables as TXT file" on page 426
 View data for chromosome and selected chromosome region only. You cannot
display data from the whole genome in Graphs tab. You can export this data for
the whole genome using the "Displaying and exporting data from the analysis
workflow" on page 93.
 Export genotype results

The Graphs Settings button opens the Graph Settings panel, enabling you to
change the style of graph, scale, and other features for the data graphs. See
"Changing graph appearance" on page 196.

Exporting Note: Exporting genotypes is not available for OncoScan or ReproSeq data.
genotype calls
1. Click the tool bar button. Alternatively, select Reports → Export Genotype
Results Text File from the menu bar.
2. In the window that appears (Figure 387 on page 348), select the array type,
results file(s) (CYCHP), and annotation database to use for the export.

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Figure 387 Export Genotype Results

3. Specify a region to export:

 SNP List: SNPs specified in a user-created SNP list (.txt).
 Selected Region: SNPs included in the chromosome region selected in the
Karyoview.
 Selected Chromosomes: SNPs on the chromosome selected in the
Karyoview.
 All Chromosomes: SNPs on all 24 chromosomes.
Note: The SNP list should include one column header named Probe Set ID or
ProbeSet_ID and one probe set name per row, as shown in Figure 388 on page 349.
The export will not proceed without one of these column headers.

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Figure 388 Example

SNP list

4. Enter the path name or click the Browse button to select a folder for the output.
5. Enter a file name prefix. If only one output file is created (see below), this will be
the file name. If multiple files are created, a suffix will be added to this string to
create the file name. Do not include the file extension here.
6. Select a Multiple File Output option which determines if a separate file will be
created for each chromosome and/or CYCHP file.

Selected Output Option(s) Files Created

None One output file will be exported that contains all chromosome and all CYCHP file data.
There will be separate data columns for each CYCHP file in the exported file.

Separate File for each Creates a separate file for each chromosome in the output data. If all chromosomes are
Chromosome selected, 24 files will be created. There will be separate data columns for each CYCHP
file in the exported file.

Separate File for each CYCHP File Creates one text file per CYCHP file. Each file contains genotype calls for all
chromosomes.

Separate File for each Create a separate file for each CYCHP file and for each chromosome. If three CYCHP
Chromosome and Separate File for files are selected and all chromosomes are reported on, this will create 72 files.
each CYCHP File

7. Click OK.
Note: Exporting of Genotypes may take several minutes to complete, as this
process is dependent on the total number of SNPs selected for export.

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Figure 389 Example of exported genotypes from a selected region of chromosome X

The exported text file (Figure 389) includes information about the analysis (for
example, array type, NetAffx annotation database, hg version, and chromosome).
Note: If the option “Separate File for each CYCHP File” was not selected, many of the
headers will be repeated for each CYCHP file. The header titles will be appended with
the CYCHP file name to indicate which file the column belongs to.
The column headers report the following information:

Column Description

Probe Set ID Probe set identifier

Call Codes Genotype call for the SNP.

Confidence Confidence value for the call.

Signal A Raw signal value for Signal A on the probe set.

Signal B Raw signal value for Signal B on the probe set.

Forward Strand Base Calls Base calls for the forward strand.

dbSNP RS ID dbSNP RS ID value

Chromosome Chromosome associated with the probe sets.

Chromosomal Position Chromosome position of the SNP.

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Variants table
For OncoScan FFPE and CytoScan HTCMA arrays only. The Variants table
(Figure 390) displays the somatic mutation information from OncoScan FFPE arrays
and/or the variant information from CytoScan HTCMA arrays.

Figure 390 Variants table

The Variants table components include:

 Tool bar (below)
 Variants table on page 351
To highlight segments in the views or in the table:
 Click the row of the table to zoom to the somatic mutation in the Karyoview,
Selected Chromosome View and Detail View.
 Click on the somatic mutation in the Karyoview, Selected Chromosome View or
Detail View to highlight the somatic mutation in the Somatic Mutations Table.
 Detected: Large, bright green circles in the graphic views denote somatic
mutations of high confidence (OncoScan) or variants called het, hom, NoCall,
NRP (anything that isn't a major homozygous call)
 Undetected: Small, dark gray dots in the graphic views denote somatic
mutations and variants in which the wild type or major homozygous genotype
was called.
Note: Calls can be removed from the table (and graph view) by de-selecting the
Undetected or Detected check box(es). in the Data Types window.

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Tool bar The Tool bar (Figure 391) provides quick access to table functions. Its standard
functions are described in "Standard tool bar controls" on page 328.

Figure 391 Tool bar

Variants table The table can display each mutation with the following information (the default set of
columns in a new user profile may include only a subset of the total columns listed
below).

CytoScan HTCMA

Column Description

Affx SNP ID Unique Thermo Fisher Scientific generated identifier for the SNP.

Alt Allele The call for the first alternate allele associated with a non-normal phenotype.

Alt Code The Call Code (A,B,C,D,...) of the Alternate Allele.

Alternate Name Displays the alternative names for the variant.

Associated Phenotype Displays the Phenotype that is associated with the variant.

c.name Displays standard variant nomenclature based on coding DNA reference sequences.

Chromosome The chromosomal location of the variant.

File Name of the sample file.

g.name Displays the genomic coordinates for the variant.

Gene Name of heritable genetic sequence that encodes proteins.

Inheritance Pattern Method of Inheritance (Example: AR (Autosomal Recessive), XLR (X-linked Recessive).

Marker Type The type of marker (Indel, SNP, CN).

Max Ending genomic position for the variant.

Min Starting genomic position for the variant.

Name/ID Thermo Fisher Scientific identifier for the probeset.

p.name Displays the change in protein translation for the variant.

Recommended A quality control metric determined by SNP Polisher algorithm that chooses the best probesets
Probeset querying a SNP.

Ref Allele The call for the reference allele associated with a normal phenotype.

Ref Code The Call Code (A,B,C) of the Reference Allele.

RSID dbSNP ID

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Column Description

Size Size in bp of the variant.

Transcript RefSeq transcript ID associated with the c.name.

Type Undetected/Detected. Detected are those mutations with any call other than the wild-type or
major homozygous genotype.

Variant Status Status of the variant based on the genotype (i.e. Not Detected, Het, Hom, NoCall, NRP).

Variant Status Alt Allele Severity status for the variant mapped to Alt Allele.

Variation ID ClinVar ID

OncoScan CNV Plus

Column Description

accession number RefSeq Gene accession number.

Channel CEL file from which the signal is measured. “A” is the AT CEL, “C” is the GC CEL.

Chromosome Chromosome on which the somatic mutation is found.

Common Name Abbreviated description of the mutations to which this ProbeSet is known to respond. The name
has the form [Gene]:[amino acid change for mutation]:[cDNA change for mutation]. In the event
that the ProbeSet cannot differentiate among multiple mutations to which it can respond, the slash
(/) delimits the multiple known mutations.

COSMIC ID The identifier of the mutation as listed in the COSMIC database, which is a catalogue of somatic
mutations in cancer. More information on these mutations can be found at:
http://cancer.sanger.ac.uk

Event Describes if the probeset is a point mutation, deletion, insertion or sequence variant.

Event Type Describes if the event is missense, frame-shift, in-frame insertion or deletion.

File Name of the OSCHP file the somatic mutation is in.

Fwd 3’ flank Sequence flanking the mutation at the 3' end.

Fwd 5’ flank Sequence flanking the mutation at the 5' end.

Genes RefSeq gene that shares coordinates with the somatic mutation.

High Threshold High confidence MutScore threshold. Measurements equal to or greater than this threshold are
called “High confidence,” describing the likelihood that the mutation is present.

Low Threshold Lower confidence MutScore threshold. Measurements with a MutScore below this value are called
“Undetected”. Measurements equal to or greater than this threshold but less than the High
Threshold are called “Lower confidence,” describing the likelihood that the mutation is present.

Max Stop position of the somatic mutation.

Min Start position of the somatic mutation.

Mutation (aa) Wild type > mutant amino acid change on the coding strand.

Mutation (nt) Wild type > mutant nucleotide change on the coding strand.

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Column Description

Mutation Syntax (aa) Encoding of which nucleotide was changed and its location in the CDS.

Mutation Syntax (cds) Encoding of which amino acid was changed and the location of the codon.

MutScore Measures somatic mutation probeset response. The stronger the response, the more likely it is
that the somatic mutation is present. The MutScore calculation depends on the algorithm version.
The newer MutScore calculation also corrects for sample-specific effects, and thereby reduces
false positive calls, which were sample specific.

For algorithm versions 1.0 - 1.2 (ChAS 3.0 and earlier, OncoScan Console 1.2 and earlier):
MutScore.old = (measured quantile normalized signal - median signal for this marker in the
reference model file) / (95th percentile signal for this marker in the reference model file - median
signal for this marker in the reference model file).

For algorithm versions 1.3 and newer (ChAS 3.1 and newer, releases of OncoScan Console after
1.2):
MutScore.new = (MutScore.old - median MutScore.old for this sample) / standard deviation of
MutScore.old for this sample (where standard deviation is calculated for all but the num-out-std
strongest MutScore.old for this sample, median is calculated for all but the num-out-med
strongest MutScore.old for this sample, and the used median is the maximum of zero and the
measured median).

Name/ID Thermo Fisher Scientific identifier for the marker.

ProbeSet Type Probeset Type is Somatic Mutation.

Size (bp) The size of the Somatic mutation in base pairs.

Source DB Cosmic database version.

Strand Coding strand of the associated gene (Forward or Reverse).

Type HighConfidence, LowerConfidence or Undetected call as to the presence of the mutation.

Note: Changes made to an OSCHP file in the Somatic Mutation Viewer Application
requires the OSCHP file to be reloaded into the ChAS Browser to reflect the change
made to the sample.

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QC and sample info tab

The QC and Sample Info tab (Figure 392) in the lower pane displays information about
the loaded Data and Region files.

Figure 392 QC and Sample Info table

Status

Data Files

Region Files

The top section displays Status for Restricted Mode (see "Using restricted mode" on
page 275)
The tables display information on:
 Loaded data files. "QC and sample information table" on page 355
 Loaded region files. "Loaded AED/BED files table" on page 361

QC and sample The QC table has six pre-loaded Table States allowing you to quickly toggle to the
information table relevant information based on array type. For detailed information, see "Saved table
states" on page 332.

Figure 393 Data Files table

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The six pre-loaded QC Table States and their column descriptions are shown below:

CytoScan QC view

Column Description

Antigenomic Ratio Ratio of median intensity antigenomic control probes/median intensity all copy number probes.

File File Name

Genome Version Build of the genome (i.e. hg19, hg38)

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

Median Raw Intensity Pre-processed Median signal of the array.

QC In or Out of QC bounds.

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

SNPQC SNP QC value. Median Absolute Pairwise Difference value. See Appendix G for detailed
information.

Waviness SD A global measure of variation of microarray probes that is insensitive to short-range variation and
focuses on long-range variation. See Appendix G for detailed information.

Waviness Segment Number of raw segments without any post-processing.

Count

Default QC view

Column Description

Algorithm Name Name of the algorithm used in processing the array.

Algorithm Version Version of the algorithm used in processing the array.

Annotation File Name of the Annotation file used to create the xxCHP file.

Array Type Type of array used in the analysis.

Autosome LOH The proportion of LOH on chromosome 1 to 22.

Cel Pair Check Inspects each pair of intensity (*.cel) files to determine whether the files have been properly paired
and assigned to the correct channel.

Created Date the xxCHP file was created.

File File Name

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Column Description

Low Diploid flag An essential part of the algorithm is the identification of "normal diploid" markers in the cancer
samples. This is particularly important in highly aberrated samples. The normal diploid markers
are used to calibrate the signals so that "normal diploid markers" result in a log2 ratio of 0 (e.g.
copy number 2). The algorithm might later determine that the "normal diploid" markers identified
really correspond to (for example) CN=4. In this case the log2 ratio gets readjusted and TuScan
ploidy will report 4. Occasionally (in about 2% of samples) the algorithm cannot identify a
sufficient number of "normal diploid" markers and no "normal diploid calibration occurs. This
event triggers "low diploid flag" = YES. In this case the user needs to carefully examine the log2
ratios and verify if re-centering is necessary.

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

Modified Date the xxCHP file was last modified.

ndSNPQC QC metric for SNP probes that is derived from polymorphic SNP probes in normal diploid
regions.

ndwavinessSD Measure of variation of probes in normal diploid regions that are insensitive to short-range
variation and focus on long-range variation.

Parameter File Name of the chasparam file used to create the xxCHP file.

QC In or Out of QC bounds.

Reference Reference Model file used in the single sample analysis.

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

SNPQC SNP QC value. Median Absolute Pairwise Difference value. See Appendix G for detailed
information.

SNPQC Type ND or non-ND

TuScan %AC If % AC = 100%, we return "homogeneous" because it could be 100% normal or 100% tumor. If
% AC =NA, the percent aberrant cells could not be determined and TuScan returns non-integer
CN calls. This metric is an algorithmically determined estimate of the % of aberrant cells in the
sample.

TuScan Ploidy The most likely ploidy state of the tumor before additional aberrations occurred. TuScan Ploidy
is assigned the median CN state of all markers, provided that %AC could be determined and
integer copy numbers are returned. If %AC cannot be determined, NA (Not Available) is reported
for both ploidy and %AC.

Waviness SD A global measure of variation of microarray probes that is insensitive to short-range variation and
focuses on long-range variation. See Appendix G for detailed information.

CytoScan HTCMA QC view

Column Description

DishQC (DCQ) Measures the amount of overlap between two homozygous peaks created by non polymorphic
probes. DQC of 1 is no overlap, which is good. DQC of 0 is complete overlap, which is bad.

File File Name

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

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Column Description

QC In or Out of QC bounds.

QC Call Rate Percentage of autosomal SNPs with a call other than NoCall (measured at the Sample QC step).

QC Het Rate Percentage of SNPs called AB (i.e. the heterozygosity) for autosomal SNPs (measured at the
Sample QC step).

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

SMN MAPD Median Absolute Pairwise Difference value calculated from the CNVMix algorithm for the SMN
pipeline.

SMN WavinessSD A global measure of variation of microarray probes that is insensitive to short-range variation and
focuses on long-range variation from the CNVMix algorithm for the SMN pipeline.

SNPQC SNP QC value. Median Absolute Pairwise Difference value. See Appendix G for detailed
information.

Waviness SD A global measure of variation of microarray probes that is insensitive to short-range variation and
focuses on long-range variation. See Appendix G for detailed information.

OncoScan QC view

Column Description

Cel Pair Check Inspects each pair of intensity (*.cel) files to determine whether the files have been properly paired
and assigned to the correct channel.

Cel Pair Check Percentage of SNPs that match between the AT and GC arrays.
Concordance

File File Name

Genome Version Build of the genome (i.e. hg19, hg38)

Low Diploid flag An essential part of the algorithm is the identification of "normal diploid" markers in the cancer
samples. This is particularly important in highly aberrated samples. The normal diploid markers
are used to calibrate the signals so that "normal diploid markers" result in a log2 ratio of 0 (e.g.
copy number 2). The algorithm might later determine that the "normal diploid" markers identified
really correspond to (for example) CN=4. In this case the log2 ratio gets readjusted and TuScan
ploidy will report 4. Occasionally (in about 2% of samples) the algorithm cannot identify a
sufficient number of "normal diploid" markers and no "normal diploid calibration occurs. This
event triggers "low diploid flag" = YES. In this case the user needs to carefully examine the log2
ratios and verify if re-centering is necessary.

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

ndSNPQC QC metric for SNP probes that is derived from polymorphic SNP probes in normal diploid
regions.

ndWaviness SD Measure of variation of probes in normal diploid regions that are insensitive to short-range
variation and focus on long-range variation.

Number nd Number of probes called normal diploid by the algorithm.

Percentage nd Percentage of probes called normal diploid by the algorithm

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Column Description

QC In or Out of QC bounds.

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

TuScan %AC If % AC = 100%, we return "homogeneous" because it could be 100% normal or 100% tumor. If
% AC =NA, the percent aberrant cells could not be determined and TuScan returns non-integer
CN calls. This metric is an algorithmically determined estimate of the % of aberrant cells in the
sample.

TuScan Log 2 Ratio Log 2 ratio determined from TuScan algorithm needed to "center" the diploid region of the
adjustment sample (around Log 2 = 0).

ReproSeq QC view

Column Description

Application (ReproSeq) Name of Application from the ReproSeq assay.

Batch File (ReproSeq) Name of the batch file downloaded from Ion Reporter.

Chr MA Ratio Ratio of Mitochondrial/Autosome.

File File Name

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

Single File (ReproSeq) Name of the current file from a Batch File downloaded from Ion Reporter.

Workflow (ReproSeq) Name of the workflow run in Ion Reporter.

SMN Sample Info view

Column Description

DishQC (DCQ) Measures the amount of overlap between two homozygous peaks created by non polymorphic
probes. DQC of 1 is no overlap, which is good. DQC of 0 is complete overlap, which is bad.

File File Name

MAPD Median Absolute Pairwise Difference value. See Appendix G for detailed information.

QC In or Out of QC Bounds.

QC Call Rate Percentage of autosomal SNPs with a call other than NoCall (measured at the Sample QC step).

QC Het Rate Percentage of SNPs called AB (i.e. the heterozygosity) for autosomal SNPs (measured at the
Sample QC step).

Sex Gender call for the sample. See "Gender call algorithms" on page 360).

SMN MAPD Median Absolute Pairwise Difference value calculated from the CNVMix algorithm for the SMN
pipeline.

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Column Description

SMN WavinessSD A global measure of variation of microarray probes that is insensitive to short-range variation and
focuses on long-range variation from the CNVMix algorithm for the SMN pipeline.

SMN1 (variant) Genotype call for SMN variant(s) as defined in the SMN.SNP.list
For more details, see the RHAS User Guide.

SMN1 CN Copy number for SMN1.

SMN1 Exon7 Copy number for Exon 7 of SMN1.

SMN1 Exon8 Copy number for Exon 8 of SMN1.

SMN2 CN Copy number for SMN2.

Other data from the header of the Sample Data file or the ARR file can also be selected
for display in the Select Columns window.
You can only hide or display columns by using the Column Select window, at the right
of the table.
Note: or samples run through the Normal Diploid Analysis for CytoScan, the
ndSNPQC and ndwavinessSD metrics can be viewed in the QC Information Tab, but
will not flag a sample as pass/fail.

Gender call The table below explains which algorithm is used to make the gender calls for the
algorithms different arrays.
The CytoScan Array uses the call “Y-gender” which gives a male/female call.
Depending on the version they were created under, various GTC 2.x and 3.x SNP6
CNCHP files use other gender calls present in their CNCHP file header.
These calls used from the CNCHP file header are NOT the same gender calls used for
those files in GTC, since the GTC-displayed gender calls were stored in GQC or
CN_SEGMENTS files which are not supported in ChAS.
Note: For more details how the array-specific algorithms call LOH segments for the X
or Y chromosome, see "LOH segments on X and Y chromosomes" on page 49.

Software/Array Type Gender Call Call Gender Call

Algorithm Confidence

ChAS 1.X, 2.X and 3.X/4.X Y-gender male/female Yes

CytoScan Arrays

GTC 3.0 to GTC 4.1/ Genome- affymetrix- male/female/unknown No

Wide SNP Array 6.0 chipsummary-Gender

GTC 2.1/ Genome-Wide SNP affymetrix- male/female No

Array 6.0 chipsummary-hasY

GTC 2.0/ Genome-Wide SNP affymetrix- male/female No

Array 6.0 chipsummary-hasY

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Loaded AED/BED This table (Figure 394) displays information about the loaded Region (AED or BED)
files table files.

Figure 394 AED/BED Files information

The Region information files section displays information on:

File File Name with Icons displayed if selected as Overlap File or CytoRegions File).

Created Date and time file was created.

Modified Date and time file was last modified.

You can only hide or display columns by using the Column Select window, at the right
of the table.

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Chromosome summary data

The Chromosome Summary Data tab has two components:
 Chromosome Summary Data
 Auto-Generated Autosome LOH Percentage
The Chromosome Summary Data table (Figure 395) summarizes particular data
across each chromosome in the loaded sample data files.
The available data types are:
Note: ReproSeq Anueploidy data is not supported within this tab.
 Min Signal – minimum Log2 Ratio value found in the chromosome
 Median Signal – median Log2 Ratio value found in the chromosome
 Max Signal – maximum Log2 Ratio value found in the chromosome
 Median CN State – median calibrated Log2 Ratio
 Mosaicism – median mosaicism mixture value
Note: The mosaicism CN state value is not an integer due to cell populations with
different CN state values. In the Chromosome Summary Data table, the mosaicism
value indicates how much the median CN state value is above or below two, the
normal CN state value for autosomes and X in females. For example, a median
mosaicism mixture CN state value of 2.48 is displayed as 0.48 in the Chromosome
Summary table.
Note: Mosaicism (median mosaicism mixture value) for normal males is -1.0 for
chromosome X and -1.0 for chromosome Y. Mosaicism for normal females is 0.0 for
chromosome X and -2.0 for chromosome Y. A mosaic XO female is treated the same
as a mosaic autosomal monosomy (i.e., the mosaicism level of chromosome X will be
between -1.0 and 0). A mosaic XXY male is also given a mosaicism level between -1
and 0 for chromosome X.
 LOH – proportion of genomic distance of LOH calls per chromosome

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Figure 395 Chromosome Summary Data, Min Signal in each chromosome

To choose the data type, make a selection from the drop-down list. (Figure 396)

Figure 396 Selecting the data type for the Chromosome Summary table

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Auto-generated Autosome LOH percentage

The percentage LOH displayed is calculated for the Autosome based on the filter size
set for LOH in the Filters Window. (Figure 397)
The Covered Autosome Length is the base pairs of the Autosome covered by probes.

Figure 397 Custom Autosomal Genome LOH Percentage

IMPORTANT! You must check the LOH Segment Data type to view the sample’s percent LOH.

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Searching results
The Search function enables you to search:
 Detected Segments
 Reference Annotations
 Loaded Region Information Files
The search can find:
 Names of Reference Annotations
 BED and AED file elements, including those in files designated as CytoRegions or
Overlap Maps
 Loaded and displayed segments
You can search by:
 File (select the files to be searched)
 ID Label
 Type

1. From the View menu, select Search or click the upper tool bar’s icon.
The Search window opens. (Figure 398)

Figure 398 Search window

2. Search all files in the File List.

Alternatively, click the All Files drop-down to select the file you want to search.
3. In the Find By ID text field, enter the ID/Name you want to search.
A wildcard (*) is not required when performing searches, however the "*" can be
used to narrow searches. For example, performing the search HOX returns SHOX
and RHOXF1 findings, while using a “*” (*HOX), returns SHOX.

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4. Optional: Use the Find By Type and/or Find By Text fields to enter a type name
(not case sensitive) for the search.
You can enter:
 Names for types of reference annotation features (Genes, DGV, etc.)
 Names for types of segments (Loss, Gain, etc.)
5. Click Search… to begin the search.
If no results are found, the following notice appears. (Figure 399)

Figure 399 No results notice

If the search takes more than a few seconds, a Searching... window appears.
(Figure 400)

Figure 400 Searching notice

If results are found, the Search Results table opens. (Figure 401)

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Figure 401 Search Results

Searching within 1. Right-click on a selected (checked) file inside the Files list pane.
a selected file
Figure 402 Searching notice

2. Click to select Search in selected file... (Figure 402)

The Search window opens. (Figure 403)

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3. Click the appropriate radio button(s), enter your search criteria, then click
Search.

Figure 403 Search window

If no results are found, the following notice appears. (Figure 404)

Figure 404 No results notice

If the search takes more than a few seconds, an In Progress notice appears.
(Figure 405)

Figure 405 Searching notice

If results are found, the Search Results window/table opens. (Figure 406)

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Figure 406 Search Results window/table

To highlight features in the views or the table:

 Double-click in a row of the table to zoom to the feature in the Selected
Chromosome and Detail Views.
 Click on a feature in the Selected Chromosome or Detail View to highlight the
feature in the Search Results table (the feature must be listed in the table to be
highlighted).
You can perform the common table operations in the Search Results table (see
"Common table operations" on page 327).
The Search Results table displays the following information:

Column Description

Chromosome Chromosome the items are located in.

Label Name or ID of the item.

Max Ending position of the item.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for the
starting probe of the segment as reported in the graphs table while the end coordinate matches the
coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic position
coordinates" on page 488).

Min Starting position of the item.

Size (kbp) Size of the item.

Type Type of item.

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Finding intersections
The Find Intersection feature enables you to find segments and regions that overlap
for different:
 Detected Segments
 Reference Annotations
 Loaded Region Information Files

1. From the View menu, select Find Intersections…

The Find Intersection window opens. (Figure 407)

Figure 407 Find Intersection window

2. Select the first file for the comparison from the File A drop-down list. (Figure 408)

Figure 408 Drop-down list

The list shows the available Sample files, Region Information Files, and
Reference Annotations.
Note: Only files that are check marked in the Files List appear in the Match File
drop-down list.
3. Select the second file from the File B drop-down list.
4. Click Find Intersection…

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The Finding Intersection notice opens. (Figure 409)

Figure 409 Finding Intersection notice

When the comparison is finished, the Intersection Results table opens.

(Figure 410)

Figure 410 Intersection Results table

The table displays the names of the A and B files above the tool bar.
To highlight features in the views or the table:
 Double-click in a row of the table to zoom to the feature for File A in the Selected
Chromosome and Detail Views.
 Click on a feature in the Selected Chromosome or Detail View to highlight the
feature in the Intersection Results table (the feature must be listed in the table to
be highlighted).
You can perform the common table operations in the Intersection Results table (see
"Common table operations" on page 327).

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The Intersection Results table displays the following information:

Column Description

% A Touching B How much of the A item is covered by the B item.

% B Touching A How much of the B item is covered by the A item.

A Identifier used for item in A file.

A CN State Copy number of the segment in file A.

A Max Ending position of the A item.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic
position coordinates" on page 488).

A Min Starting position of the A item.

A Size (kbp) Size of the A item.

A Type Type of item in A file with overlap.

B Identifier used for item in B file.

B CN State Copy number of the segment in file B.

B Max Ending position of the B item.

For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table (see Appendix E, "Genomic
position coordinates" on page 488)

B Min Starting position of the B item.

B Size (kpb) Size of the B item.

B Type Type of Item in B file with overlap.

Chromosome Chromosome the items are located in.

Shared Size (kbp) Size of the overlap.

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Segment Prioritization enables the sorting of copy number segments based on user-
defined relevance with overlapping annotations.
Thermo Fisher Scientific offers multiple ways to help quickly annotate segments in
order to reduce interpretation time for each sample.
Segment prioritization options:
 "ChAS Professional version of Franklin by Genoox"
 "Tier-based prioritization in ChAS" on page 376
 "Score-based prioritization in ChAS" on page 381

Note: The following NetAffx Genomic Annotation files are required for full use of all the
parameter in Segment Prioritization:
 NetAffxGenomicAnnotations.Homo_sapiens.hg19.na20221201/
 NetAffxGenomicAnnotations.Homo_sapiens.hg38.na20221201 (or more
current) for optimal segment prioritization results.

IMPORTANT! All data results from the Segment Prioritization process should be manually
reviewed.

ChAS Professional version of Franklin by Genoox

Sample data can be uploaded to your Franklin account automatically using ChAS AIR
(Automated Interpretation and Report) tokens. Use these tokens to take advantage of
Franklin's ACMG classification. phenotype to gene relationships, literation searching,
and access community and historical data. For more information on ChAS AIR tokens,
contact your local sales representative.

ChAS AIR tokens  Contact your local sales representative to purchase AIR Tokens in quantities of 24,
96 or 384 samples.
 Your sales representative will provide a link for setting up an account in Franklin
(required for new accounts only).
 The ChAS AIR Tokens will be deposited into your Franklin account.
 One token is deducted from your AIR token balance for each CHP file you upload
to Franklin (1 CHP file = 1 AIR token).

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Uploading your 1. Load the CHP files into the ChAS Browser
sample(s) to 2. Review the QC metrics to ensure the sample quality prior to interpretation.
Franklin
3. Review the breakpoints of each segment using the Detail View to compare the
segment and the probe level data. Make any necessary adjustments/edits, as
described throughout Chapter 10, "Segment modification" on page 223.
Note: Segments in the mosaic segment track will not be published. For these
segments to be included in the upload to Franklin, they must first be promoted to
the Gain/Loss Copy Number track See "Promoting mosaic segments" on page
243. Promoting is done to mitigate redundancy of Whole Integer Copy Number
segments and Mosaic copy number segments in the same region.
4. In the File window, right-click on the sample filename(s) you want to upload to
Franklin, then click Send File(s) to Franklin... (Figure 411)

Figure 411 Send File(s) to Franklin

A window appears confirming what data type and filters are going to be uploaded
to Franklin. (Figure 412)

Figure 412 Publish to Franklin window

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 Click Cancel to make adjustments to the segment type and/or filter criteria.
 Click OK to keep the displayed settings.
After clicking OK, an Enter credentials window appears prompting you to log into
your Franklin account. If you do not have a Franklin account or do not know your
account credentials, contact [email protected].
5. After entering your Username and Password, click OK.
Note: Your Franklin credentials are saved until ChAS is closed. This eliminates
the need to log in for each additional CHP file you want to upload.
A message appears confirming your files have been successfully sent. If ChAS
was unable to connect to Franklin, an Error message will appear. If it does, check
your Internet connection to the genoox.com website.
6. After Franklin processes your sample(s), go to genoox.com to view their analysis.
Note: If edits were made to a file already uploaded to Franklin, you will not be
charged an additional AIR token for uploading and reanalyzing the file again.

IMPORTANT! Do not delete the open case in Franklin, simply re-upload the edited file(s) to
Franklin to overwrite the existing data.

Returning to an 1. To access a previously uploaded file in Franklin from ChAS, go to the File
open case in window, right-click on the file(s), then click Open Case in Franklin. (Figure 413)
Franklin from
ChAS Figure 413 Open Case in Franklin

The Franklin web page opens displaying the details of your open case.
Note: Before you can review a segment from the Franklin website in ChAS, the HTTP
service in ChAS must be enabled. From the ChAS Browser, click Preferences →
Configure HTTP Service. Confirm the Enable box is checked and Port 8348 is
displayed. Also make sure Port 8348 is not blocked by your firewall.

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Tier-based prioritization in ChAS

The tier-based prioritization assigns Tiers 1-5 to copy number segments that overlap
defined annotations. Copy number segments that overlap an annotation with an
assigned tier will get have that tier assignment. If a copy number segment is assigned
multiple tiers, the lowest tier number will be assigned to the copy number segment.
The exception to this general rule are annotations for DGV-GS and ChAS DB Count
both. If a segment is meets the criteria for either of these annotation, the tier
assignment will take priority over lower number tiers.

Configuring the 1. From the Segment Table tool bar, click the button.
tier-based option The Segment Prioritization Options window appears. (Figure 414)

Figure 414 Segment Prioritization Options window

2. Click the View/Edit Tier-Based Rules button.

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The Select Tier Rules window appears. (Figure 415)

Figure 415 Select Tier Rules window

3. To prioritize your copy number segments in a tier-based order, assign a tier value
to the rule(s) you want to use. To do this, click the drop-down arrow adjacent to
the rule, then click the tier value (1-5) you want to assign to it. A Tier 1 assignment
denotes the highest rule priority, while Tier 5 is the lowest.
Note: Not every Rule requires an assigned tier. See the table below for Rule
definitions.

IMPORTANT! For copy number segments that meet rule(s) with different tier assignments, the
highest tier (lowest number) will be assigned to the segment. Example: A copy number segment
overlaps a rule assigned as Tier 1 and also a rule that is Tier 3, the segment will be assigned as a
Tier 1 since that is the higher of the 2 tiers. Two Rules are exceptions: DGV-GS and DB-B, if either
of these rules are met, the assigned tier overrides any other tiers. If both of these rules are met, the
tier assignment for DGV-GS is assigned.

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Tier-based Description
rule/evidence

DGV-GS Database of Genomic Variants - Gold Standard. The copy number segment is completely contained within
an entry of like type (Gain or Loss) from the Gold Standard DGV track and meeting a defined frequency.
Default frequency is >=1%. This rule WILL override higher ranked tiers based on the tier selected in this
rule.

DB-B ChAS DB Both. Compare the copy number segment to the ChAS DB Both column data. If the number of
entries in this column exceeds the defined threshold, then the copy number segment will be assigned the
tier associated with this rule (unless the DGV-GS rule is also met). This rule WILL override rules with higher
ranked tiers (with the exception of DGV-GS).

DB-F ChAS DB - Filtered. Compare the copy number segment to the Filtered ChAS DB Both column. Example:
Set the Filtered ChAS DB query to filter on segments in the database with the Call 'unknown significance'.
If the copy number segment overlaps enough segments in your ChAS DB called 'unknown significance'',
then the selected Tier will be assigned.

OM-3 Any OMIM Genes annotation that is dark green in color. Dark Green is assigned for phenotype map key 3
OMIM records indicating the molecular basis is known; a mutation has been found in the gene.

OM Any OMIM Genes annotation that is NOT dark green in color. See OM-3 (above).

Cyto-R CytoRegions file. The segment overlaps any region in the assigned CytoRegion file. For more information
on CytoRegions, see "Using CytoRegions" on page 267.

TS Triplosensitivity. The copy number segment overlaps an entry in the Triplosensitivity track which has an
assigned TS_score of 3.

HI Haploinsufficiency. The copy number segment overlaps an entry in the Haploinsufficiency track which has
an assigned HI_score of 3.

RS RefSeq. The copy number segment overlaps an entry in the Protein Coding Genes Track.

EN User-editable field populated by a user-configurable drop list of Calls

P-HI The copy number segment overlaps a Protein Coding Gene or Protein Coding Ensembl Gene with
predicted haploinsufficiency values meeting the defined thresholds. pLI derived from gnomAD (https://
gnomad.broadinstitute.org/) and %HI derived from DECIPHER (https://decipher.sanger.ac.uk/).

NoGene The copy number segment does not overlap any known Protein Coding Gene or Protein Coding Ensembl.

4. Once all desired rules have an assigned tier, click OK to save the selections and
return to the Segment Prioritization Options window.
Click Cancel to return to the Segment Prioritization Options window without
saving any tier assignment changes.
Click Restore Defaults to return to the installation settings.

Tier to call You can assign a Call to represent each tier. The contents of the drop-down list was
settings generated from the Calls Vocabulary list. There are a set of default 'Calls", but this list
can be customized, as detailed in "Using the calls feature" on page 253.
1. Click on the drop-down list adjacent to the Tier(s) you want to assign a Call to,
then click on a selection, as show in Figure 416.

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Figure 416 Tier to Call drop-down lists

Note: Tiers are not required to have a Call assigned. Unassigned Tiers will appear
blank in the Segment Table’s Calls From Prioritization column.
2. After your Tier to Call assignments are complete, click OK.

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Viewing segment Three new segment prioritization columns now appear in the Segment Table, as
prioritization in shown in Figure 417.
the segments
table

Figure 417 New Segment Table columns

 Call From Prioritization: Displays the Call associated with the Tier assigned to the
copy number segment.
 . .Evidence: Displays the abbreviation representing the rules met based on which
annotations the copy number segment overlaps. See the Tier-based rule/
evidence table of definitions above for more details.
Note: A copy number segment that does not overlap any rules with an assigned
tier will display No rules match.
 Tier or Score: This will be a number from 1-5 representing the Tier that was
assigned to the copy number segment based on the user-defined Tier-Based rules
selected.
If the Call from Prioritization assignments are correct, they can be accepted as the
Calls for each segment. To do this:

1. Click the button.

The Call from Prioritization assignments will be copied into blank cells in the Call
column. Note: Any Calls manually assigned will remain in the Call column and not
be overwritten. Segments hidden by the filters will not have calls copied from the
Calls from Prioritization column.
A confirmation message appears (Figure 418) summarizing the Call from
Prioritization assignments are to be copied into the Call column.

Figure 418 Confirm copy into Call column

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2. Click Yes to acknowledge the message.
Note: Any Call can be manually adjusted by clicking on the Call cell and selecting
a new option from the drop-down list, as detailed in "Using the calls feature" on
page 253.

Score-based prioritization in ChAS

The Score-Based prioritization is a research-based adaptation that is similar, but not
identical to, the guidelines proposed in the Riggs et al. 2019 paper: Genetics in
MEDICINE, Published online: 06 November 2019.
This segment prioritization method assigns numeric values (i.e. scores) based on the
overlap of a copy number segment with public and/or private annotations. Default
score assignments are based on the aforementioned paper.
 A copy number segment's final score is summed based on the rules the segment
matches.
 The score assigned to a copy number segment is then associated with a call based
on user defined thresholds.
 Overlap between copy number segments and annotations are performed on all
transcripts for a given gene that are >=90% of the size of the gene coordinates in
the Triplosensitivty and Haploinsufficiency tracks and have identical gene symbols.
 Segment prioritization applies to the following segment types: Gains, Mosaic
Gains, XON Region Gains, Loss, Mosaic Loss, and XON Regions Loss.

Configuring the 1. From the Segment Table tool bar, click the button.
score-based The Segment Prioritization Options window appears. (Figure 419)
option

Figure 419 Segment Prioritization Options window

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2. Click on the Use Score-Based radio button.

View/Edit Score-Based Rules for Gain Segments

1. Click the View/Edit Score-Based Rules for Gain Segments button.
The Select Score Options for Gain window appears. (Figure 420)

Figure 420 Select Score Options for Gain window

2. Use the text field adjacent to the Rule to enter a new numerical. Click the
Restore Defaults button to return to the factory values. See the table below for
Score-based rule/evidence, descriptions, and default value information.

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Score-based Description Default

rule/evidence value

1A The Gain copy number segment fully or partially overlaps at least 1 annotation in the Protein 0
Coding Genes track.

1B The Gain copy number segment does not fully or partially overlap any annotation in the -0.6
Protein Coding Genes track.

2A The Gain copy number segment completely overlaps an annotation in either the 1
Triplosensitivity or Recurrent/Curated Regions track with a TS Score = 3.

2B The Gain copy number segment partially overlaps an annotation in either the Triplosensitivity 0
or Recurrent/Curated Regions track with a TS Score = 3. Partial overlap indicates one
breakpoint of the Gain segment is located within the TS_Score = 3 gene/region.

2C/2F The Gain copy number segment contains the same gene content as a Triplosensitivity or -1
Recurrent/Curated Regions annotation with a TS Score = 40. The copy number Gain segment
might be larger than the gene/region, but contains the same gene content as listed in the
Triplosensitivity or Recurrent/Curated Regions tracks.

2D/2E Both breakpoints of the Gain copy number segment are contained within an annotation -1
having a TS Score = 40 in either the Triplosensitivity or Recurrent/Curated Regions.

2H The Gain copy number segment completely overlaps an annotation in either the 0
Haploinsufficiency or Recurrent/Curated Regions track with a HI Score = 3.

2I Both breakpoints of the Gain copy number segment are contained within an annotation 0.3
having a HI_ Score = 3 in either the Haploinsufficiency or Recurrent/Curated Regions. The
copy number Gain segments is smaller than the user defined threshold (Default >=90%).

2I+ Both breakpoints of the Gain copy number segment are contained within an annotation 0.9
having a HI_ Score = 3 in either the Haploinsufficiency or Recurrent/Curated Regions. The
copy number Gain segments is larger than the user defined threshold (Default >=90%).

2J/2K The Gain copy number segment partially overlaps an annotation in either the 0
Haploinsufficiency or Recurrent/Curated Regions track with a HI Score = 3. Partial overlap
indicates one breakpoint of the Gain segment is located within the HI_Score = 3 gene/region.

3A The Gain copy number segment (partially or completely) overlaps at least 1 Protein Coding 0
Gene annotation. Default is 1-34 genes.

3B The Gain copy number segment (partially or completely) overlaps more Protein Coding Gene 0.45
annotations than in 3A. Default is 35-49.

3C The Gain copy number segment (partially or completely) overlaps more Protein Coding Gene 0.9
annotations than in 3A or 3B. Default is > =50.

4O-DB-B The Gain copy number segment overlaps/covers a defined number of segments in your ChAS -1.0
database (DB Count Both column). Default is 400 segments. Configuration of DB Count Both
parameters can be found in "Querying a segment from the segment table" on page 392.

4O-DGV-GS Both breakpoints of the Gain copy number segment are contained within an annotation in the -1.0
DGV-GS Gain (blue). The DGV-GS annotation must have an NR frequency greater than track
defined. Default NR frequency is 1%.

CY The Gain copy number segment overlaps an annotation in the customer supplied 0
CytoRegions File(s). For more information on CytoRegion files, see "Using CytoRegions" on
page 267.

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3. After your score assignments are complete, click OK.

View/Edit Score-Based Rules for Loss Segments

1. Click the View/Edit Score-Based Rules for Loss Segments button.
The Select Score Options for Loss window appears. (Figure 420)

Figure 421 Select Score Options for Loss window

2. Use the text field adjacent to the Rule to enter a new value. Click the Restore
Defaults button to return to the factory values. See the table below for Score-
based rule/evidence, descriptions, and default value information.

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Score-based Description Default

rule/evidence value

1A The Loss copy number segment fully or partially overlaps at least 1 annotation in the 0
Protein Coding Genes track.

1B The Loss copy number segment does not fully or partially overlap any annotation in the -0.6
Protein Coding Genes track.

2A The Loss copy number segment completely overlaps an annotation in either the 1
Triplosensitivity or Recurrent/Curated Regions track with a TS Score = 3.

2B-r The Loss copy number segment partially overlaps an annotation in the Recurrent/Curated 0
Regions track with a HI Score = 3. Partial overlap indicates one breakpoint of the Loss
segment is located within the HI Score = 3 region.

2B-g The Loss copy number segment partially overlaps an annotation in the Haploinsufficiency 0
track with a HI Score = 3. Partial overlap indicates one breakpoint of the Loss segment is (static
located within the HI Score = 3 gene. If 2B-g is met, then move on to 2C - 2E to assess a value,
value based on location of the partial overlap. further
assessmen
t required)

2C-1 The Loss copy number segment overlaps the 5'UTR and some CDS of a gene with HI score 0.9
= 3 in the Haploinsufficiency track.
TIP: Right-click on the transcript, choose View/Edit Annotation Properties, then select the
Structure tab to view the exons and CDS coordinates.
Note: All transcripts for a gene are assessed as long as the transcript is =< 90% of the
length of the gene as defined in the Haploinsufficiency track and have identical gene
symbols.

2C-2 The Loss copy number segment overlaps the 5'UTR, but no CDS of a gene with HI score 0
= 3 in the Haploinsufficiency track.
TIP: Right-click on the transcript, choose View/Edit Annotation Properties, then select the
Structure tab to view the exons and CDS coordinates.
Note: All transcripts for a gene are assessed as long as the transcript is =< 90% of the
length of the gene as defined in the Haploinsufficiency track and have identical gene
symbols.

2D-1 The Loss copy number segment overlaps the 3'UTR only, no CDS is involved for a gene 0
with HI score = 3 in the Haploinsufficiency track.
TIP: Right-click on the transcript, choose View/Edit Annotation Properties, then select the
Structure tab to view the exons and CDS coordinates.
Note: All transcripts for a gene are assessed as long as the transcript is =< 90% of the
length of the gene as defined in the Haploinsufficiency track and have identical gene
symbols.

2D2/2D3 The Loss copy number segment overlaps the 3'UTR AND the last exon in the coding region 0.3
for a gene with HI_score = 3 in the Haploinsufficiency track.
TIP: Right-click on the transcript, choose View/Edit Annotation Properties, then select the
Structure tab to view the exons and CDS coordinates.
Note: All transcripts for a gene are assessed as long as the transcript is =< 90% of the
length of the gene as defined in the Haploinsufficiency track and have identical gene
symbols.

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Score-based Description Default

rule/evidence value

2D-4 The Loss copy number segment overlaps the 3'UTR AND multiple exons in the coding 0.9
region for a gene with HI_score = 3 in the Haploinsufficiency track.
TIP: Right-click on the transcript, choose View/Edit Annotation Properties, then select the
Structure tab to view the exons and CDS coordinates.
Note: All transcripts for a gene are assessed as long as the transcript is =< 90% of the
length of the gene as defined in the Haploinsufficiency track and have identical gene
symbols.

2E Both breakpoints of the Loss copy number segment are contained within an annotation 0.3
having a HI_ Score = 3 in either the Haploinsufficiency track or Recurrent/Curated Regions
track. The copy number Loss segment is smaller than the annotation in the track by less
than the user defined threshold (Default >=90%).

2E+ Both breakpoints of the Loss copy number segment are contained within an annotation 0.9
having a HI_ Score = 3 in either the Haploinsufficiency track or Recurrent/Curated Regions
track. The copy number Loss segment is larger than the annotation in the track by less than
the user defined threshold (Default >=90%).

2F Both breakpoints of the Loss copy number segment are contained within an annotation -1
having a HI_ Score = 40 in either the Haploinsufficiency track or Recurrent/Curated
Regions track.

2H The Loss copy number segment overlaps a Protein Coding Gene or Protein Coding 0.15
Ensembl Gene with predicted haploinsufficiency values meeting the defined thresholds.
pLI derived from gnomAD (https://gnomad.broadinstitute.org/) and %HI derived from
DECIPHER (https://decipher.sanger.ac.uk/).

3A The Loss copy number segment (partially or completely) overlaps at least 1 Protein Coding 0
Gene annotation. Default is 1-24 genes.

3B The Loss copy number segment (partially or completely) overlaps more Protein Coding 0.45
Gene annotations than in 3A. Default is 25-34.

3C The gain copy number segment (partially or completely) overlaps more Protein Coding 0.9
Gene annotations than in 3A or 3B. Default is > =35.

4O-DB-B The Loss copy number segment overlaps/covers a defined number of segments in your -0.9
ChAS database (DB Count Both column). Default is 400 segments. Configuration of DB
Count Both parameters can be found in "Querying a segment from the segment table" on
page 392.

40-DGV-GS Both breakpoints of the Loss copy number segment are contained within an annotation in -0.9
the DGV-GS gain (red). The DGV-GS annotation must have an NR frequency greater than
track defined. Default NR frequency is 1%.

CY The Gain copy number segment overlaps an annotation in the customer supplied 0
CytoRegions File(s). For more information on CytoRegion files, see "Using CytoRegions"
on page 267.

3. After your score assignments are complete, click OK.

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Configuring the 1. From the Segment Prioritization Options window, go to the Score to Call pane.
score-based (Figure 422)
option
Figure 422 Score to Call pane

 Define the Score Thresholds: In the appropriate text field, enter a Call based on the
segment score as defined above. Your entered threshold values for each Call will
be populated in the Segment Table’s Call from Prioritization column.
 Select Calls: Use the drop-downs adjacent to each threshold to assign a Call that
will be associated with a range of scores.
Note: Calls in the drop-down lists can be customized by adding to the Calls
Vocabulary window in the User Configuration.
In the example below (Figure 423), a copy number segment with a Score of 1.3 would
have a Call from Prioritization assignment of "Level 1". A copy number segment with
a score of -0.96 would have a Call from Prioritization assignment of "Probably
nothing".

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Figure 423 Score to Call drop-down lists

2. Click OK to accept the Score thresholds and Calls or click Cancel to return to the
ChAS Browser without saving any new assignments. Click the Restore Defaults
button to return to the factory values.

Viewing segment Three new segment prioritization columns now appear in the Segment Table.
prioritization in (Figure 417).
the segments
table

Figure 424 New Segment Table columns

 Call From Prioritization: Displays the "Call" associated with the score threshold
ranges.

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 Evidence: Displays the rules met based on which annotations the copy number
segment overlaps.
 Tier or Score: This will be a numeric value representing the score generated and
assigned to the copy number segment based on the user-defined Score-Based
rules selected.
If the Call from Prioritization assignments are correct, they can be accepted as the
Calls for each segment. To do this:

1. Click the button.

The Call from Prioritization assignments will be copied into blank cells in the Call
column.
Note: Any Calls manually assigned will remain in the Call column and not be
overwritten. Segments hidden by the filters will not have calls copied from the
Calls from Prioritization column.
A confirmation message appears (Figure 425) summarizing the Call from
Prioritization assignments are to be copied into the Call column.

Figure 425 Confirm copy into Call column

2. Click Yes to acknowledge the message.

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A segment can be queried against the ChAS Database for intersecting segments from
previously published samples. Using both the Overlap Threshold and Coverage Threshold
can focus the query results to segments that are of approximately the same size as the
segment in the current sample.

Note: ReproSeq Aneuploidy data can not be published into the ChAS DB.

Setting up a ChAS DB query

1. From the ChAS Browser, click Preferences → Edit User Configuration.
2. Click the DB Query window tab. (Figure 426)

Figure 426 User Configuration - DB Query window/tab

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Setting up query Note: When querying on a copy number segment in the Browser, the values set in the
parameters for a Copy Number Query Parameters section are used.
copy number 1. Enter minimum percentage values for both Overlap and Coverage using the text
search boxes or click and drag the appropriate slider bar. (Figure 427) Note: The default
values are set to 50%.

Figure 427 Copy Number Query Parameters

2. Check the Match only same gain/loss type check box if you want to query the
database for only similar copy number types (gains only or losses only). Uncheck this
check box if you want to query all copy number segment types.
3. Check the Include Exon Regions check box if you want to include Exon Region
Segments in your query.
4. Check the Include LOH box to include LOH segments in your query.
5. Click OK to save your changes or click Restore Defaults to return the parameter
settings back to their default settings.

Setting up query Note: When querying on an LOH segment in the Browser, the values set in the LOH Query
parameters for an Parameters section are used.
LOH segment 1. Enter minimum percentage values for both Overlap and Coverage using the text
search boxes or click and drag the appropriate slider bar. (Figure 428) Note: The default
values are set to 50%.

Figure 428 LOH Query Parameters

2. Click OK to save your changes or click Restore Defaults to return the parameter
settings back to their default settings.

Setting up query Note: When querying on an XON Region segment in the Browser, the values set in the
parameters for an Exon Region Query Parameters section are used.
XON region 1. Enter minimum percentage values for both Overlap and Coverage using the text
segment search boxes or click and drag the appropriate slider bar. (Figure 429) The default values are
set to 50%.

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Figure 429 XON Regions Query Parameters

2. Check the Match only same gain/loss type check box if you want to query the
database for only similar XON Region segment types (gains only or losses only).
Uncheck this check box if you want to query all XON Region segment types.
3. Check the Include Copy Number Segments check box to include Copy
Number Segments in your query.
4. Click OK to save your changes or click Restore Defaults to return the parameter
settings back to their default settings.

Querying a segment from the segment table

To view what segments in the database intersect with the currently loaded segment,
you must first make the DB Count Both column visible. The DB Count Both column
displays the number of segments in the database that meet the criteria set in the DB
Query tab.
1. Right-click in the DB Count Both cell for the segment(s) you want to view, then
click Query ChAS DB for "DB Count Both". (Figure 430)
Note: Segments matching ONLY the Coverage OR Overlap thresholds can also
be returned in the Segment Intersections window by right clicking in either the DB
Coverage Count or DB Overlap Count columns respectively. You can also right
click on the segment in the Detail View and choose Query ChAS DB to return
segments meeting either the Coverage OR the Overlap thresholds. See "Filtering
DB count columns" on page 401. If you want to add column(s) to your Segment
table, see "Selecting columns to display or hide" on page 329.

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Figure 430 Query ChAS DB for “DB Count Both”

Segment The Segment Intersections view appears with the results from the query.
intersections (Figure 431)
The Segment Intersections view shows samples in the database that contain
segments that meet the criteria set in the DB Query.
The middle portion of this view contains table information about the samples in the
database including any Call, Interpretation or Inheritance information assigned to the
segments for the samples shown in the example above. To display or hide columns
within this table, click (upper right corner).
The lower portion of the view provides the same external annotations available in the
Detail View. To display an annotation track, go to the ChAS Browser’s Files Menu and
check the box. The annotation track will then be displayed in both the Detail View and
the Segment Intersections View. (Figure 431)
You can return segments from the database based on either DB Overlap or DB
Coverage. These segments meet either one of the overlap or coverage threshold
criteria.

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Note: Segment Intersection search results are limited to 1000 intersecting segments.
When querying on a copy number segment in the Browser, the Copy Number Query
Parameter Thresholds are used for all segment types. When querying on an LOH
segment in the Browser, the LOH Query Parameter Thresholds are used for all
segment types.
Example: You have a gain segment in the ChAS Browser and run a query to retrieve
intersecting segments. Both Gain and LOH segments counts appear in DB Count
Both, the LOH segment being returned are using the Copy Number Query Parameter
Thresholds since the original segment is a GAIN.

Figure 431 Query ChAS DB - Segment Intersections window

Segment Intersections Table

This segment example is represented as a loss (in the sample currently loaded in the browser).

Blue lines represent break points of the Segment

Segment Intersections
Graph

External Annotations

Click the Side-by-Side icon (upper right) to split the Segment Intersections window, as
shown in Figure 432 on page 395.
Note: Columns with a pad and pencil icon represent a segment field that can be
edited. All edits are stored directly to the database.

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Figure 432 Query ChAS DB - Segment Intersections window (Side-by-Side)

The Segment Intersection View table has the following columns:

Note: Columns listed with an adjacent icon denote the column is user-editable.

Column Description

Call User-editable field populated by a user-configurable drop list of Calls.

Inheritance User-editable field populated by user-configurable drop-down list of Inheritance.

Oncomine Displays the Oncomine Reporter terminology assigned to the segment.

Reporter

Segment Displays Segment Interpretation assigned to this sample.

Interpretation

% of Overlap Item The percentage of the Overlap Map Item covered by the segment.
covered by Segment

Call from The Call term assigned based on Tier or Score Classification at the time the sample was published
Prioritization (Stored) to ChAS DB.

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Column Description

Chromosome Chromosome on which the item is located.

CN State Copy Number State.

CytoRegions Names of the CytoRegions with which the segment shares coordinates.

DB Coverage Number of segments in the database meeting the minimum Percent Coverage Count.

DB Overlap Number of segments in the database meeting the minimum Percent Overlap Count.

DGV List of DGV variations that share coordinates with the segment.

Evidence (Stored) Provides information on which annotations the segment overlapped at the time the sample was
published to ChAS DB.

Genes List of RefSeq genes from the Genes track that share coordinates with the segment. Identically
named gene isoforms are NOT repeated.

Interpretation User-editable field for free-text interpretation on the segment.

Label Identifier for the item.

Max Zero-based index position of the last base pair in the sequence, plus one. Adding one ensures that
the length of any (hypothetical) segment containing a single marker would be one, and ensures that
the coordinates match the coordinate system used in BED files.
For all segments, the segment start coordinates are always lower by one bp from the coordinate for
the starting probe of the segment as reported in the graphs table while the end coordinate matches
the coordinate for the ending probe as reported in the graphs table

Min Zero-based index position of the first base pair in the sequence.

OMIM Genes List of OMIM Genes that share coordinates with the segment.

Overlap Map Item(s) in the Overlap Map which overlap the segment.

Overlap Map Items The percentage of the segment that is overlapped by the Overlap Map Item.

Phenotype Displays Phenotype annotation assigned to this sample.

Published Displays the date and time of your query.

Publisher Displays Publisher’s name.

Sample DB ID A xxCHP file ID automatically assigned when the xxCHP file is published to the database.

Sample Type Displays the Sample Type assigned to this xxCHP file.

Sample UUID Unique identifier for the CHP file.

Segment DB ID An ID automatically assigned to each segment when the xxCHP file is published to the database

Segment ID The unique identifier for the copy number segment.

Segmental List of Segmental Duplications that share coordinates with the segment.
Duplications

Sex Displays Male or Female.

Size (kpb) Size of the item.

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Column Description

Tier or Score (Stored) The assigned Tier or Score value based on the Segment Prioritization method selected at the time
the sample was published to ChAS DB. When using Tier based, the column will display the assigned
Tier. When using Score based, the column will display the score value based on the annotations the
segment overlaps.

Type Type of segment (Gain, Loss, GainMosaic, LossMosaic LOH) or annotation.

Additional segment intersection information

Additional Segment Intersection information becomes available after querying a ChAS
DB that has been remapped from a previous genome build that includes additional
columns that are populated in the Segment Intersection Table. These remapped
segments, are also represented in different graphical patterns, as shown in Figure 433
and detailed in Figure 434.

Figure 433 Additional Segment Interaction Information example

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Figure 434 Additional Segment Interaction Legend

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The additional Segment Intersection table columns and their definitions, are as
follows:

Column Description

Original location Chr:start-stop genome location of the original genome build for the segment.

Markers in original segment Total number of markers in the original segment.

Added markers Number of markers to the segment added by remapping.

Removed markers Number of original markers removed from the segment from remapping.

Segment length difference Size difference in the segment (Original - Remapped).

Original Genome Build Genome Build from the original analysis prior to remapping.

Markers in remapped segment Total number of markers in the remapped segment.

Downloading segments from a sample file in ChAS DB

From the Segment Intersection window, all the segments for a selected sample can
be downloaded and viewed in the Segments Table and Detail View. Only the segment
data and annotations from the sample are displayed.
Note: Files downloaded from ChAS DB can not be opened in the MSV.

Downloading and viewing Segments from a sample(s) stored in ChAS DB

1. From the Segment Intersections window, right-click on the sample(s) in either the
table or the graphical view.
2. Select Download file(s) from ChAS DB. (Figure 435)

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Figure 435 Segment Intersections - Download file(s) from ChAS DB

Note: As shown in Figure 436, sample files downloaded from ChAS DB are listed in the
Files Tree with a database symbol. Segments from samples files downloaded from
ChAS DB are listed in the Segments Table with a database symbol in the File column.

Figure 436 Segment Intersections - Download file(s) from ChAS DB

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Note: Downloaded segments can be deleted when in Edit Mode, but no other segment
modifications are enabled as the underlying data is unavailable.

Updating downloaded segment annotations

Segment annotations in the ChAS DB can be updated using the following methods:
 Right-clicking on the segment and selecting View/Edit Annotation Properties →
Curation Tab.
 Clicking on a column/field pad and pencil icon to edit the segment annotation(s).
 Right-clicking on the Filename in the Files tree, select View/Edit Properties → Sample
Properties.

Filtering DB count columns

Filtered DB count columns are available in the Segment Table and reflect the number of
segments in the database matching the filtered criteria.
Note: The DB count columns reflect the number of segments in the database meeting the
Minimum Percent Overlap/Coverage criteria only. The Filtered DB count columns allow
you to display segments that not only meet the Minimum Percent Overlap/Coverage
criteria, but also additional filters such as Call or Gender.
1. Click Edit User Configuration, then click on the Filtered DB Query tab. (Figure 437)

Figure 437 User Configuration - Filtered DB Query window/tab

2. Refer to "Setting up a ChAS DB query" on page 390 for how to set the Percent
Minimum Overlap/Coverage Thresholds.

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3. Return to the Filtered DB Query window tab.
4. The Filtered DB Query window tab displays the current filter setting. To change
it, click Change Filter Parameters.
A Set Filter Parameters window appears. (Figure 438)

Figure 438 Set Filter Parameters window

5. Use the windows check boxes, radio buttons, and selections to change your
filter parameters.
6. Click OK.
Your new query parameters are saved and displayed at the bottom of the Filtered
DB Query window tab, as shown in Figure 439.

Figure 439 Displayed Filter Parameters example

To reset the Filtered DB Query Parameters back to default settings, click Restore
Defaults. For more information see, "Filtering DB count columns" on page 401.
Figure 440 shows the DB Count Both and Filtered DB Count Both columns. It
illustrates that DB Count Both queries the database for all segments matching the
Minimum Percent Overlap/Coverage and gain/loss/LOH parameters. The Filter DB
column reflects the additional Filter Criteria.

Figure 440 Displayed Filter Parameters example

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Querying overlapped segments

1. Right-click on a Segment of interest within the Detail View. (Figure 441)
2. Click Query ChAS DB.

Figure 441 Query ChAS DB from Detail View

The results returned when querying a segment in the detail view will contain segments
that meet the DB Coverage filter or the DB Overlap filter set up previously. (Figure 426
on page 390)

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Changing or refining the DB query criteria

1. From the upper left corner, click Search → Search Again... (Figure 442)

Figure 442 Segments Intersections window

The Search parameters window appears. (Figure 443)

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Figure 443 Search Parameter window

2. Use the provided radio buttons, check boxes, and text fields to customize your
search, then click OK.
Note: Altering these parameters only affects the current segment query. The
following fields, Sample Types, Array Types and Calls are populated based on
what has been published by the user into the ChAS database If the ChAS
Browser is unable to contact the database, these fields are populated based on
the library file and vocabularies entries.

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Publishing data to the database

Once sample and its segments have been analyzed, curated and annotated, it can be
added to a database by a process called publishing.

IMPORTANT! You MUST have Manager or Admin Role permissions to publish data to the
database. For details, see "Administration" on page 456.

Publishing data or Method 1

multiple data to 1. In the File tree, right-click on a file name, then click Publish File(s) to Database...
the database (Figure 444)

Figure 444 Example: Multiple files selected for

publishing to the database

Method 2
1. Click to highlight the sample name(s), then click the tool bar's Publish to
Database icon .
A summary of uploaded segments/Publish? appears. (Figure 445)

Figure 445 Publish? window

2. Acknowledge the message, then click OK.

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Note: Only segments in the copy number, XON region and LOH segment tracks
can be uploaded. Segments uploaded are reflective of the current filters and
settings applied.
Note: Only segments listed as enabled and filtered will be published. If a
segment category is listed as not enabled, click Cancel and check the check box
in the Data Types File tree and then right click on the sample filename(s) to start
the publishing again.
Note: Publishing time is dependent on the number of segments in the sample.
Note: Segments in the Mosaic track are not uploaded to the database. Mosaic
segment must be promoted to the copy number state track in order to be
published to the database. See "Promoting mosaic segments" on page 243.
Note: If a xxCHP file has been previously Published to the database, you will
receive a warning indicating this sample already exists in the database. You can
choose to overwrite the existing information or cancel to keep the existing
information.
Note: The Segment Table Columns DB Count and Filtered DB Count are
automatically updated.
Note: If ChAS is set to manual mode, the histogram need to be manually updated
to include recently published samples. To update the histograms, click
ChAS DB → Refresh ChAS DB data.

Publishing to Important rules and restrictions

database  A sample cannot be published if it is in Edit Mode. See "Using edit mode" on page
224.
 Only samples that are highlighted (not checked) are published to the database.
 Samples published using hg18 cannot be published to the database.
 Multiple filenames can be highlighted and published at the same time.
 Segments from xxCHP files analyzed using hg19 analysis files cannot be loaded
into a ChAS Database genome version hg38. The opposite is also true.
 Mosaic Segments can not be published.
 To promote mosaicism in the database, the Mosaic Segment should be
assigned a copy number value and promoted to Copy Number segments using
the edit function. For more details, see "Promoting mosaic segments" on page
243.
 You must be logged in as an administrator or manager (with manager role
permissions) to publish data.
 Previously published samples can be edited and published again, however
publishing a second time overwrites the original database entry.

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Manual or automatic connection mode

By default, ChAS starts in automatic connection mode.
While in automatic connection mode, the DB count columns and histograms are
refreshed/updated whenever a file is published.
If you do not want to wait for the data to be refreshed/updated each time a file is
published, choose manual connection mode. In manual mode, the DB count columns
and histograms are only be updated when you click ChAS DB → Refresh ChAS DB
data or click the icon.
There are two ways to switch from automatic to manual connection mode.
 At start up, select a user (as you normally would), click on the Manual connection
check box, then click OK. (Figure 446)

Figure 446 Select User window

 During a ChAS session, go to the upper bar of icons and click on for
automatic connection or click on for manual connection.
Or
 Click ChAS DB → Auto-Connect, then click on the check box to toggle between
connection modes, as shown in Figure 447.

Figure 447 ChAS DB drop-down menu

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Querying samples in the ChAS database

1. Click ChAS DB → Query Samples or click the Query Samples tab, then click
the Query Samples button.
The Query Samples window appears. (Figure 448)

Figure 448 Query Samples window

2. Use the provided radio buttons, check boxes, and text fields to customize your
query, then click OK.
The Query Samples table populates with your filtered search results. (Figure 449)
The contents for columns in which the headers have an Edit Icon can be
modified. Changes will apply directly to the ChAS database.
Columns with a chip/pencil icon represent sample properties that can be
edited.

Editing column 1. Double click on a cell to be edited.

contents An Edit Value window appears. (Figure 449)
2. Enter or change the value in the window.
3. Click OK.
Your changes are now saved to the ChAS Database.

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Editing multiple 1. Highlight the cells you want to edit.
cells with the 2. Right-click, then select Edit Property Values.
same value
An Edit Value window appears. (Figure 449)
3. Enter a new value or edit the existing displayed value.
4. Click OK.
Your changes (for the multiple cells you selected) are now saved to the ChAS
Database.

Figure 449 Query Samples window tab table - Filtered search results

For instructions on how to use the table’s features, see "Common table operations"
on page 327.
Note: The following fields, Sample Types, Array Types and Calls are populated
based on what has been published by the user into the ChAS database. If the ChAS
Browser is unable to contact the database, these fields are populated based on the
library file and vocabularies entries. Queries are not automatically refreshed when
publishing to or deleting from the ChAS DB. Queries must be re-run to reflect changes
to the database made after the initial query.

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Removing a sample from the query window

You can remove a sample from the query window, however this action does NOT
remove the sample from the database.
1. Highlight the sample(s) you would like to remove from the results display.
2. Right-click, then click Remove Query Results. (Figure 450)
A warning message appears asking you to confirm the removal of the file(s) from
the results window.
3. Click OK to remove the files from the results. Click Cancel to return to the main
screen.

Figure 450 Remove Query Results

Deleting sample(s) from the ChAS database

WARNING! You must have manager or admin permissions for the ChAS database to delete
samples.

Sample(s) deleted from the ChAS Database are permanently deleted and cannot be retrieved. There
is no undo delete feature.

Deleting a single To remove a single sample in a database, use the Query Samples window to locate
sample the file to be deleted.
1. In the Query Samples window (Figure 448 on page 409), enter the file’s Filename
or Sample ID, then click OK.
The sample appears in the table. (Figure 451)

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Figure 451 Query Samples window tab table - Deleting a sample

2. Right-click on the sample, then click Delete.

When a sample is deleted from a database, the reason for the deletion is
required. Enter the reason in the Enter delete reason window. (Figure 452)
Note: This reasoning you enter is captured in the ChAS DB and it can be
exported. For details, see "Exporting a deletion log" on page 437.

Figure 452 Enter deletion reason window

3. Click OK to delete. Click Cancel to return to the query window.

The sample is removed.

Deleting multiple 1. Multiple samples can be highlighted to delete. They can be selected using the
samples following keyboard and mouse combinations: Ctrl click, Shift click or Ctrl a..
(Figure 453)

Figure 453 Query Samples window tab table - Deleting multiple samples

2. Right-click on the highlighted area, then click Delete.

The samples are removed.

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Querying segments to the ChAS database

1. Click ChAS DB → Query Segments or click the Query Segments tab, then click
the Query Segments button.
The Query Segments window appears. (Figure 454)

Figure 454 Query Segments window

2. Use the provided radio buttons, check boxes, and text fields to customize your
query, then click OK.
The Query Segments table populates with your filtered search results.
(Figure 455)
The contents for columns in which the headers have an Edit Icon can be
modified. Changes will apply directly to the ChAS database. Editable columns
are: Call, Segment Interpretation, Inheritance, Oncomine Reporter.

Editing column 1. Double click on a cell to be edited.

contents An Edit Value window appears. (Figure 455)
2. Enter or change the value in the window.
3. Click OK.
Your changes are now saved to the ChAS Database.

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Editing multiple 1. Highlight the cells you want to edit.
cells with the 2. Right-click, then select Edit Property Values.
same value
An Edit Value window appears. (Figure 455)
3. Enter a new value or edit the existing displayed value.
4. Click OK.
Your changes (for the multiple cells selected) are now saved to the ChAS
Database.

Figure 455 Query Segments window tab table - Filtered search results

For instructions on how to use the table’s features, see "Common table operations"
on page 327.
Note: To delete sample files from the Query Segments tab, follow the same
instructions outlined in "Deleting sample(s) from the ChAS database" on page 411.
This procedure deletes the entire sample file and all file information associated with it.

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IMPORTANT! Edit Mode must be OFF before exporting from ChAS.

Chromosome Analysis Suite includes the following tools for reporting results:
 Export the Karyoview, Selected Chromosome View, and Detail View as a DOCX,
PDF or PNG file. See "Exporting graphic views".
 Export to a DOCX file. See "Creating signature and background profiles".
 Export table data as a DOCX, PDF, TXT file, or copy selected data onto your
clipboard. See "Exporting table data".
 Combine PDF reports. See "Combining PDFs into a single PDF"
 Use a ClinVar export template. See "Exporting with ClinVar".
 Export copy number and variant data as VCF. See "Exporting VCF files".

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

Note: If you have trouble displaying non-English characters on screen or in exported

PDF files, make sure that the font “Arial Unicode MS” is installed on the machine.
Open the “C:\Windows\Fonts” folder and search for a ARIALUNI.TTF file.

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Exporting graphic views

You can export the Karyoview, Selected Chromosome View, and Detail View in the
following formats:
 PDF - "Exporting as a PDF"
 MS Word (DOCX) - "Exporting as Word (DOCX) format" on page 420
 PNG graphic file - "Exporting as PNG" on page 422

Exporting as a ChAS provides a variety of options for exporting graphic views as PDFs. The PDF
PDF Report displays the graphic with basic information about data files and settings.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

1. From the Exports menu, select the PDF option you want to use.
 Export application window PDF - Creates PDF with entire software screen and
information about data files
 Export Karyoview PDF - Creates PDF with Karyoview and information about
data files.
 Export Selected Chromosome PDF - Creates PDF with Selected Chromosome
View and information about data files.
 Export Detail View PDF - Creates PDF with selected Detail View and information
about data files.
 Export Segments Table PDF - Creates PDF with Segment Table
 Export QC and Sample Info PDF - Creates PDF with the QC and Sample
Information
 Export Chromosome Summary Data PDF - Creates PDF with the Chromosome
Summary Data

An Export Details window appears. (Figure 456)

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Figure 456 Export Details window

2. Optional: If you have added a Sample Interpretation in the View/Edit Sample

Properties window, the information will be populated into the Interpretation
dialog box. You can also type free text into the Interpretation box.
3. Optional: Select the option for adding page numbers.
4. Optional: Select the option for adding to an existing report, if desired. See
"Combining PDFs into a single PDF" on page 430.
5. Click Select File.
The Save window opens.
6. Select a folder location for the PDF using the navigation tools.
This folder location is automatically selected when exporting other PDFs during
a session.
7. Enter a name for your PDF file.
If you are adding the graphic to an existing PDF, select the PDF file.
8. Click Save.
You are returned to the Export Details window.
9. Optional: Leave the Auto Launch Export check box checked, if you want your
newly saved PDF to open automatically after clicking OK.
10. Click OK.
A PDF is created with your selected export details saved.

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Creating signature and background profiles

Signature profiles Signature Profiles, including a logo, address, reviewer name and credentials, can be
added to a DOCX export. Use saved signature profiles for quick recalls with any DOCX
export
1. Click on the Preference Menu, then select Edit User Configuration.
2. Click the Exports Tab.
3. Click the Summary Exports tab, then click the Summary Export tab. (Figure 457)

Figure 457 Summary Export window - Signatures

Creating a new signature

1. Click the New button.
2. Complete the text fields.
3. Optional: Click on the Upload Logo button to add your organization’s logo.
4. Click OK to save.
Your saved signature name will be the same as your organization name.
5. Optional: Repeat steps 1-4 to create additional signatures.

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Editing a saved Signature
1. Highlight the Signature name you would like to modify.
2. Click the Edit button.
3. Modify the appropriate fields.
4. Click OK to save your updated signature.

Deleting a signature
1. Highlight the Signature name you would like to delete.
2. Click the Delete button.
3. Click OK to permanently remove the signature.

Background Background profiles (Figure 458) provide saved text(s) that can be added to each
profiles DOCX export. For example, a noteworthy background about the assay profiles you
want to save.

Figure 458 Summary Export window - Backgrounds

Creating a new background

1. Click on the New button.
2. Name the Background using the Title field.

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3. Enter the text for the background information that you want to appear on the export.
4. Click OK to save.
5. Optional: Repeat steps 1-4 to create additional Backgrounds.

Editing a saved background

1. Highlight the Background name you want to modify.
2. Click the Edit button.
3. Modify the text.
4. Click OK to save your updated background.

Deleting a background
1. Highlight the Background name you would like to delete.
2. Click the Delete button.
3. Click OK to permanently remove the Background.

Exporting as 1. From the Exports menu, select Export - Word (docx) Format.
Word (DOCX) The Export Details window opens. (Figure 459)
format
Figure 459 Export Details window

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Note: In order to export a graph (Karyoview, Whole Genome View, Detail View,
Selected Chromosome View), the graph must be visible in the ChAS Browser before
export.
2. Single-click, Ctrl-click, or Shift-click on the Available Exports (left pane), then click
the right double arrow button (Figure 459) to add them to the Selected Exports (right
pane). Use the Up and Down buttons to define each report’s order within the master
report.
3. Optional: Select a saved Signature and/or Background from the drop-down lists to
add them to your DOCX export.
If you previously entered Sample Level Interpretations, they will appear in the
Interpretation field.
Note: Before adding an entry in the Interpretation field, the Selected Exports pane
must first display Sample Analysis Information, as shown in Figure 459.
4. Optional: Click the Add to Existing Export check box to add this new report to an
existing one. After checking this check box, click on the Select File button to
navigate to and select an existing DOCX file.
5. Optional: Click the Convert to paragraph style for Segments Table check box if
you want your Segments Table data translated into a paragraph-style format, as
show in Figure 460.

Figure 460 Segments Table to paragraph-style format example

6. Optional: Click the Include Row Number check box to add row numbers to the
Segment Table.
7. Optional: Click the Hide Y Chromosome check box to export the Karyoview without
the Y chromosome ideogram for female samples.

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8. Click the Select File button to navigate to a saved report location, enter a
filename, then click Save.
The name of the file defaults to the name of the filename.
9. By default, the report automatically opens in MS Word after it is generated.
Uncheck the Auto Launch Export check box to disable this feature.
10. Click OK to generate the DOCX report. Click the Reset button to return the
Report Details window back to its factory defaults.

Exporting as PNG You can also create a PNG screen shot of the entire software screen.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

1. From the Exports menu, select Export application window PNG.

A Save As window opens.
2. Select a folder location for the file using the navigation tools.
This folder location is automatically selected when exporting other screen shots
during a session.
3. Enter a name for the PNG file in the File Name box.
4. Click the Save button.
The PNG file screen shot is saved in the selected location.
The PNG file can be cropped in a graphics program like Paint and inserted into a
word processing document if desired.

Exporting table data

ChAS provides several options for exporting table data:
 "Exporting table data into a PDF"
 "Exporting views and tables as a DOCX file"
 "Exporting tables as TXT file"
 "Exporting a segments table with modified segments to a TXT file"

Exporting table For information on how to choose and export preset column content (from previously
data into a PDF saved table states). See “Saved table states” on page 332.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

Note: You can export data from the Segment Table by selecting Export Segment
Table PDF from the Exports menu, but you cannot export graph table data in a PDF
format.
In order to track which of your segments have been modified (merged, created de
novo, deleted, had their start or end coordinates edited, or had their type or state

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changed), you MUST perform the following BEFORE exporting the Segments Table
to PDF. The only PDF format capable of tracking which segments have been modified
is the Segments Table PDF, all other PDFs show NO visual or textual distinction
between modified and non-modified segments.
BEFORE exporting table data into a PDF file:
1. Click (top right of Segments table).
The Select Columns window appears.
2. Scroll down, locate, then click to check the Modified Segment check box.
3. Click OK.
The Modified Segment column is now added to your Segments table.

Exporting table data into a PDF file

1. At the Segments table upper tool bar, click the PDF button .
The Select Columns and Files window appears. (Figure 461)

Figure 461 Select Columns and File window for Segment Table PDF

If you have added a Sample Interpretation in the View/Edit Sample Properties window,
the information will be populated into the Interpretation dialog box. You can also type
free text into the Interpretation box. You must check the Include Sample Properties
check box in order to enable the Interpretation field

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2. Enter the appropriate text in the Interpretation field.
To add the other Sample Properties, check the Include Sample Properties
check box. If these fields have been populated, they will be exported in the PDF.
3. Select the columns to be displayed and the columns truncation rules. The
Column Selection and Preferences window (Figure 462), include:
 Column Name: Header of the column in the table.
 Add Column: Click the check box to display the column in the PDF report.
 Column Truncation Options:
No_Truncation - Field is exported as is, using wrap-around if necessary.
Truncate_Beginning - Truncates content at the beginning of the field, leaving
as many characters as specified in Truncated Length box.
Truncate_Middle - Truncates content in the middle of the field, leaving
characters at the beginning and end, with ellipses (…) to mark the truncated
characters.
Truncate_End - Truncates content at the end of the field, leaving as many
characters as specified in Truncated Length box.
 Truncated Length: Number of characters displayed after truncating the data.

Figure 462 Column Selection and Preferences

4. Select the option for adding page and row numbers, if desired.
5. Select the option for adding to an existing report, if desired. See "Combining
PDFs into a single PDF" on page 430.
6. Click the Select File button.

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The Save As window opens. (Figure 463)

Figure 463 Save As for Segment Table PDF

7. Select a folder location for the file using the navigation tools.
8. Enter a name for the PDF file, or select a file for the information to be appended
to.
9. Click Save in the Save As window.
10. Click OK in the Select Columns and File window.
A PDF file is created with the selected data type saved.
The PDF report displays:
 Table type
 Information on chromosome and genome region
 Interpretation
 Data files
 Genome or CytoRegion Segment Filters used
 Settings for Data Processing
 Microarray Nomenclature
 Details of the table data

Exporting tables tips

Follow the tips below to improve the export of table data in a PDF file:
 Use truncation.
 Select only columns you need or select columns from a saved table state. See
"Saved table states" on page 332.
 Use filtering options (Segment filters, displaying only results for a chromosome or
area in the detail view, etc.) to limit the number of values being exported.

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Exporting views You can save the currently viewed table in a new or existing DOCX report.
and tables as a 1. While in a desired View or Table, click the DOCX button .
DOCX file
A Save window appears.
Do one of the following:
 New Reports: Enter a filename to create a new DOCX file, then click Save.
 Adding to an existing report: Click to select an existing DOCX file. Click Save.
The message window, You will be adding contents to an existing file. Continue?
appears. Click Yes to append the currently displayed table contents onto an
existing file.

IMPORTANT! Before adding a file, it must be closed.

Exporting tables The TXT file format enables you to transfer data to other software for analysis.
as TXT file
IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

Exporting table information as a text file

1. Perform pre-filtering on the data in the table. (Figure 464)

Figure 464 Segments table with data filtered

2. In the Table tool bar, click the Export TXT button.

The Save as TXT window opens. (Figure 465)

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Figure 465 Save as TXT window

3. Select a folder location for the file using the navigation tools.
4. Enter a name for the TXT file.
5. Click Save.
The TXT file is saved in the selected location (Figure 466).
It can be opened using a text editing or spreadsheet program, or in other
software designed to use Tab Separated Value TXT format.

Figure 466 TXT file opened in Excel

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Exporting a In the Segments Table:
segments table  Materially Modified segments are shown in italic text when Edit Mode is ON, but
with modified not italicized when Edit Mode is OFF.
segments to a  Calls and Interpretations don't cause a segment's row text to be italicized in Edit
TXT file Mode.
 Deleted segments are shown in strike-through text when Edit Mode is ON, and are
not present in the table when Edit Mode is OFF.
 In the TXT Exports of the Segments Table table, please note that Deleted segments
will be part of the export when Edit Mode is ON, and will not be part of the export
if Edit Mode is OFF
Figure 467 is an example of a Segment Table with Edit Mode ON. Note its italicized
text representing materially modified segments and the strike-through text showing
deletions.

Figure 467 Segment table - Edit Mode ON

Figure 468 is an example of a Segment table that has been exported with the Edit
Mode ON. Note the 4th row of the Use in Report column. In the case of this segment,
it reads FALSE, because this segment was deleted.

Figure 468 Segment table TXT EXPORT - Edit Mode ON

Figure 469 is an example of a Segment Table with Edit Mode OFF. The italicized text
representing materially modified segments is no longer present. The deleted segment
and strike-through text showing a deletion (shown in Figure 467 and Figure 468) also
do not appear.

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Figure 469 Segment table - Edit Mode OFF

Figure 470 is an example of how an exported TXT table appears with Edit Mode OFF.
Note the deleted segment shown in Figure 467 and Figure 468 is not present.

Figure 470 Segment table TXT EXPORT - Edit Mode OFF

Transfer to You can copy data from selected cells to the clipboard for pasting into a text or
clipboard spreadsheet file.
1. Select the cells you want to copy in the table. (Figure 471)

Figure 471 Segment table with cells selected

2. Click the Copy to Clipboard button in the table tool bar.

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The selected data is copied to the clipboard.
You can paste the data on the clipboard into a text or spreadsheet file
(Figure 472).

Figure 472 Data pasted into text file

Combining PDFs into a single PDF

You can combine different PDFs into a single PDF with multiple pages and content.
You can do this by:
 Adding new data to an existing PDF file.
 Merging two or more existing PDF files.

IMPORTANT! The results from ChAS are for Research Use Only. Not for use in diagnostic
procedures.

Adding a new 1. When exporting a table or graph as a PDF, click the Add to Existing Export
PDF export to an check box in the Export Details window. (Figure 473)
existing PDF file
Figure 473 Export Details window with Add to Existing Export selected

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2. Click Select File and select an existing PDF file for the data to be added to.
The Save As window opens. (Figure 474)

Figure 474 Save As window

3. Select a PDF file, then click Save in the Save As window.

A confirmation message appears, asking if you want to overwrite or add to the
data (Figure 475).

Figure 475 Confirmation message

4. Click Yes in the Confirm Rewrite notice to append the data in the selected file.
5. Click OK in the Select Columns and File or Export Details window.
The new report data is combined with the existing report.

Combining two 1. Click Exports → Combine PDFs.

existing PDF files The Combine PDF Exports window opens. (Figure 476)

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Figure 476 Combine PDF Exports window

2. Click Add Files….

The Select PDF Files to combine window opens. (Figure 477)

Figure 477 Select PDF Files to Combine window

3. Select the PDF files to combine, then click Open in the Select PDF Files window.
The selected files are displayed in the Select Input Files list.
You can use the Remove File button to remove a selected input file.
Click and drag on a file in the list to change the order of data in the Combined
PDF.
4. Click the Select Output File button.

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The Save As window opens. (Figure 478)

Figure 478 Save As window

5. Enter a file name for the combined PDF file, then click Save in the Save As
window.
You are returned to the Combine PDF Exports window.
6. Click OK.
Your selected PDFs are combined.

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Exporting with ClinVar

The ClinVar export enables exporting of copy number data using the ClinVar Full
Template for easy submission directly to ClinVar. A ClinVar Submission Profile must
be created to use this Export. For details on the template, go to:
www.ncbi.nlm.nih.gov/clinvar/docs/submit/

IMPORTANT! ChAS is a research use only application and any submission to ClinVar is the
responsibility of the submitter.

All fields exported into the ClinVar submission template are selected and defined by the user.
Standard ClinVar nomenclature is provided for required submission fields and can be customized
as shown in "Adding vocabulary content" on page 435.

Creating a ClinVar 1. Click Preferences → Edit User Configuration.

submission The User Configuration window appears.
profile
2. Select the Exports tab, then select the ClinVar tab. (Figure 479)

Figure 479 ClinVar window tab

3. In ClinVar Submission Info pane, click the New button to create a new
submission profile.
An Edit Profile window appears.
4. Complete all the appropriate fields. Fields with an * are required by ClinVar.
5. Click OK to save the profile.
6. Optional: To create additional ClinVar profiles, repeat steps 3-5

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Editing an 1. Highlight the profile name in the ClinVar Submission Info list box that is to be
existing ClinVar modified.
profile 2. In ClinVar Submission Info pane, click the Edit button.
3. Edit the appropriate fields.
4. Click OK to save your changes.

Deleting a profile 1. Highlight the profile name in the ClinVar Submission Info list box you want to
delete.
2. Click the Delete button.
3. Click OK to confirm the profile deletion, or click Cancel to keep the profile.

Adding By default, recommended ClinVar vocabularies are stored for certain required fields,
vocabulary but additional terms can be added to any field.
content 1. Click Preferences → Edit User Configuration.
The User Configuration window appears.
2. Click the Exports tab, then click the ClinVar tab.
3. Select a category you want to add a term(s) to, then use the text field (Figure 479)
to enter the additional term(s).
4. From the ClinVar vocabularies drop-down, select the category that you want to
add a term(s) to.
5. Use the text field (at the bottom) to enter the additional term(s).
6. Click the Add button to add the term to the category’s list.

Removing 1. From the ClinVar vocabularies drop-down list, select a category that contains the
vocabulary term you want to remove.
content 2. Highlight the term, then click Remove.

Exporting in There are certain fields that are required before uploading to ClinVar. It is
ClinVar format recommended you use the ClinVar Table State in the Segments Table to expose all
required fields. To use the ClinVar Table State, refer to "Saved table states" on page
332.
1. In the Segments Table, apply the ClinVar Table State.
2. Select the segments to be exported using the Use in Export check box.
3. Fill in all columns for the selected segments, as all columns in the ClinVar Table
State are required before you can upload to Clinvar.
4. In the Exports Menu, select ClinVar Export.
A browse window appears.
5. Select a location to save the export, then use the File Name text box to name the
export, then click OK.
A Submission Info/Segment Data window appears.
6. Select the ClinVar Profile you want to use for this export.

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7. Optional: If you want to add any additional comments to the export, click on the
Segment Data tab to enter them within this tab.
8. Click OK to export.

Note: You can open the ClinVar export in Excel to add information to the optional
fields. Opening the ClinVar export from ChAS, auto-populates all currently required
ClinVar fields.

Table 20 Variant tab: Auto-populated columns into the ClinVar submission template (all other optional columns are blank upon
export).

Auto-populated column Description

Chromosome Populated from Segment Table (Chromosome)

Variant type Populated from Segment Table (Gain/Loss)

Variant length Populated by ClinVar upon submission

Copy Number Populated from Segment Table (Gain/Loss)

Variation identifiers Populated using OMIM track

Condition category Populated from ClinVar Vocabulary

Clinical significance Populated from Segment Table (Call)

Date last evaluated Uses date of export unless otherwise specified on the Submission Info window before
exporting.

Comment on clinical Populated from Segment Table (Segment Interpretation)

significance

Collection method Populated from ClinVar Vocabulary

Allele origin Populated from ClinVar Vocabulary

Affected status Populated from ClinVar Vocabulary

Structural variant method/ SNP Array

analysis type

Platform type Microarray

Platform name Populated based on the Microarray used

Software name and version Chromosome Analysis Suite 4.4

Table 21 Case Data tab: Auto-populated columns into the ClinVar submission template (all other optional columns are blank
upon export).

Auto-populated column Description

##Linking ID Populated from Segment Table (Full Location)

Collection method Populated from ClinVar Vocabulary

Allele origin Populated from ClinVar Vocabulary

Affected status Populated from ClinVar Vocabulary

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Table 21 Case Data tab: Auto-populated columns into the ClinVar submission template (all other optional columns are blank
upon export).

Auto-populated column Description

Structural variant method/ SNP Array

analysis type

Clinical Features Populated from Sample Properties (Phenotype)

Tissue Populated from Sample Properties (Sample Type)

Sex Populated from Gender determination

Platform type Microarray

Platform name Populated based on the Microarray used

Software name and version Chromosome Analysis Suite 4.4

Exporting a deletion log

The user, time, filename and reason why a file is deleted or republished to a ChAS
database can be exported.
1. Click ChAS DB → Download Deletion Log (Figure 480)

Figure 480 Download Deletion Log

Your default Internet browser opens.

2. Enter your ChAS Database credentials, as you normally would.
3. Depending on your Internet browser, you may be prompted to either download
the file or save it. To save it, click File → Save As.
4. To view your exported log file, open it in Excel. (Figure 481)

Figure 481 File viewed in MS Excel example

Deletion Logs can also be exported from the ChAS DB Tools Maintenance Page.
See "Downloading deletion logs" on page 454.

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20
ChAS provides many options for customizing the display of data and annotations.
The User Profiles and Named Settings functions enable you to save your analysis and
display settings.

Types of settings
ChAS provides two ways to store setup information. User profiles and Named
settings. Each way works differently and performs different functions.

User profiles A ChAS Browser User Profile stores your selections for various display settings as
they were when the software was last shut down while using that user profile.
A new user profile can be created or selected only when starting the software.
The user profile saves the following display settings:
 Screen size, displayed tabs, and sizing of display areas
 The views displayed in ChAS, and the size of the display panes
 Available Named Settings: Different users can have different lists of named
settings to choose from
 Name of the currently selected named setting
 Copies of the user’s custom (not shared) named settings
 Data Display Configurations
 Region information files selected for CytoRegions and Overlap Map
 Which types of graph and segment data are turned on or off
 Display options for graph data (height, grid, values, etc.)
 Chromosome and area displayed.
 Selected Reference Annotation database (ChAS Browser NetAffx Genomic
Annotations file)
 Loaded AED and BED files
 The files and Reference Annotations (Genes, DGV, etc.) that are checked or
unchecked
 Custom color rules

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Named settings A Named Setting stores the user’s choices for:
 Which types of graph and segment data are turned on or off
 Segment Filter Settings
 Restricted Mode on/off
The Named Setting doesn’t save a particular CytoRegion file, but does inform
you if no file is selected when you select a setting with restricted mode on.
It is possible to apply a Named Setting with restricted mode using a different
CytoRegion file than was selected for the initial creation of the setting.
You can switch between different Named Settings in the same user profile to look at
different types of data.
ChAS provides pre-configured (shared) Named Settings indicated by the icon as
described in the table below. These named settings cannot be deleted.

Named Setting Genome Segment CytoRegion Data Types

Filters Segment Filters

Standard Gain: Gain: Gain

Marker Count = 50 Marker Count = 50 Loss
Size (kbp) = 400; Size (kbp) = 400 GainMosaic
Loss: Loss: LossMosaic
Marker Count = 50 Marker Count = 50 Copy Number State
Size (kbp) = 400 Size (kbp) = 400 Weighted Log2 Ratio
Allele Peaks
Allele Difference

High Resolution Gain: Gain: Gain

Marker Count = 50 Marker Count = 25 Loss
Size (kbp) = 100; Size (kbp) = 50 GainMosaic
Loss: Loss: LossMosaic
Marker Count = 50 Marker Count = 25 Copy Number State
Size (kbp) = 100 Size (kbp) = 50 Weighted Log2 Ratio

LOH only LOH: LOH: LOH

(3Mb and 50 SNPs) Marker Count = 50 Marker Count = 50 Genotype Calls
Size (kbp) = 3000 Size (kbp) = 3000 Allele Peaks
Allele Difference

Differential Gains and Gain: Gain: Gain

Losses Marker Count = 50 Marker Count = 25 Loss
Size (kbp) = 400; Size (kbp) = 50 GainMosaic
Loss: Loss: LossMosaic
Marker Count = 50 Marker Count = 25 Copy Number State
Size (kbp) = 100 Size (kbp) = 50 Weighted Log2 Ratio

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Named Setting Genome Segment CytoRegion Data Types

Filters Segment Filters

OncoScan Defaults 0 0 0

XON-Level 1 XON Level: 0 XON Region Gain,

Level 1 = On XON Region Loss,
Level 2-4 = Off LOH Segments, Log2
XON Gain/Loss Marker: Ratio, Smooth Signal,
Count = 0 Allelic Difference
Size (kbp) = 0

Creating and using user profiles

You can only select or create user profiles upon starting ChAS.
1. Double-click on the ChAS icon on the desktop; or
From the Windows Start Menu, select Programs → Thermo Fisher Scientific
→ Chromosome Analysis Suite → Chromosome Analysis Suite.
The ChAS Splash Screen and the Select User window open. (Figure 482)

Figure 482 Select User window

2. Click Create New in the Select User window.

The Create New User window opens. (Figure 483)

Figure 483 Create New User window

3. Enter a name for the new profile in the User ID field.

4. Click OK in the Create New User window.

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The new user appears in the drop-down User list in the Select User window.
(Figure 484)

Figure 484 Select User window with new user

profile

5. Select the new user, then click OK.

Any changes you make to the setup of the software that is listed in "User profiles"
on page 438 will be saved when you shut down the software and used the next
time the software is opened with this user profile.

Deleting a user 1. Go to the Windows folder where the user profiles are stored and delete the folder
profile with the profile name you want to delete.
You can see the location of the folder in the About window, as described in
"Analysis file locations in Windows 10" on page 26.

Creating and using named settings

You can save a snapshot of your favorite settings as a Named Setting. To apply a
particular Named Setting to the active data (check marked in the Files List), make a
selection from the Named Setting drop-down list. Some pre-configured Shared
Named Settings may be available for use by all users. Only an administrator can add
or remove Shared Named Settings, but any user can apply them to their data.

Saving a named 1. Set the display data settings as desired.

setting These can include:
 Which graphs and segment types are turned on or off
 Segment Filter Settings
 Restricted mode on/off
2. From the Preferences menu, select Save Named Setting.

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The Setting Name window opens. (Figure 485)

Figure 485 Named Setting List

3. Enter a name for the setting you want to create, then click OK.
The setting is saved and appears in the Named Setting drop-down list.
(Figure 486)

Figure 486 Named Setting drop-down list

Note: The Named Setting saves the settings at the time it was created. Subsequent
changes to the settings will not be saved in the Named Setting.

Selecting a 1. From the Named Setting drop-down list, select the setting. (Figure 487)
named setting
Figure 487 Named Setting drop-
down list

Alternatively, from the Preference menu, select Apply Named Setting…

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The Select Named Setting window opens. (Figure 488)

Figure 488 Select Named Setting window

2. Select the Named Setting from the drop-down list, then click OK.
The selected setting is applied. Note: A Named Setting is not modified by any
changes that you make to the settings in ChAS. If you want to keep a copy of your
new settings, you will need to save them as a new Named Setting.

Deleting a named 1. From the Preferences menu, select Delete Named Setting.
setting The Delete Setting window opens. (Figure 489) Note: Shared Named Settings
(the icon in the Named Setting list) do not appear in the Delete Setting drop-
down list. Users cannot delete or modify a shared Named Setting.

Figure 489 Delete Setting window

2. Select the setting you want to delete from the drop-down list, then click OK.
The setting is deleted.

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Exporting and importing preferences 20

Exporting and importing preferences

Preferences functions enable you to transfer most of the settings in a User Profile between
one system and another.
Note: If you import “exported” preferences that reference a Shared Named Setting which
no longer exists, such as a Shared Named Setting from ChAS 1.0.1 or ChAS 1.1, the profile
will be changed to point to the default Shared Name Setting.

Exporting 1. From the Preferences menu, select Export Preferences…

preferences The Select Directory to export preferences to window opens. (Figure 490)

Figure 490 Select Directory to export preferences to

2. Use the navigation features of the window to select or create a directory for the
preferences. Note: The software creates a folder named “preferences” in the
directory you select or create. If you select a directory that already contains a
“preferences” folder, it will be overwritten. When you want to import the preferences,
select the directory that contains the “preferences” folder that is indicated by the
icon.

3. Click Select Directory.

If the directory already contains a “preferences” folder, the Overwrite notice appears.
(Figure 491)

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Figure 491 Overwrite notice

4. Click Yes to export the preference files to the directory that you selected.
You can then transfer the preferences to another user profile or system.

Importing 1. From the Preferences menu, select Import Preferences…

preferences The Select Folder to import preferences from window opens. (Figure 492)

Figure 492 Select Folder to import preferences from

Directory that contains the

“preferences” folder

2. Use the navigation features of the window to select the directory that the
preferences were exported to (directories that contain a “preferences” folder are
indicated by the icon.)
3. Click Open to import the preference files.
If you selected a directory that doesn’t contain the “preferences” folder, the
following notice appears. (Figure 493)

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Figure 493 Error notice

Click OK and repeat steps 1 through 3, selecting the correct folder.

The Restart notice appears. (Figure 494)

Figure 494 Restart notice

Note: The imported preferences will not be applied until you restart ChAS.

Importing External websites may update their links from time to time. To remedy this, a feature
hyperlinks as been added to update an outdated link(s) within ChAS.
1. Click Preferences → Import Hyperlinks.
The Load Hyperlinks Configuration window opens.
2. Navigate to your updated hyperlinks (.chaslink) file, click to highlight it, then click
Select File.
3. Restart the ChAS Browser to apply the link update(s).
Note: For .chaslink file help, contact Technical Support.

Configuring the The HTTP service may enable external applications to interact with the ChAS Browser.
HTTP service By default, this service is off. Please contact Technical Support before activating this
feature.
1. Click Preferences → Configure HTTP Service.
The Configure HTTP Service window opens.
2. Click the check box to enable the service, then enter the designated Port
number.
3. Close the window.
The service and Port are now activated.

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21
Connecting to a remote ChAS DB server
The ChAS v4.4 browser cannot point to a ChAS v3.0/3.1/3.2/3.3/4.0/4.1/4.2/4.2.1/4.3
database.
You must upgrade the ChAS v3.0/3.1/3.2/3.3/4.0/4.1/4.2/4.2.1 database to ChAS
v4.4 through the Backup and Restore process. See "Backing up a database" on page
451 and "Restoring a database" on page 451.
1. From the Preferences drop-down menu, click Edit Application
Configuration…
The Configuration window appears.
2. Click the Server tab.
The Server window/tab appears. (Figure 495)
3. Type in the name or IP address of the computer/server name that you would like
to connect to in the Hostname or IP Address text field or contact your IT
Department for help completing this form.
Note: Up to three Hostnames/IP Addresses can be saved/stored.

Figure 495 Server window/tab

4. Click OK.

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Accessing the ChAS DB server tools 21
If a connection to the ChAS DB cannot be established or the server/computer
containing ChAS DB is not turned on, the following message appears
(Figure 496). Please check the name/IP address and make sure the server/
computer is turned on.

Figure 496 Error message

Accessing the ChAS DB server tools

Note: The screen captures used in this chapter may vary depending on which
Browser you are using.
1. From the Chas DB drop-down menu, click to select Database Tools.
(Figure 498)

Figure 497 Select User window

The following web page appears. (Figure 498)

IMPORTANT! The ChAS Server Home Page requires an active Internet connection, requires a
browser (Chrome and Internet Explorer v11 are recommended). Also, if you are using the local
ChAS DB, an active Internet connection is not required.

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Accessing the ChAS DB server tools 21

Figure 498 Sign in to ChAS window

2. Log in using the installer’s factory default Username: admin and Password:
admin. After logging in, it is recommended new users go to "Administration" on
page 456 to create a New User(s) and/or edit User(s) roles.
Note: Make sure you look in the URL field to identify which ChAS database the
ChAS Database Tools is accessing.
The ChAS DB Home Page appears. (Figure 499)

Figure 499 ChAS DB Home Page

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Status page 21

Status page
Use this page to view how many samples and segments are in the Database.
(Figure 500)

Figure 500 ChAS DB Status Page

Maintenance
Use this page to perform a backup, restore, and database clean up. (Figure 501)

Figure 501 ChAS DB - Maintenance

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 Chapter 21 Database tools
Maintenance 21
Backing up a 1. Click Backup Database, then click the Backup button.
database A backup is automatically generated and is stored in the Affymetrix directory shown
in Figure 502.
(\Affymetrix\ChAS\PostgreSQL\Backups\ChASDB_yyMMdd_HHmmss.backup)
Note: A backup is automatically done whenever a Restore operation is performed.

IMPORTANT! It is strongly recommended that you perform scheduled routine backups of the
database.

Figure 502 ChAS DB - Backup Database

Note: The ChAS installer creates a disabled Windows Task that automatically backs up
the ChASDB database on a weekly basis once it is enabled.

Restoring a Note: Restoring a backup file created in ChAS 3.0/3.1/3.2/3.3/4.0 automatically upgrades
database it to ChAS 4.1.
1. Click Restore Database, then click the Choose File button. (Figure 503)
An Explorer window opens.
2. Navigate to the location where your ChAS DB was last backed up, then click Open.
By default, a backup of your current database is stored/resides here:
\\Affymetrix\ChAS\PostgreSQL\Backups
3. Click Restore to start the restore process.

IMPORTANT! Do not leave this page once choosing the Restore button until you see the
message that the database has been successfully restored. Also, once the restore process has
successfully completed, you must click ChAS DB → Refresh ChAS DB Data to view the data in the
database using the ChAS Browser.

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Merging ChAS databases 21

Figure 503 ChAS DB Home Page

IMPORTANT! After restoring the database, you must click ChAS DB → Refresh ChAS DB data
to view the newly restored data from the database.

Merging ChAS databases

When merging the contents of two ChAS databases into a single database, one database
should be restored into ChAS and the other database must exist as a backup.db file.

When merging the segments from two databases, if a duplicate entry is found then the
merge keeps the entry for the database currently active in ChAS. The duplicate from the
backup.db is skipped.

Merging two
ChAS databases
IMPORTANT! The two ChAS databases to be merged, must be from the same version of ChAS.
Also, the library files for CytoScan HD and OncoScan CNV Plus must be present in your Library
folder before merging the two databases.

Make sure one of the ChAS databases is restored into ChAS (for details on how to Restore
a ChAS DB, see page "Restoring a database" on page 451). Since any duplicate segments
between the databases will keep the copy from the actively restored database, make sure
the database with the more complete content is the one that is actively restored in ChAS.
1. From the ChAS browser, go to ChAS DB → Database Tools.
If prompted, log into the ChAS database as you normally would.

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Merging ChAS databases 21
2. Click on the Maintenance link.
3. Click on the Merge database link.
4. Click the Browse button to navigate to the backup.db file you want to merge with
the current database.
5. Click Merge.

Merging an older If you want to merge a database (from an older version of ChAS) with a current ChAS 4.0
ChAS database database, perform these steps:
1. Backup your current ChAS 4.0 database.
2. Restore the database from (e.g.) ChAS 3.1. See "Restoring a database" on page 451.
During the restore process, the older ChAS database is automatically upgraded and
is now compatible with ChAS 4.0.
3. Backup the 3.1 database you just restored.
4. Restore the ChAS 4.0 database you backed up in Step 1.
Note: If the databases to be merged contain duplicate entries, the copy that is in the
currently restored database will be kept. The entry from the backup.db that is being
merged will be skipped.
5. From the ChAS browser, go to ChAS DB → Database Tools.
If prompted, log into the ChAS database as you normally would.
6. Click on the Maintenance link.
7. Click on the Merge database link.
8. Click the Browse button to navigate to the backup.db file you want to merge with
the current database.
9. Click Merge.

Cleaning up a ChAS DB will automatically run re-indexing scripts to maintain optimal performance. You
database can also run these scripts manually if desired.
Note: You must have a Manager or an Admin role to clean up a database.
1. Click the Clean up database button (Figure 504) to run the Vacuum Analyze and
Reindex Database optimization process.

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 Chapter 21 Database tools
Downloading deletion logs 21

Figure 504 ChAS DB - Cleanup Database

Downloading deletion logs

Use this feature to export a list of filenames that were deleted from ChAS DB.
1. Click the Download Log of Deleted Files
2. If asked, provide your ChAS DB Username and Password.
3. Save the genome-model log file.
4. Open with Microsoft Excel for easier viewing.

Creating a blank ChAS DB

Use this feature to create a blank hg19 or hg38 ChAS DB. Make sure you backup your
previous database prior to creating an empty ChAS DB, as the database will be erased
and recreated.
Note: xxCHP files are only compatible with a ChAS DB of the same genome version.
1. Back up the current ChAS DB.
2. Click on the Reset to Empty (hg19 or hg38) ChAS DB
3. Use the drop-down to select the genome version for your new database.
(Figure 505)

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Deidentifying Files 21

Figure 505 ChAS DB - Cleanup Database

4. Check the box to have a backup of the current ChAS DB before the database is
deleted and an empty DB is created.
5. Click Delete all data and reset database.

Deidentifying Files
Deidentifying files will remove potentially sensitive information from the ChAS DB. By
running Deidentification, the file names stored in the ChAS DB will be replaced by an
alpha numeric ID.
Note: If you have included sensitive information in custom database fields, this
process will not remove that information.
1. Click on De-identify Files.
2. (Optional) Create a backup of the database to preserve the original content, then
click the Start De-identification button to replace the file names in your ChAS
Database.

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Administration 21

Administration
Note: You must have an Admin role to perform Administration functions. Log files for
the ChAS database can be found in: \ProgramData\Affymetrix\ChAS\Log
1. Click Administration.
The following window appears: (Figure 506)

Figure 506 ChAS DB - Administration

2. Click Edit Users.

The following window appears: (Figure 507)

Figure 507 ChAS DB - Administration (Edit Users)

Do one of the following:

 Click the Edit button to edit a current Username.
 Click Add User to add (grant privileges to) a new ChAS DB user.

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Administration 21
Permission Guidelines
 User Role has permission to query the database, edit segments, add segment and
sample annotations, but does not have permission to upload data to the database,
run backup/restore, maintenance or edit users.
 Manager Role has permission to query the database, edit segments, add segment
and sample annotations, upload data to the database, run backup/restore,
maintenance, but does not have permission to edit users.
 Admin Role has permissions to run all functions in ChAS Browser and ChAS DB.

Using a shared
ChAS database
while off-line
IMPORTANT! If your Windows Firewall is enabled during the installation of ChAS and you want
to Backup the ChAS Database and Restore it to your local ChAS DB, a message may appear
indicating that you cannot connect to the shared folder. If this message appears, contact your IT
department for help in allowing file sharing through the Windows Firewall.

Working off-line using a ChAS database that resides on a shared server

1. Connect to the shared ChAS DB server click Preferences → Edit Application
Configuration, ChAS DB server tab. For details on connecting to another ChAS
DB, see "Connecting to a remote ChAS DB server" on page 447.
2. Follow the procedure to perform a back up, locate the back up, then copy it to
your local computer.
3. Return to Preferences → Edit Application Configuration, ChAS DB server
tab, then click on the default to redirect to your local ChAS DB server.
See "Restoring a database" on page 451 for instructions on how to restore the back
up database - you just copied from the server.

IMPORTANT! You must have a Manager or Admin role and make sure you log back into the local
host before restoring your computer. While performing a restore from a backup of a shared server,
the roles associated with the shared server are displayed, therefore any roles that were created on
the local server are replaced by those used on the shared server (until local host ChAS DB is
restored again).

Publishing data you have analyzed in off-line mode to the shared ChAS DB
server
1. Log back into the shared ChAS DB server. To do this. click Preferences → Edit
Application Configuration, ChAS DB server tab, then enter the server name/IP
address.
2. Click OK.
Note: After you are logged into the shared ChAS DB server, publish the samples to
the database as you normally would. See "Publishing data to the database" on page
406. If a xxCHP file has been previously Published to the database, you will receive a
warning indicating this sample already exists in the database. You can choose to
overwrite the existing information or cancel to keep the existing information.

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Remapping a hg19 ChAS DB to hg38 21

Remapping a hg19 ChAS DB to hg38

A ChAS DB populated with data from hg19 analyses can be remapped to hg38
coordinates using the ChAS DB Remapper feature.
The ChAS DB Remapper maps the segments from your hg19 ChAS DB to the hg38
genome. All segments in ChAS DB start and end with a marker currently mapped in
hg19. The Remapper takes the probe locations for all markers in the segment from
hg19 and remaps them to hg38. It locates the best representation of the remapped
segment in hg38 by taking into account the number of additional markers in the
remapped segment, as well as the number of markers removed from the original
segment.
Remap confidence = (originalMarkerCount - addedCount - 2*removedCount)/
originalMarkerCount
For remapped segment definitions in a ChAS DB, see the table on page 395.
Segments with a Remap confidence >0.75 are remapped to the hg38 ChAS DB. The
Remapper makes a copy of the database prior to remapping. However, always make
a backup or copy of the ChAS DB that you would like to remap for safe keeping.
1. Click on ChAS DB -→ ChAS DB Remapper.
2. Click the Browse button (Figure 508) to select a ChAS db.backup to be
remapped to hg38.

Figure 508 ChAS DB Remapper

3. Click Start.
Note: Depending on the size of the ChAS DB.backup to be remapped, this
process may take several minutes.
The ChAS Remapper window appears. (Figure 509)

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Remapping a hg19 ChAS DB to hg38 21

Figure 509 ChAS DB - Cleanup Database

The following files are generated in the same folder as your original ChAS DB select
to remap:
 ChAS DB.hg38.backup - this backup can be restored as the active ChAS DB for
querying within the Browser.
 A TXT file listing all original segments - provides a text file of the original segment
information and the remapped segment information along with success or fail
criteria.
 A TXT file listing the segments that failed to remap to hg38 - provides s text file of
the original segments that did not remap to the new genome build.

For more information on viewing a remapped database, see "Additional segment

intersection information" on page 397.

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 ChAS Database Loader (CDL)
22
CDL is now part of the ChAS Browser. CDL enables uploading of xxCHP files from any
previous (including the current) version of ChAS. You may upload up to 500 xxCHP
files at one time (as long as they are all analyzed from the same genome build).
CDL supports the following array types:
 Genomewide SNP 6
 CytoScan 750K
 CytoScan HD
 CytoScan Optima
 CytoScan XON
 CytoScan HTCMA
 OncoScan CNV Plus
 OncoScan CNV
 Cytogenetics 2.7M

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 Chapter 22 ChAS Database Loader (CDL)
Starting CDL 22

Starting CDL
1. Click ChASDB → ChAS Database Loader
The ChAS Database Loader window appears. (Figure 510)

Figure 510 Main CDL window

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 Chapter 22 ChAS Database Loader (CDL)
Adding files to CDL 22

Adding files to CDL

1. From the main CDL window, click Files → Add Files (Figure 511)

Figure 511 Add Files

An Explorer window appears. (Figure 512)

Figure 512 Add Files

By default, the Files of Type is set to All Supported Types. (Figure 511) If you
want to view a specific supported file type, click the drop-down, then select the
file extension you want to display.
2. Single click, Ctrl click, Shift click or Ctrl a (to select multiple files).
3. Click Open.
Your selected files now appear in CDL’s main window. (Figure 514)
Repeat steps 1-3 if you want to add files (up to 500) from different saved
locations.

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Adding files to CDL 22
Sample info 1. If you want to view the properties of the files displayed in the Explorer window,
click .

The Sample Info window appears. (Figure 513)

Figure 513 Sample Info window

2. Single click, Ctrl click, Shift click or Ctrl a (to select multiple files).
3. Click Open Selected Files.
Your selected files now appear in CDL’s main window.
Note: A special icon is used to indicate a CHPCAR or “sidecar” file, as shown in
Figure 514. For more information on sidecar files, "Editing segment data
overview" on page 223.

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Adding files to CDL 22

Figure 514 Main CDL window populated

IMPORTANT! File level properties are optional fields that are available to CHP files analyzed in
ChAS 3.0 or higher. Any file level properties entered are stored in the CHPCAR file, these properties
will not populate in the CDL window. However, if those properties were entered for a CHP file and
are contained in the CHPCAR file, they will be published to the database. Entries in a CHPCAR file
supersede entries in the text file. File level properties for your xxCHP files can be added directly to
the database after publishing has completed. For more details, see "Interacting with the ChAS
database" on page 390.

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Publishing to the ChAS database 22
Adding files to be Files can be loaded into CDL using a tab-delimited text file. Place the file names,
published using a including their paths in the first column, then label the first column header CHP File
text file as shown in Figure 515.

Figure 515 Tab-delimited text file Header 1 example

1. Click on Import File List or click Files → Import file list.

An Explorer window appears.
2. Navigate to, then select the tab-delimited text file containing path to the xxCHP
files to be loaded into CDL.

Publishing to the ChAS database

IMPORTANT! Before you use CDL to publish your files, it is highly recommended you backup
your ChAS database first. For instructions on how to access and backup your database, refer to
Chapter 21, "Database tools" on page 447. Also, xxCHP files can ONLY be published to a ChAS
DB of the same genome version assignment.

Testing your Before publishing, you may want to test your ChAS database connection. To do this:
connection 1. Click ChAS DB → ChAS Database Loader
(optional)
2. Click Tools → Test Connection
A message appears if there is a successful connection to the ChAS database.

Verifying the 1. From the ChAS Browser, click the Preferences drop-down menu, then select
ChAS database Edit Application Configuration…
The Configuration window appears.
2. Click the Server tab.
The Server window/tab appears. (Figure 516)

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Publishing to the ChAS database 22

Figure 516 Server window/tab

3. Verify the ChAS DB you are publishing to is correct, then click OK.

Before publishing Before publishing files, you must check the Genome dialog box (Figure 517) to make sure
files your desired filter settings and data types are enabled.

Figure 517 Genome dialog box

Note: QC thresholds and Smooth/Joining settings in the ChAS Browser will be used when
publishing xxCHP files using CDL. To use different QC thresholds and/or Smoothing and
Joining settings, see "Setting QC parameters in the ChAS browser" on page 133.

Changing 1. Click on the Filter icon (or click Files → Segments Filters).
segment filters The Segments Filters window opens. (Figure 518)
(optional)

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Publishing to the ChAS database 22

Figure 518 Segments Filters window

2. Update the appropriate filters using the provided check boxes, text boxes and
sliders.
3. Click X to save your changes and close the window.

Managing data 1. Use the Segments Filters window (Figure 518) to click the check box of the data
types (optional) type(s) you want to publish.
2. Click X to save your changes and close the window
3. Review the Genome dialog window (Figure 517) again to make sure your data
types to be published are displayed.

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Publishing to the ChAS database 22
Publishing your 1. Check your table before publishing, as all displayed files are published. Note: If
files there are specific files you do not want published, single click, Ctrl click, or Shift
Click to highlight them, click the Clear drop-down menu, then click Clear
Selected. (Figure 519)

Figure 519 Selecting files not to publish

IMPORTANT! You must have ChAS DB Manager or Admin privileges before you can publish. For
information on setting up ChAS DB role assignments, see "Administration" on page 456.

2. Click .
A Publish? window appears. (Figure 520)

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Publishing to the ChAS database 22

Figure 520 Publish? window

3. Acknowledge the message, click to check its check box, then click OK.
4. An Overwrite? message may appear. (Figure 521) Click the appropriate button
to continue.

Figure 521 Overwrite? message

The publishing process begins. (Figure 522)

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Publishing to the ChAS database 22

Figure 522 Publishing in progress example

To pause the publishing process, click . While in pause mode, you can
add more files to the table, as described in "Adding files to CDL" on page 462.
After the publishing process is complete, each Status column is marked with a result
icon.

 = The file was successfully published to the ChAS database.

 = The file was skipped over and not published, because it was already found
in the database or it did not meet the assigned QC thresholds.

 = The file failed and was not published.

Note: Refer to the table’s Status Message column (Figure 522) for details regarding a
skipped or failed file.

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Clearing Table Data 22

Clearing Table Data

Clear Published After publishing, click Clear → Clear Published to remove all files that successfully
published.
After clicking Clear Published, files with a Skipped or Failed status remain in the
table. Click Export properties... to export these files for further investigation.

Clear All Click Clear → Clear All to remove all files from the table.

Figure 523 Clear

table data drop-down
menu

Closing CDL
1. Click Close CDL or click File → Close CDL.

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 Analysis parameters
A
Analysis parameters for single sample analysis
 For information on CytoScan algorithm parameters and their values, go to:
http://media.affymetrix.com/support/developer/powertools/changelog/apt-
copynumber-cyto.html

Reference model file creation

Reference Model File Creation is done with fixed parameters in the Reference Creation
workflow.
It is essential that the input for Reference Model Creation include at least 44 total CEL
files and at least 20 males and 20 females.
There are no user-adjustable parameters for the Reference Model File Creation
 For information on CytoScan algorithm parameters and their values, go to:
http://media.affymetrix.com/support/developer/powertools/changelog/apt-
copynumber-cyto.html

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 AED file format
B
Affymetrix Extensible Data (AED) files contain data that annotate positions on a
genome. AED allows custom, typed fields, can be edited in the ChAS Browser’s AED
Editor feature ("Viewing and batch editing AED file contents" on page 306), and
supports internationalization.
This appendix covers the formatting and use of Affymetrix Extensible Data (AED) files
with ChAS.
 "AED file description"
 "Property name elements"
 "Compatibility"
 "References"
AED files can be created by Chromosome Analysis Suite (ChAS) and loaded into ChAS
as region information files to:
 Define CytoRegion and Overlap Map regions
 Record information of interest about features in the genome
AED files can be produced and edited in:
 ChAS (Recommended)
 Text-editing software (Not Recommended)
 Spreadsheet software such as Microsoft Excel (Not Recommended)

AED file description

An AED file contains a list of annotations, descriptions of features on a biological
sequence such as a chromosome. This description is comprised of several
properties—either properties defined by this specification, such as the annotation
start and stop positions; or properties defined by users or third parties.
An AED file may also provide metadata which describe the particular group of
annotations in the file as a whole, such as the author of the file or the genome
assembly for which the annotations were produced.
Properties and metadata have certain types which define the semantics and constrain
the range of values they may have. Properties should begin with a lowercase letter,
while types should begin with an uppercase letter.
The AED file format uses a tab-delimited text format with the *.aed file extension. It
uses Unicode character sets and has the following components: (Figure 524)

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 Appendix B AED file format
AED file description B

Figure 524 AED file in Excel with required header fields for properties and metadata

Header Row
Metadata

Annotations

IMPORTANT! AED supports only Unicode, which can be stored in one of various encodings
(charsets such as UTF-8, UTF-16LE, and UTF-16BE). The AED file indicates the charset with an
initial Byte Order mark (BOM). An AED file with no initial BOM is not recommended. An AED file
that does not begin with a BOM will be interpreted as containing only the ASCII subset of Unicode,
resulting in an error if any characters lie outside the range of ASCII. (With no indication of a charset,
it is not possible to determine which non-ASCII characters were intended. File formats such as
BED that make assumptions about non-ASCII characters have the potential to corrupt data when
transported between systems.)

 "Header row": Names the properties that can be used in the annotations
 "Metadata records" on page 475 Optional: Provides information about the AED
file itself and the group of annotations it contains.
 "Annotations Rows" on page 476: The annotation row displays values for the
properties listed in the header rows (for each feature that is annotated).

Header row The header row of an AED file is a tab-delimited list of the properties that can be used
to describe a region of the genome.
Each AED file header represents a property. Normal records in the file represent
annotations, and the record fields represent annotation properties. Special metadata
records represent metadata properties for the file as a whole, rather than for a
particular annotation.
A property name has the following format:
namespacePrefix:propertyIdentifier(namespacePrefix:TypeIdentifier)
 namespacePrefix
• A namespacePrefix is optional. It assigns the property or type to a vocabulary
grouping called a namespace. The lack of a namespace prefix indicates that the
property has been created by a user and is not part of the formal AED
specification.
The lack of a namespacePrefix indicates that the property is in the default/
custom namespace; this namespace enables users to add properties to an
annotation just by adding new columns, such as foo(aed:String) or
bar(aed:Integer).

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 Appendix B AED file format
AED file description B
 propertyIdentifier
• The propertyIdentifier names the property that the values in the column are for.
Each annotation can be assigned an unlimited number of properties. Each property
has a certain meaning, and this meaning is usually defined by the documentation for
the property namespace. The purpose of the AED file is to indicate values for certain
properties for each annotation. For example, by use of the aed:name(aed:String)
column, the AED file indicates a string value to be used as the name each annotation).
 TypeIdentifier
• The TypeIdentifier (always capitalized) specifies the data type of the value to be used
for the property in the AED file. Examples include:
– bio:sequence(aed:String)
– aed:value(aed:String)
– medianMarkerDistance(aed:Integer)
 Required Fields
• Fields may appear in any order, except that the following predefined fields must
always appear in the following order at the beginning of the header:
– bio:sequence(aed:String)
– bio:start(aed:Integer)
– bio:end(aed:Integer)
– aed:name(aed:String)
– aed:value(aed:String) Optional: You must use this property if you are including
metadata information in the file.

IMPORTANT! ChAS verifies the property types when importing an AED file. If a file header
specifies a known property, but includes an incorrect data type for the property, the file will not be
loaded. For example, “fish:score” is a known property with “whole number” data type. An AED file
header that specifies “fish:score(aed:String)” would be treated as an error.

Metadata records Some records, instead of providing annotation about a location on a genome assembly,
provide metadata information about the AED file itself (Figure 525). These metadata
records are identified by the presence of an empty string in the bio:sequence field. The
bio:start and bio:end fields must also be left blank for metadata records. If there are
metadata records present, the aed:value field is required.
In a metadata record, the value in the aed:name field is interpreted as the name of the
metadata property, with type identification rules identical to those of the header fields. The
value in the aed:value field is interpreted as the value of the metadata property, and the
characters that make up its string value must follow the lexical and semantic rules
specified by the type indicated in the aed:name field.

Figure 525 Metadata entries

Metadata property names Metadata property values

Blanks for bio:sequence and other properties

All other metadata record fields should be blank.

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 Appendix B AED file format
Property name elements B
Annotations The rows below the Metadata properties are the annotations. Each row is a tab-
Rows delimited list of values. Each value must have the correct data type, as described in
the property name for that value.

Property name elements

The property name elements are described in more detail in the following sections:
• "Namespaces"
• "Properties" on page 477
• "Types" on page 479

Namespaces The name of each type and property in AED is considered part of a vocabulary
grouping called a namespace. Namespaces prevent clashes between names defined
by disparate parties, as well as unambiguously identify commonly used types and
properties so that identical semantics may be assured. A namespace is identified by
a Uniform Resource Identifier (URI) as defined in RFC 3986.
A type or property identifies its namespace by a namespace prefix followed by a colon
character. If no namespace prefix is present, the type or property is considered part
of the AED default namespace. The part of the type or property after the namespace
prefix is considered its simple name.
AED has several build-in namespaces, with predefined namespace URIs and prefixes:

Table 22 Namespaces

Namespace Prefix Description Examples

- Custom and experimental properties not yet established as standard. foo

bar
myProperty

aed AED-specific properties and types. aed:name

aed:Integer

bio Descriptions of biological entities. bio:sequence

bio:Strand

style Information related to information representation, visually or otherwise. style:color

If any other namespace is used in an AED file, it must be declared in the metadata
section of the file using the special namespace prefix. The simple name of the
metadata header indicates the prefix being declared, and the value (of type aed:URI)
indicates the namespace to be associated with the prefix. For example, to associate
the prefix “example” with the URI http://example.com/namespace/, and the “affx”
with the URL http://affymetrix.com/ontology/, then use the following metadata record:

namespace:example(aed:URI) http://example.com/namespace/

namespace:affx (aed:URL) http://affymetrix.com/ontology

Chromosome Analysis Suite (ChAS) User Guide 476

 Appendix B AED file format
Property name elements B
Properties This section describes the properties defined by the AED specification. By convention
property names begin with lowercase letters. A predefined property is only required if
indicated. Some properties are only useful as metadata, and these are so indicated.

AFFX properties
This section describes the properties defined by the AED specification. By convention,
property names begin with lowercase letters. A predefined property is only required if
indicated. Some properties are only useful as metadata, and these are so indicated.

Table 23 AFFX Properties

Name Type Description

Affx:ucscGenomeVersion aed:String (Metadata) The genome assembly version using UCSC

(aed:String) names, for example “hg19”.

AED properties
These properties are parts of the AED namespace.

Table 24 AED Properties

Name Type Description

aed:application aed:String (Metadata) The name of the application that produced the AED file, if metadata, or
the annotation.

aed:category aed:String Identifies the group and optionally subgroups into which the resource is classified.
Subcategories, if any, should be delimited using the forward slash character '/'
(U+002F) with no whitespace. (Example: copynumber/gain)

aed:created aed:DateTime (Metadata) The point in time the data was created; this is not necessarily the time the
file was created.

aed:counter aed:Integer A general purpose field to be incremented when user-defined circumstances occur.
A common use for this field is to indicate, the number of samples in which the
condition has been observed.

aed:modified aed:DateTime (Metadata) The point in time the data was modified; this is not necessarily the time
the file was modified.

aed:name aed:String (Required.) Indicates the name of the record.

In a metadata record, this value is interpreted as the name and type of the metadata
property.

aed:note aed:String A user-defined explanation or comment regarding the annotation.

aed:value aed:String (Required only if metadata records are present.) In a metadata record, this value is
interpreted as the value of the metadata property. An AED processor must ignore
this field for all non-metadata records.

aed:uuid aed:UUID (Metadata) The universally unique identifier of the resource. Although allowed, it is
not always advised to identify user-editable resources such as AED documents with
UUIDs, as copying and manually editing such resources can result in multiple such
resources with identical UUIDs, negating the purpose of UUIDs.

Chromosome Analysis Suite (ChAS) User Guide 477

 Appendix B AED file format
Property name elements B
Biology properties

Table 25 Biology Properties

Name Type Description

bio:assembly aed:URI (Metadata) A URI indicating the genome assembly used. Currently the DAS
GlobalSeqIDs are recommended.

bio:state aed:Rational The algorithm-determined state (e.g. copy number) of an annotation.

bio:confidence aed:Rational A value between 0.0 and 1.0, inclusive, indicating the confidence that an annotation
call is accurate.

bio:end aed:Integer (Required) The zero-based ending position, exclusive, of the record along the
sequence.

bio:markerCount aed:Integer The number of markers such as probes that intersect an annotation.

bio:sequence aed:String (Required) The name of the chromosome (e.g. chr3, chrY), contig (e.g. ctg5), or
scaffold (e.g. scaffold90210).
The special value of an empty string (“”) indicates that the record is a metadata
record, giving special meaning to values in other fields in the record.

bio:start aed:Integer (Required) The zero-based starting position, inclusive, of the record along the
sequence.

bio:strand bio:Strand The sequence strand on which a feature lies.

Style properties
Style properties are used to control the display of the annotation.

Table 26 Style Properties

Name Type Description

style:color aed:Color The color to be used when visually depicting the annotation.

Chromosome Analysis Suite (ChAS) User Guide 478

 Appendix B AED file format
Property name elements B
Types AED defines the following types. By convention type names begin with an uppercase
letter. The lexical form is applied to the resulting character sequence derived after
following the quoting rules of RFC 4180.

Table 27 Types
Type Description Lexical Form Examples

aed:String A sequence of Unicode characters. character* • Abc

• a "fun" test!

aed:Integer The positive whole numbers, the [-] digit+ • 123

negative whole numbers, and zero. •0
• -5000

aed:Rational A rational number. Currently only [-]digit+.digit+ • -123.0

rational numbers with finite decimal [e[+|-]digit+] • 0.0
expansion are allowed. AED The lexical form • 123.45
processors typically implement this “NaN” is explicitly • 1.2e+5
type using floating point values. prohibited.
This type does not allow floating
point not-a-number (NaN) values.

aed:Boolean A binary true/false value. “false” | “FALSE” • false

| “true” | “TRUE” • FALSE
• TRUE

aed:URI A Uniform Resource Identifier (URI). See RFC 3986. • http://example.com/

• urn:uuid:f81d4fae-7dec-11d0-a765-
00a0c91e6bf6
• mailto:[email protected]

aed:DateTime A timestamp with the absolute date YYYY-MM- • 2008-09-12T18:45:43.779-07:00

and time and an identified time DDThh:mm:ss.s+
zone. The lexical form is a subset of (+|-)hh:mm
ISO 8601 with required
milliseconds and time zone offset.

aed:Color A color. Currently only supports rgb(digit+, digit+, • rgb(0, 0, 0)

colors in the RGB color space. The digit+) • rgb(200, 50, 128)
lexical form represents red, green, • rgb(255, 255, 255)
and blue components, respectively,
each supporting a decimal integer
value 0-255)

bio:Strand Represents a sequence strand One of the •+

relative to the landmark or following •-
assembly. The lack of an indicated characters:
strand encompasses the semantics + (U+002B)
of “unknown”, and “non-stranded.” Forward strand.
- (U+002D)
Reverse strand.

aed:UUID A Universally Unique Identifier xxxxxxxx-xxxx- • f81d4fae-7dec-11d0-a765-

(UUID) as specified by RFC 4122 (in xxxx-xxxx- 00a0c91e6bf6
canonical form, not as a URN). xxxxxxxxxxxx

Chromosome Analysis Suite (ChAS) User Guide 479

 Appendix B AED file format
Compatibility B

Compatibility

UCSC Browser The BED file format, developed at UCSC, is widely used for transfer of simple region
Extensible Data coordinates. However, the format has been interpreted and implemented in multiple
(BED) ways by various software within and outside of UCSC. Some implementations require
a TAB delimited format, others require a space-delimited format, and still others
accept both. Characters outside of the ASCII character set are not well supported. We
created the AED format with very strict and explicit definitions so as to avoid some of
these compatibility issues.
Although the AED format is preferred, ChAS supports both the import and export of
data in BED format. When exporting data in BED format, ChAS exports only the basic
4-column tab-delimited BED format containing the position and name of each item. If
the names of any of your items contain spaces or non-ASCII characters, there is no
guarantee that all programs will be able to interpret those names correctly.
When importing data in BED format, ChAS supports the reading of BED files with
anywhere from 4 to 12 columns.
 The file must be TAB delimited
 Only ASCII characters should be used
 The values for thickStart and thickEnd will be ignored for display purposes
 The value for itemRgb will be honored for display purposes
 The values for blockCount, blockSizes and blockStarts can be used to import
and display data with intron/exon structure, such as genes.
 Formatting rules in the BED header are ignored
 BED files containing multiple tracks are not supported; use a separate BED file
for each track.
The UCSC Browser, as well as ChAS, uses the strict definition of BED where
chromStart is not allowed to be greater than chromEnd. ChAS will accept import of
BED files even if this convention is violated, but will auto-correct and export BED files
properly with chromStart < chromEnd.
AED has been structured to facilitate as much as possible migration of data rows to
and from BED. Starting with existing AED and BED files, data records from AED may
be transferred to BED by using:
 The “Export” function from inside ChAS (recommended)
 A text editor (not recommended) if the AED files are first prepared in the following
manner:
• Remove all fields except for bio:sequence, bio:start, bio:end, and aed:name.
• Ensure that no non-ASCII characters are included. (The treatment of non-ASCII
characters by a BED processor is undefined.)
• Ensure that no name contains whitespace characters.
• Data rows from the first four columns of a BED file can be transferred to AED with
no constraints as long as the columns are delimited by TAB.

Chromosome Analysis Suite (ChAS) User Guide 480

 Appendix B AED file format
References B
Microsoft Excel Though not recommended, an AED file may be edited using most spreadsheet
and other programs that support tab-separated value (TSV) files and that recognize a byte order
spreadsheet mark (BOM). An AED file can be edited in Microsoft Excel, for example, using the
following rules:
applications
When loading an AED file into Microsoft Excel as a TSV file, make sure that the
Unicode code page for the correct encoding is selected (preferred), or accept the
default “Windows (ANSI)” code page (which should still recognize Unicode characters
if the correct BOM is present in the file).
When saving an AED file from Microsoft Excel, make sure the “Unicode Text” type is
selected. This will result in a file encoded in UTF-16LE, which is still a valid AED file as
it begins with the appropriate BOM.

Microsoft Though not recommended, an AED file may be edited by any text editor that supports
Notepad and Unicode and that uses a byte order mark (BOM) to indicate the charset. The version
other Text editors of Microsoft Notepad in Windows XP, for example, will both correctly read text files
marked with a BOM and save text files using the appropriate BOM if the following rules
are followed:
When saving an AED file from Microsoft Notepad, make sure the encoding is set to
“UTF-8” or “Unicode”.
For other text editors, make sure the correct preferences are set both to recognize and
write BOMs for files.

Text Editors
EmEditor <http://www.emeditor.com/> is a commercial text editor that has extremely
good Unicode and BOM support, and is able to open up gigantic text files.
PSPad <http://www.pspad.com/> is a free text editor that has particularly extensive
Unicode and BOM support and is available in many localizations.
UniPad <http://www.unipad.org/> is a shareware text editor that correctly handles
Unicode and BOM, and provides a wide range of built-in glyphs for representing
Unicode code points that cannot be viewed on most other text editors.

References
ISO 8601: ISO 8601:2004(E): Data elements and interchange formats — Information
interchange — Representation of dates and times. International Organization for
Standardization, 2004-12-01.
Microsoft Byte Order Mark: http://msdn.microsoft.com/en-us/library/
ms776429(VS.85).aspx
RFC 3986: RFC 3986: Uniform Resource Identifier (URI): Generic Syntax. T. Berners-
Lee, R. Fielding, and L. Masinter. Internet Engineering Task Force, 2005. http://
tools.ietf.org/html/rfc3986
RFC 4122: RFC 4122: A Universally Unique IDentifier (UUID) URN Namespace. P.
Leach, M. Mealling, and R. Salz. Internet Engineering Task Force, 2005. http://
tools.ietf.org/html/rfc4122
RFC 4180: RFC 4180: Common Format and MIME Type for Comma-Separated Values
(CSV) Files. Y. Shafranovich. Internet Engineering Task Force, 2005. http://
tools.ietf.org/html/rfc4180
Unicode Byte Order Mark FAQ: http://unicode.org/faq/utf_bom.html

Chromosome Analysis Suite (ChAS) User Guide 481

 ChAS properties and types
C
Starting with version 1.1.0, ChAS has adopted the framework underlying AED files as
its native framework for identifying and storing properties and value types. Every
property of annotations, files, and other objects within the software is now identified
by a URI behind the scenes. Furthermore, the types of values given to these properties
are the same types available within AED files.
The AED framework therefore provides a consistent and pervasive approach to
describing entities throughout the application and seamlessly across AED files and
other types of files such as xxCHP files.

Identifying properties within ChAS

Standard AED Because every user-accessible property within ChAS complies with the AED
property style framework, any property may be entered in standard prefix:simpleName style, just
as it would appear in an AED file. For example, the creation date of an entity may be
entered using the aed:created property name.
The predefined AED prefixes defined for AED files may always be used. Unlike AED
files, which allow declaration of arbitrary prefixes with additional namespaces, ChAS
has an additional list of predefined namespace prefix associations valid only within the
context of the ChAS user interface.
These prefixes may be used to refer to the corresponding namespaces with no explicit
namespace declaration. For example, the fish prefix may be used to refer to FISH
namespace properties (e.g. fish:labs) with no need to explicitly associate the FISH
namespace URI with the namespace.
Table 28 lists the namespace prefixes recognized within the ChAS user interface.

Table 28 ChAS namespace prefixes

Namespace URI Prefix Label

http://affymetrix.com/ontology/aed/ aed General

http://affymetrix.com/ontology/aed/biology/ bio Biology

http://affymetrix.com/ontology/aed/style/ style Style

http://affymetrix.com/ontology/aed/default/ (none) Custom

http://affymetrix.com/ontology/ affx Affx

http://affymetrix.com/ontology/algorithm/ alg Algorithm

http://affymetrix.com/ontology/algorithm/option/ algopt Algorithm Option

Chromosome Analysis Suite (ChAS) User Guide 482

 Appendix C ChAS properties and types
ChAS property style C
Table 28 ChAS namespace prefixes
Namespace URI Prefix Label

http://affymetrix.com/ontology/algorithm/state/ algstate Algorithm State

http://affymetrix.com/ontology/arr/ arr ARR

http://affymetrix.com/ontology/chp/ chp CHP

http://affymetrix.com/ontology/netaffx/ netaffx NetAffx

http://affymetrix.com/ontology/genome.ucsc.edu/bed/ bed BED

http://affymetrix.com/ontology/projects.tcag.ca/variation/ dgv DGV

http://affymetrix.com/ontology/www.genome.ucsc.edu/fishClones/ fish FISH

http://affymetrix.com/ontology/www.ncbi.nlm.nih.gov/omim/ omim OMIM

http://affymetrix.com/ontology/www.pubmed.gov/ pubmed PubMed

http://affymetrix.com/ontology/www.ncbi.nlm.nih.gov/RefSeq/ refseq RefSeq

http://affymetrix.com/ontology/www.genome.ucsc.edu/genomicSuperDups/ superdup Segmental

Duplications

ChAS property style

Properties may also be entered by the user in a more attractive format specific to ChAS,
consisting of the property simple name followed by a space and a special label in
parentheses to identify the namespace.
The namespace label is presented in the table above. For example, the fish:labs property
may also be entered as labs (FISH).
The ChAS style is the default format for display within ChAS. Regardless of what format
you use to enter a property, it will be displayed in its ChAS style.

Full URI property style

Any property, including those with predefined namespace prefixes, may be entered using
its full canonical URI. This allows entry of unknown third-properties in other namespaces.
If the property is in a known namespace, it will be displayed using the ChAS property style
described above. For example, the fish:labs property may be entered using the full URI
http://affymetrix.com/ontology/www.genome.ucsc.edu/fishClones/labs; the property will
be displayed as labs (FISH).
Properties may be entered in ChAS three different ways:
 ChAS style (default): labs (FISH)
 AED style: fish:labs
 AED URI: http://affymetrix.com/ontology/www.genome.ucsc.edu/fishClones/
labs

Chromosome Analysis Suite (ChAS) User Guide 483

 Appendix C ChAS properties and types
Identifying value types within ChAS C

Identifying value types within ChAS

With the incorporation of the AED framework, ChAS now uses the same AED types
used within AED files. Because there is a small, fixed set of types, within the
application user interface these types are always selected using a prepopulated list
such as a drop-down list control.
The types are displayed using special user-friendly names, even though they refer to
the same corresponding types within AED files.
These types and their ChAS style labels appear as follows:
 aed:Boolean - Boolean
 aed:Color - Color
 aed:DateTime - DateTime
 aed:Integer - Whole Number
 aed:Rational - Decimal Number
 aed:Strand - Strand
 aed:String - Text
 aed:URI - URI
 aed:UUID - UUID
Some of the types listed above may not be available in some contexts.

Automatic conversion of xxCHP headers to properties

The file format used by xxCHP files uses a separate approach for describing
properties and value types. However, there exist equivalent AED types for the types
used by xxCHP files. Moreover, the header names used in xxCHP files are logically
grouped into categories by certain prefixes. ChAS uses these groupings to place
xxCHP headers into AED namespaces when loading xxCHP files. ChAS also modifies
the names of the headers to make them more readable and to provide consistency
with other AED properties used throughout the application.

Header name ChAS uses the following namespaces when converting CHP header names based on
conversion the header name prefix, as shown in Table 29.

Table 29 CHP header name conversion to AED namespace

CHP Header Name Prefix AED Namespace

affymetrix-algorithm- http://affymetrix.com/ontology/algorithm/

affymetrix-algorithm-param- http://affymetrix.com/ontology/algorithm/

affymetrix-algorithm-param-option- http://affymetrix.com/ontology/algorithm/
option/

affymetrix-algorithm-param-state- http://affymetrix.com/ontology/algorithm/state/

Chromosome Analysis Suite (ChAS) User Guide 484

 Appendix C ChAS properties and types
Automatic conversion of xxCHP headers to properties C
Table 29 CHP header name conversion to AED namespace
CHP Header Name Prefix AED Namespace

affymetrix-chipsummary- http://affymetrix.com/ontology/chp/summary/

(all others) http://affymetrix.com/ontology/chp/

After determining the appropriate namespace to use, ChAS removes the header name
prefix and modifies the remaining characters according to the following rules (simplified):
1. All beginning uppercase letters are converted to lowercase.
2. All separator characters (such as ʹ-ʹ and ʹ_ʹ) are removed.
3. The characters immediately following separators are converted to uppercase. For
example, the CHP header:
affymetrix-algorithm-param-option-gender-override-file is
converted to optionGenderOverrideFile and placed in the http://
affymetrix.com/ontology/algorithm/ namespace.

Converted ChAS performs further special conversions on the following header parameters for
properties historical and consistency reasons, as shown in Table 30.

Table 30 Converted Properties

CHP Header Name Property

affymetrix-array-type http://affymetrix.com/ontology/arrayType

affymetrix-chipsummary-snp-qc http://affymetrix.com/ontology/chp/summary/snpQC

affymetrix-chipsummary-MAPD http://affymetrix.com/ontology/chp/summary/mapd

Derived The following properties are each assigned to a file property derived from one or more
properties header parameters, xxCHP file attributes, or other information, in the given order:
http://affymetrix.com/ontology/aed/created (aed:created)
 The file creation time in the Calvin generic data header.
 The create_date header parameter.
 The create-date header parameter.
http://affymetrix.com/ontology/aed/modified (aed:modified)
 File system last modified date.
 http://affymetrix.com/ontology/algorithm/annotationFile (alg:annotationFile)
 The affymetrix-algorithm-param-state-annotation-file header parameter.
 The affymetrix-algorithm-param-cn-annotation-file header parameter.
 The affymetrix-algorithm-param-mapfile header parameter.
 The affymetrix-algorithm-param-option-annotation-file header parameter.
http://affymetrix.com/ontology/algorithm/parameterFile (alg:parameterFile)
 The affymetrix-algorithm-param-state-config-file header parameter.
 The affymetrix-algorithm-param-config-file header parameter.

Chromosome Analysis Suite (ChAS) User Guide 485

 Appendix C ChAS properties and types
Automatic conversion of xxCHP headers to properties C
 The affymetrix-algorithm-param-paramfile header parameter.
 The affymetrix-algorithm-param-option-config-file header parameter.
http://affymetrix.com/ontology/algorithm/referenceFile (alg:referenceFile)
 The affymetrix-algorithm-param-state-reference-file header parameter.
 The affymetrix-algorithm-param-reference-file header parameter.
 The affymetrix-algorithm-param-reference-mdlfile header parameter.

Chromosome Analysis Suite (ChAS) User Guide 486

 ChAS browser NetAffx Genomic
D Annotations

Homo Sapiens database files

NetAffx Genomic Source of content

Annotation files  NetAffx Genomic Annotation files are used by the ChAS Browser to display
recent snapshots of genomic annotations downloaded from public databases.
 The UCSC Genome Browser is the source of the data that populates the
following Browser tracks: Genes, Ensembl, Segmental Duplications, sno/miRNA,
and Cytobands. UCSC was also the source of OMIM data for ChAS Browser file
versions NA31-NA33.1 and 32.1. NA33.2 and NA36 no longer contain annotation
information for BACs and FISH Clones.
 The Database of Genomic Variants is the source of the data displayed in the DGV
track.
 The ClinGen Resource is the source of the data displayed in the Triplosensitivity,
Haploinsufficiency, and Recurrent/Curated Regions tracks.
 The OMIM database (with curation and processing assistance from UCSC and
NCBI) is the source of the data displayed in the OMIM Genes, OMIM Phenotype
Loci, and OMIM Region Phenotype Loci tracks.

IMPORTANT! Starting with ChAS v3.3, the naming convention of the NetAffx Genomic
Annotation database file will change. This file will now include a date (as opposed to a specific
NetAffx build number) and will be updated more regularly than its current schedule of being
updated with each software release. The new naming convention is as follows:
NetAffxGenomicAnnotations.Homo_sapiens.hg38.naYYYYMMDD.db

For optimal use of the Segment Prioritization methods described in Chapter 17, "Prioritizing
segments" on page 373, you must download the NetAffx Genomic Annotation files released with
ChAS 4.4 or use more current ones when available.

IMPORTANT! It is VERY highly recommended to confirm findings obtained using the ChAS
Browser's NetAffx Genomic Annotations file contents by linking out to external databases using
the ChAS software coordinates for the most current annotation information. See "Linking to
external websites" on page 213.

Chromosome Analysis Suite (ChAS) User Guide 487

 Genomic position coordinates
E
There are multiple conventions and file formats to describe locations in chromosomal
DNA sequences. This appendix describes a few issues that relate to ChAS.

Genome assemblies
First, it is important to know which set of DNA sequences is being used as the
reference. For the human genome, the reference assembly is available for download
from public sources such as UCSC and Ensembl. Those two sites currently use
identical genome assemblies, but refer to them by different names. UCSC uses names
such as “hg18”, “hg19” and “hg38”. The identical genome assemblies are known as
“NCBI36”, “GRCh37”and “GRCh37”at Ensembl. Assemblies at NCBI can have a
decimal point as well, for example, “36.3” or “37.1”. For positions on the
chromosomes 1-22, X and Y, there is no difference between assemblies “36.1”, “36.2”
and “36.3” and we expect the same will be true for future “point” releases.

SNP and marker positions

When referring to individual positions on a chromosome, such as the positions of
SNPs, it is sufficient to give a single coordinate. There are different conventions about
whether to consider the first DNA base pair on the chromosome as position 0 or
position 1.
For SNP marker positions, all of the following consistently use a 1-based index
position coordinate: CYCHP files, CNCHP files, NetAffx detail pages for SNP markers,
NCBI pages for SNP positions of dbSNP entries, and the Graphs Table in ChAS .
Consider the (randomly-chosen) SNP marker"S-3SRJC" from the CytoScan HD array.
This marker is designed to correspond to the SNP with ID “rs4376202" in the dbSNP
database. The NCBI website reports the position as chr4:1822637 on GRCh38. On the
NetAffx website, the identical coordinate is also given for this SNP. The same
coordinate value is given in CYCHP files and in the ChAS graphs table. Refer to http:/
/www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=7641618 for this particular
example.
For copy number markers which are not based on SNP positions, we continue to use
a 1-based index position. For these markers, we continue to use a 1-based index
position. Unlike the case for SNPs, there is no particular single base pair that the
marker corresponds to. The convention in CYCHP files is to use the position of the
first DNA pair corresponding to the position where the marker hybridizes with the
DNA. When two or more markers have the same start position on a chromosome, the
coordinate of one of them will be shifted by one or occasionally a few more bases such
that each marker is reported at a unique position.

Chromosome Analysis Suite (ChAS) User Guide 488

 Appendix E Genomic position coordinates
Segment positions E

Segment positions
BED and AED file formats are used for storing and sharing region files between software.
The BED format was created by UCSC for use with their genome browser, and is also used
in other software. The AED format was created by Thermo Fisher Scientific for use with
ChAS and possible future software, but used the BED format as a starting point.
The BED file format is explicitly defined to use a 0-based coordinate system where the
second column (chromStart) in the file is the position of the first base-pair and the third
column (chromEnd) is the position of the last base-pair plus one. Another way of saying
this is that the start index is inclusive and the end index is exclusive. As an example, to
refer to the first 100 based on the chromosome, you would use chromStart=0 and
chromEnd=100. The length of any region is always given simply by chromEnd minus
chromStart.
The UCSC browser strictly requires that chromStart not be larger than chromEnd. In order
to support file outputs from non-conforming programs, ChAS will accept BED files where
chromStart > chromEnd. It will simply switch those two coordinates and act as if the
coordinates were given in the correct order.
Since a SNP has, by definition, a length of one base-pair, the proper way to represent a
SNP position is with chromEnd = chromStart + 1. The UCSC browser does allow
chromStart to be equal to chromEnd. But this is used for representing insertion points, and
is not used to represent SNP positions. Because the AED format was intended to be
compatible with BED format, we use the same coordinate system.
For example, suppose there are three markers with the following positions on a
chromosome given in the CYCHP file: Marker A at 1000, Marker B at 2000, Marker C at
3000. Marker positions in the CYCHP file are 1-based index positions. To represent these
in a BED file, we would need a file like this:
 Chr3 999 1000 markerA
 Chr3 1999 2000 markerB
 Chr3 2999 3000 markerC
If there were a segment starting at markerA and ending at markerC, we would need to
represent it in a BED or AED file as:
 Chr3 999 3000 segment_1

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 Editing BED files
F
A BED file is essentially a tab-delimited text file, as shown in Figure 526.

Figure 526 Example BED file

hg version

Using a text editor such as MS WordPad and MS NotePad (not a spreadsheet

application like Microsoft Excel) to edit BED files is recommended and work well.
Editing a BED file using a spreadsheet application such as Excel is not recommended
because these programs may not preserve the correct BED file format. For example,
when exporting data from Excel into tab-delimited text, Excel may add quotation
marks around some text, which would cause the file to be invalid and unusable with
ChAS or other applications.
There is no easy way to prevent Excel from adding extra quotation marks which
corrupt the output. Advanced Excel users can use macro programming to create
special output formats. Other options include:
 Do not use Excel to edit BED files. You may use a text editor, but be certain to
separate the columns with TAB characters and do not use non-ASCII characters.
The BED format was not designed with such characters in mind; therefore,
problems may occur when you try to share these files with others. ChAS will
reject BED files containing non-ASCII characters, and will never export non-ASCII
characters into a BED file.

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F
 After exporting a BED file from Excel, edit the file in another application to remove
extra quotation marks.
 Use AED format for the data, then use ChAS to export to BED format if needed.
 Be careful to create a BED file that does not cause Excel to add quotation marks.
Do not include the itemRgb column, quotation marks, or special characters in a
track line. For example, the following is an acceptable track line: Track db=hg19
name=My_Track description=This_is_my_data

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 CytoScan algorithms and QC
G metrics

Algorithm overview
This section provides a high level overview of how copy number calls are generated
within the software. The copy number workflow starts with the intensities on the array,
include normalization and scaling, reference set ratios, Log2 transformation, CN state
segmentation, and how CN segment calls are made.
Note: For CytoScan HTCMA algorithm and QC, see the RHAS User Guide.

Feature GeneChip Cartridge Microarrays are scanned on the GeneChip Scanner and
identification and processed by the AGCC/GCC scanner software package. AGCC/GCC aligns a grid
signal extraction on the DAT file (the original scanned image) to identify each microarray feature and
calculates the signal from each feature. This process uses the DAT file, containing the
raw signal, and creates a CEL file, which contains a single signal intensity for each
feature. The CEL file is used for all downstream analyses.

Single sample Beginning with the raw signal data in the CEL file, the Single Sample CytoScan
CytoScan Workflow implements a series of steps that perform probe set summarization,
workflow normalization, removal of variation caused by known properties and residual variation,
and completing with calling genotypes, copy number segments and LOH segments.
A brief overview of each step performed by the CytoScan Workflow is shown in
Figure 528 on page 494. In addition, a rough sketch of Analysis Pipeline (for Single
Sample Analysis) is demonstrated in Figure 528 on page 494.

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Algorithm overview G

Figure 527 CytoScan Workflow Overview. Steps related to probes used for copy
number determination run down the left and those steps used for SNP probes run down
the right side of the diagram

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Algorithm overview G

Figure 528 Rough sketch of Analysis Pipeline (for Single Sample Analysis)

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Dual quantile normalization G
Signal-level The first level of covariate adjustors operate on the raw signal.
covariate
adjustors Fragment adapter covariate adjustor
After the Nsp I restriction digest, an Nsp I-specific adaptor is ligated onto the cohesive
end termini. Since Nsp I is a 6-nucleotide cutter with degenerate sites, meaning that
they contain one or more base pairs that are not specifically defined, these ends are
of various sequences and the ligated adaptors are a variety of sequences. The exact
sequences of the cut site and ligation adaptor have an effect on the overall efficiency
of ligation and subsequent PCR amplification. The Adaptor Covariate Adjustor
corrects for these differences by normalizing the signals for each adaptor/cut site
sequence class to an overall median.

Fragment length covariate adjustor

The length of each Nsp I fragment impacts the efficiency of PCR amplification and
therefore the signal. Fragments of 300-500 bp are amplified with the highest efficiency
and the degree of amplification tapers off as the fragments get longer. The Length
Covariate Adjustor corrects for these differences by normalizing the signals for a
series of fragment size bins to an overall median.

Dual quantile normalization

Dual quantile normalization is simply a two-phase process where probes used for
copy number detection and probes used for SNP genotype detection are normalized
separately. In both cases, a normalization sketch is built using the autosomal probes
in the reference set. The normalization sketch is the prototype distribution of probe
intensities that defines what this distribution looks like for all arrays. The single sample
autosomal probes are fit to the sketch and the X and Y probes are interpolated into
the distribution.
Quantile normalization makes the assumption that the distribution of probes on the
array is fairly consistent from array to array. Since the X-chromosome is one of the
largest chromosomes (155Mbp, ~5% of the genome), differences between males and
females would stretch this assumption. That is why the quantile normalization focuses
on creating an autosomal sketch and normalizing the autosome to it. The X and Y
chromosome probes are then handled in a special way. Each of them is matched to
the closest pre-normalization signal value. Based on that match, their normalized
signal should be close to the signal for the very same autosomal probe. So the
normalized values for X and Y probes are simply “looked-up” in the pre-normalization
autosomal sketch, and transformed to the post-normalization value.

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Copy number workflow G

Copy number workflow

Log2 ratio Log2 Ratios for each marker are calculated relative to the reference signal profile. The
calculation Log2 Ratio is simply Log2(samplem) – Log2(referencem), for each marker, “m”.

High pass filter Since most probes map to genomic markers associated with a normal copy number,
image correction most Log2 Ratios should be centered at a value of zero. Also, since markers from any
genomic region are scattered across the surface of the microarray, regions of altered
copy number will not appear as regional changes on the microarray image.
Some samples do reveal spatial trends away from zero that are gradual and this
spatial bias when scattered back across the genome exhibits itself as added noise in
the Log2 Ratios. The High Pass Filter Image Correction identifies these gradual spatial
trends and adjusts Log2 Ratios to remove the spatial bias and lower the level of
noise.Log2 Ratio-Level Covariate Adjustors

Log2 ratio-level Super GC covariate adjustor

covariate The GC content of genomic DNA sequence impacts probe signal dose-response and
adjustors therefore probe Log2 Ratios. The sequence GC content of the microarray probe
impacts hybridization kinetics. In addition, the genomic GC content of the Nsp I
fragment and the 500 kbp surrounding the probe (local GC) all impact the efficiency
of target preparation in the genomic region of each probe. The super GC covariate
adjustor combines the probe GC content, the fragment GC content and the local GC
content into one covariate that corrects for Log2 Ratio differences based on the
combination of GC contents associated with each probe.

Reference intensity covariate adjustor

Probes in different intensity categories have different dose responses in Log2 Ratio
space. Using the Reference Set probes to define bins based on probe intensity, the
single sample probes are binned and the median of the distribution of Log2 Ratios
within each bin is adjusted to the median Log2 Ratio of the corresponding bin from
the reference set.

Marker Type Covariate Adjustor

Polymorphic probes designed for SNP detection and non-polymorphic probes
designed for copy number detection have different properties and different dose
responses. The Marker Type Covariate Adjustor normalizes the median Log2 Ratios
of SNP and CN markers to account for differences in Log2 Ratios between the two
groups.

Median This final level of normalization simply shifts the median Log2 Ratio of the autosomes
Autosome to a copy-number state equal to 2, i.e. a Log2 Ratio of 0.
normalization

Systematic Even after all of the Covariate Adjustors, there is some residual variation with unknown
residual variability origins. During product development we have introduced variation into the protocol in
removal an attempt to capture other forms of unanticipated variation. The Systematic Residual
Variability Removal step matches sample variability to the residual variability of the
reference set, and when matched, corrects the data to remove the residual.

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Copy number workflow G
Signal restoration Signal restoration is an application of Bayes wavelet shrinkage to the Log2 Ratios
associated with markers. The result of this transformation is an overall reduction in
variation around the local mean of Log2 Ratios. In this context, “local” means a region
consisting of a small set of markers upstream and downstream from a given marker.
The resulting data can be viewed as the Weighted Log2 Ratio in ChAS and serves as
the input to the segmentation algorithm. The wavelet shrinkage method is augmented
by a reduction of influence of outliers when local means are computed.

Segmentation Copy Number Calls for each Marker based on Log2 Ratios
For CytoScan arrays, markers are individually assigned a copy number call by a
Hidden Markov model (HMM). The sample specific inputs to the HMM are the
Weighted Log2 Ratios generated by the Signal Restoration module.
The weighted Log2 Ratios are centered on copy number (CN) = 2. In theory, when
Log2 Ratio = 0 then CN = 2, when Log2 Ratio = -1 the CN = 1, etc. In truth,
microarrays, or any hybridization-based technology, exhibit Log2 Ratio compression
due to many factors, so the Log2 Ratios never exhibit the amplitude expected by the
math. The following table shows theoretical and actual Log2 Ratios for different Copy
Number States.

Table 31 Copy number states and Log2 Ratios

Copy Number Truth Theoretical Log2 Ratio Actual Log2 Ratio

1 -1 -0.45

2 0 0

3 0.58 0.3

The actual Log2 Ratios observed are best derived from a very large data set with well-
characterized copy number changes. To this end, we have analyzed over 1400
samples that have copy number changes across 75% of the genome and have
established stable empirical values for these expected Log2 Ratios. These values, as
well as the dispersion characteristics of the Log2 Ratio data, are used as inputs to the
HMM along with the weighted Log2 Ratios of the sample data.
The HMM uses these inputs to convert observed Log2 Ratios into a CN state for each
marker. It uses a table of transition probabilities that express the probability of
changing from any CN state to another. As can be seen in the following example
(Figure 529), there are many potential paths through the possible CN states of a set of
markers.

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Copy number workflow G

Figure 529 Potential CN paths through a set of markers

The HMM uses the Viterbi algorithm to calculate the most probable path through the
set of markers using the transition probabilities between each pair of CN states.
Essentially, the graph of potential CN states is the “hidden” layer of the HMM, and the
measure Log2 Ratios are the observed layer. The HMM algorithm finds the most
probably CN states given the observed Log2 Ratios.

Segment Formation
Once markers are assigned Copy Number States by the HMM, contiguous stretches
of adjacent markers ordered by chromosome position having the same state are
aggregated into segments. These segments are described in a segment table within
the resulting CYCHP file that provides for each segment, the common Copy Number
State, the number of markers in the segment, the genomic marker position that
initiates the segment and the genomic marker position that terminates the segment.

Enforce Minimal Segment Length

Default parameters enforce a minimum segment length of 5 markers. This is a
subjective choice of parameter that implicitly states that the user is not interested in
segments with fewer markers than the minimum. The algorithm that enforces
minimum segment size distributes markers from any segment with fewer than the
minimum to its larger neighboring segments by changing the copy number call on the
modified markers to conform with those of the neighbors.

Smoothing & Joining

To stabilize the calling of copy number gains or losses, the ChAS software implements
a smoothing step. Smoothing will combine adjacent segments that are both gains,
even if they are not the same Copy Number State. For example, smoothing will
combine a set of adjacent segments of Copy Number State 3 and 4 into one segment
and assign it the most prevalent Copy Number State of the markers in the original
segments, (rounding up for gains and rounding done for losses in case of a tie).
Smoothing will also combine Copy Number States 0 and 1. But smoothing will not
combine gains with losses or either with normal segments.

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Copy number workflow G
Joining combines segments of gains or losses if they are separated by small spans of
normal copy number segments. The default value defining “small spans” in ChAS is
≤50 markers and ≤200 kbp. Small segments of less than 50 markers/200kbp of normal
copy number are removed, and the adjacent gain segments are joined. Likewise for
flanking loss segments. This is a dynamic process in ChAS, in that smoothing and
joining can be turned on and off, and parameters altered, resulting in modifications of
the displayed segments, but not altering the underlying CNState graph.

Segment table The final result of the copy number pipeline is a table of segments identified in the
output sample. The table in the CYCHP file includes segments of normal and non-normal
copy number. Segments called on the X- and Y-chromosomes are characterized as
normal or non-normal using gender information and adjusting for the Pseudo
Autosomal Regions (PAR) that are present on the X and Y. In ChAS, the segment table
display only shows segments of non-normal copy number.

Mosaicism The algorithm for detection of copy number aberrations in the presence of mosaicism
segment considers single copy deletions and gains. The algorithm is tuned to be most accurate
algorithm when the normal/expected Copy Number State is two. The algorithm targets detection
of changes of approximately 3MB or more in size (for CytoScan HD). Copy number
change events less than this size may be detected; however, sensitivity and specificity
will be reduced.

Limitations in mosaicism segmentations

 The algorithm is designed to detect only mosaicism between approximately15%-
70% mosaicism for copy numbers between 1 and 3 for regions on the order of
3MB in size or larger for autosomes and chrX .
 The algorithm is designed to detect only mosaicism between approximately
15%-70% mosaicism for copy numbers between 0 and 2 for regions on the order
of 3MB in size or larger for chrY.
 The algorithm will not call events below 1MB in size irrespective of number of
markers.
 The algorithm will not call events below 10% mosaicism irrespective of genomic
size or number of markers.
 The algorithm does not use allelic difference or BAF data for segmentation
purposes. It is recommended that allelic difference and/or BAF data tracks be
examined in conjunction with the reported mosaicism segmentation.

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SNP marker workflow G

SNP marker workflow

Signal CytoScan arrays contain six probes for each SNP probe set, three targeting each
summarization allele. The first step of the SNP-specific workflow is to summarize the previously-
normalized probe intensities for the A and B alleles, yielding allelic signal values.

Allelic signal For each marker, the Allelic Difference is calculated as the difference between the
computation summarized signal of the A allele minus B allele, standardized such that an A-allele
genotype is scaled to a positive value, and the B allele is scaled to a negative value.
The standardization is determined based on median values for this difference under
different genotype configurations determined by the reference set. In this way a
homozygous AA maps to approximately +1, and a homozygous BB allele maps to
approximately -1, with the heterozygote mapping to approximately 0. Additionally,
single A and B allele signals will map to 0.5 and -0.5, respectively. This scaling
provides a useful way of discerning two copies of an A allele from a single copy,
enabling detection of regions of copy-neutral LOH (e.g. IBD) from hemizygous LOH.

Genotyping Genotyping for CytoScan arrays is accomplished using the BRLMM-P algorithm
described in the White Paper: BRLMM-P: A Genotype Calling Method for the SNP
Array 5.0 (2007).

Allelic difference Systematic changes in Allelic Differences can be related to differences in GC content.
GC correction For instance, on a given sample Allelic Differences representing AA and BB genotype
markers might get progressively closer or further from each other as the GC content
changes. It is assumed that such changes represent unwanted variability. The Allelic
Difference GC correction determines differences in the structure of the allelic
differences associated with GC and then removes these differences. For CytoScan
HD the super GC covariate is used. For CytoScan 750K the Local GC covariate is
used.

Detection of LOH The LOH algorithm frames the problem in terms of a statistical hypothesis test. Given
a specific region containing N SNP markers with heterozygous and homozygous
genotype calls, decide between the following two hypotheses:
Null Hypothesis: Region is LOH
Alternative Hypothesis: Region is non-LOH
To decide between the two hypotheses the number of heterozygous calls is compared
with a critical value that is computed for each sample. When the number of
heterozygous calls is above the critical value, then the alternative hypothesis is
favored, i.e. region is not LOH. If there are not a sufficient number of heterozygous
calls then the decision is made in favor of LOH. The algorithm moves the region of N
markers along the genome to determine LOH events. Further details are provided in
the While Paper: The Loss of Heterozygosity (LOH) Algorithm in Genotyping Console
2.0.

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Array data QC metrics G

Array data QC metrics

This section provides a high level overview of the key QC metrics used with the
CytoScan arrays.

Median of the MAPD is a global measure of the variation of all microarray probes across the genome.
Absolute values It represents the median of the distribution of changes in Log2 Ratio between adjacent
of all Pairwise probes. Since it measures differences between adjacent probes, it is a measure of
short-range noise in the microarray data. Based on an empirical testing dataset, we
Differences have determined that array data with MAPD > 0.25 (for CytoScan 750K and HD, MAPD
(MAPD) > 0.29 for CytoScan Optima) has too much noise to provide reliable copy number
calls.

Waviness SD Waviness-SD is a global measure of variation of microarray probes that is insensitive

to short-range variation and focuses on long-range variation. Based on an empirical
testing dataset, we have determined that array data with Waviness-SD > 0.12 has
either sample or processing batch effects that will reduce the quality of the copy
number calls. Elevated Waviness-SD is not always an indication of too much noise.
Elevated Waviness with good MAPD and SNPQC metrics can occur in samples with
many copy number changes or very large regions of change. It is therefore advised to
check the data when observing elevated Waviness with good MAPD and SNPQC.

SNPQC SNPQC is a measure of how well genotype alleles are resolved in the microarray data.
Based on an empirical testing dataset, we have determined that array data with
SNPQC < 15 (for CytoScan 750K and HD, SNP QC < 8.5 for CytoScan Optima) is of
poorer quality than is required to meet genotyping QC standards.

ndSNPQC (SNP Quality Control of Normal Diploid Markers)

The metric, SNPQC is a measure of how well genotype alleles are resolved in the
microarray data. ndSNPQC is the same metric but only applied to normal diploid
markers (that is those that have been determined to have Copy Number =2 in the
sample). Larger ndSNPQC values are better.

ndWavinessSD (Normal Diploid Waviness Standard Deviation)

ndWavinessSD is a global measure of variation of microarray probes that is insensitive
to short-range variation and focuses on long-range variation. ndWavinessSD is
computed on normal diploid markers.

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MAPD – Detailed Description G

MAPD – Detailed Description

For quality assessment purposes, we define metrics that assess whether the
microarray data is useful for copy number (CN) analysis. One of these metrics is
Median of the Absolute values of all Pairwise Differences (MAPD).
MAPD is defined as the Median of the Absolute values of all Pairwise Differences
between Log2 Ratios for a given chip. Each pair is defined as adjacent in terms of
genomic distance, with SNP markers and CN markers being treated equally. Hence,
any two markers that are adjacent on the genome are a pair. Except at the beginning
and the end of a chromosome, every marker belongs to two pairs (Figure 530).

Figure 530

Formally, if xi: is the Log2 Ratio for marker i:

MAPD = median(|xi-1 – xi|, with i ordered by genomic position)
MAPD is a per-microarray estimate of variability, like standard deviation (SD) or
interquartile range (IQR). If the Log2 Ratios are distributed normally with a constant
SD, then MAPD/0.96 is equal to SD and MAPD*1.41 is equal to IQR. However, unlike
SD or IQR, using MAPD is robust against high biological variability in Log2 Ratios
induced by conditions such as cancer.
Variability in Log2 Ratios in a microarray arises from two distinct sources:
 Intrinsic variability in the starting material, hybridization cocktail preparation,
microarray or scanner
 Apparent variability induced by the fact that the reference may have systematic
differences from this microarray
Regardless of the source of the variability, increased variability decreases the quality
of CN calls.

Effect of MAPD As a measure of performance, we measured copy number gain and loss using
on functional samples with large chromosome aberrations that spanned approximately 70% of the
performance genome. With this dataset of nearly 1500 microarrays we measured the sensitivity for
detecting regions of copy number change across all of these regions. The sensitivity
of detecting an aberration on each array was binned into groups of varying
sensitivities, and plotted versus MAPD for each array in the following graph.
(Figure 531)

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Waviness-SD – Detailed Description G
s

Figure 531

The bins of detection sensitivity are displayed as coordinates along the x-axis, with
0% detection at the left and 100% at the right. The number of arrays is listed above
each box plot. The majority of the arrays had sensitivities above 90%. Based on this
analysis, we established a QC cutoff for MAPD of 0.25. Arrays with MAPD above 0.25
cannot be reliably used to determine copy number.

Waviness-SD – Detailed Description

For quality assessment purposes, we define metrics that assess whether the
microarray data is useful for copy number (CN) analysis. In addition to MAPD (above)
we define an alternate form of measurement of variance in the array data that is called
Waviness-SD, where SD stands for Standard Deviation.
Waviness refers to an effect seen in all genomic microarrays (see Maroni et al. (2007)
Genome Biology 8:R228) where long-range variation is observed, often associated
with regional genomic differences like local GC-content changes.
Waviness-SD is a QC metric that focuses on measuring these long-range effects. As
described separately, MAPD is a metric that measures short-range variation, the
variation of adjacent probes. The long-range variation measurement is accomplished
by calculating the variation in Log2 Ratios across the whole genome and subtracting
out the short-range variation, specifically, for autosomal probes:
Define:
Xi as the Log2 Ratios of autosomal probes
And Zi as the variance between adjacent probes:
Zi = X2i+1 – X2i
Waviness-SD is the total variance (Xi) minus the local variance (Zi):
Waviness-SD = sqrt(Var(Xi)-Var(Zi)/2)
While this metric is useful in most cases, it does make the assumption that most of the
genome is of normal copy number. This assumption may not be reasonable for some
types of cancer samples with large amounts of genomic copy number variations, or
for multiple-chromosome constitutive trisomies, where a considerable fraction of the
genome is duplicated.

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SNPQC – Detailed Description G
For most samples, a Waviness-SD value below 0.12 for CytoScan arrays indicates
that the long-range variation is within levels that can be accommodated by the
CytoScan algorithms. But a high Waviness-SD measure on a sample with good MAPD
and SNPQC metric values should be checked for the presence of large regions of
copy number change to assess whether it is a sample effect or a QC failure.
Waviness-SD can be a good indicator of process drift since it measures long-range
variation relative to the CytoScan HD or CytoScan 750K reference profile. A general
rise of Waviness-SD for all samples coming from your laboratory may be an indication
of a change of protocol, technique or reagents.

SNPQC – Detailed Description

SNPQC is a metric that estimates the distributions of homozygous AA, heterozygous
AB and homozygous BB alleles and calculates the distance between them. The better
the separation of these distributions, the better the ability to identify a genotype based
on its cluster position (Figure 532).

Figure 532

Propose we go towards a “single chip FLD” like metric

SNPQC correlates well with genotype performance, as measured by Call Rate and
Concordance to published HapMap genotypes. To establish this relationship, we
scored 380 microarrays from the Reference Set by calculating SNPQC, Call Rate and
Concordance. The following graphs show the relationships between SNPQC and the
other two metrics (Figure 533).

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Effect of SNPQC on Functional Performance G

Figure 533
Call Rates and Concordance also tied closely to SNPQC

The left panel shows that when SNPQC > 15, Call Rate is above 98%. The right panel
shows that when SNPQC > 15, Concordance is above 99%. This functional mapping
of SNPQC has allowed us to set a functional threshold for this QC metric at 15.
Microarrays with SNPQC > 15 are considered of high quality and interpretation of the
data is possible.

Effect of SNPQC on Functional Performance

SNPQC provides insight into the overall level of data quality from a SNP perspective.
The key consideration when evaluating the SNPQC value is to ensure the threshold is
exceeded. The quality of the SNP allele data is compromised, and is noisier and more
difficult to interpret when the SNPQC values are below the recommended acceptance
threshold as illustrated in the figure below. When the SNPQC value is below 15, the
noise within the array is higher than normal which compromises the overall data
quality and clarity of results. However, when the SNPQC value is above 15, the data
is of excellent quality and can be relied upon as robust with regard to performance
(Figure 534).

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Effect of SNPQC on Functional Performance G

Figure 534 Examples of Allele Track data quality at various levels of SNPQC. The lower row of
figures show data for a CN=2 and the upper for CN=3 regions. The panels from left-to-right
represent increasing SNPQC quality. The functional threshold for SNPQC is 15, so all values
above 15 show excellent data quality.

The key consideration is whether the SNPQC value is above or below the threshold
value and not the absolute magnitude. As long as the SNPQC value exceeds the
threshold there is a retention in the data quality as illustrated by the graphs to the right
which demonstrate clear allelic data across a broad range of SNPQC values which
exceed the recommended threshold. SNPQC is one of the metrics used to assess
array quality and should be helpful towards determining which experimental data sets
are of satisfactory quality to continue with subsequent interpretation.
Note: For detailed information on algorithms and QC metrics for the OncoScan array,
refer to the OncoScan Console User Manual (P/N 703195).

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TuScan algorithm G

TuScan algorithm
The TuScan algorithm uses B-allele frequencies (BAFs) and log2 ratios to estimate the
ploidy and percentage of aberrant cells in the sample (%AC) which in turn are used to
calculate copy number calls (CN). The BAFs and log2 ratios contribute equally to CN
determination. TuScan first uses the BAFs and log2 ratio data to identify segments of
equal CN. Next TuScan uses the BAFs, log2ratios and segment data to find the
combination of %AC and ploidy that best fits the data. When TuScan can successfully
determine %AC, the algorithm assigns each aberrant segment an integer copy
number representing the copy number in the tumor portion of the sample. This is
possible because CN is well approximated by an integer when the tumor is nearly
homogeneous. If the tumor is highly heterogeneous (i.e., lacks a dominant clone), or
contains a large amount of “normal” cells %AC cannot be determined. In other words,
if the percentage of aberrant cells contributing to the various aberrations in the sample
varies across all aberrations, %AC and ploidy cannot be determined. When %AC
cannot be determined, the segmentation algorithm will still identify segments of equal
CN, but the CN in just the aberrant cells cannot be determined. In this case, TuScan
bins the copy numbers and returns fractional CN values in 1/3 increments (e.g., 2,
2.33, 2.66, 3 etc.). This fractional copy number is derived from the normal
contamination as well as the heterogeneous population of tumor cells; therefore, the
fractional CN calls represent the average CN observed for that segment. Users should
look at the value of %AC to determine whether the CN value represents the CN in the
tumor (%AC= number) or the average CN in the sample (%AC=NA). Tumor
heterogeneity also affects the interpretation of the CN number calls when %AC cannot
be determined. For example, a TuScan call of 2.33 can result from 40% of the aberrant
cells having 3 copies, 10% of aberrant cells having 5 copies, or a more complex
heterogeneous mixture of copy numbers. Since nearly every tumor sample will have
some amount of normal contamination combined with tumor heterogeneity it is not
possible to predict how often TuScan will be able to determine the %AC, it will vary
depending on the sample.

Manual re-centering algorithm (OncoScan)

TuScan identifies normal diploid markers in a sample of interest, determines the copy
number for these markers (2, 4 or 6) and ensures that markers with CN=2 have a log
ratio of 0. This is referred to as "centering" the sample.
When no or an insufficient number of normal diploid markers are found, the automatic
recentering does not occur. In addition, occasionally the automatic recentering misses
the true CN =2 markers and does not correctly center the sample. In these cases, it is
advised to center the sample manually to get correct CN calls. Manual recentering is
now available through the CHAS software and the recentered sample is re-run through
TuScan (described above) to provide integer copy number.
The new RC.OSCHP files can be viewed in ChAS or the BioDiscovery software,
Nexus.
To manually recenter samples, an offset (median log2 ratio) is provided that tells the
algorithm how much a sample should be pushed up (positive value) or pushed down
(negative value) so that this region resides at the log 2 ratio = 0, indicative of normal
diploid.

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 Appendix G CytoScan algorithms and QC metrics
Copy number effect on somatic mutations G
In the example below (Figure 535) the sample should be centered at chromosome 4q.
The median log ratio on 4q is -0.17, therefore the manual recentering adjustment
would be given this offset value, resulting in an increment adjustment of 0.17 for all log
ratios.

Figure 535

Copy number effect on somatic mutations

Somatic mutation probesets in the OncoScan FFPE Assay are designed to selectively
respond to the presence of mutation sequences. However, large copy number
amplifications spanning the somatic mutation targets can sometimes lead to falsely
reporting the presence of mutations in amplified regions.
If the copy number state is greater than ~15, you may observe false positive somatic
mutation calls. The only region for which we have observed this problem is the EGFR
gene, which is prone to very high copy number in certain cancer types.
In the example below (Figure 536), the predicted copy number state for the EGFR
gene is greater than 30, which affects the somatic mutation score. Another side effect
shown in the example below is that three mutations are called in the high Copy
Number region, a contradictory event for at least two of these mutations.

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 Appendix G CytoScan algorithms and QC metrics
Copy number effect on somatic mutations G

Figure 536

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 Appendix G CytoScan algorithms and QC metrics
CytoScan XON region calling algorithm G

CytoScan XON region calling algorithm

For CytoScan XON arrays a region focused calling algorithm was developed to
distinguish between neutral, gain and loss copy number. Regions are defined by
genomically contiguous stretches of closely spaced markers. Each region is assessed
independently.
A three state conditional random field (CRF) model is used to segment each region.
The CRF model uses the log2 ratio measurements corresponding to that marker and
four markers on either side, plus the state of the previous marker, to assess whether
a given marker is in one of the three states. Before using the CRF model the log2 ratio
is independently adjusted for every marker to account for expected differences in
responsiveness to copy number.
For resistance to outliers, the t-distribution is used for computation of emission
probabilities. The mean parameter for the emission distributions are fixed for each
state across all markers, but the standard deviation parameter includes a component
that differs for each marker, based on expected marker variability. Adjacent regions
with the same copy number determination are not joined into larger segments so large
copy number aberration events may be represented by multiple region based calls.

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 Recommended CytoScan XON
H array workflows

IMPORTANT! The Segment Prioritization feature outlined in Chapter 17, "Prioritizing segments"
on page 373 can be used in conjunction with the recommended steps below to quickly prioritize
XON regions.

Whole exome analysis

The markers on the CytoScan XON array have been categorized into these four levels
(based on the annotation in the region of the genome).
 Level 1: Includes genes with the highest level of evidence: developmental delay,
epilepsy, ASD, XLID, Metabolic disorders, hereditary cancer OMIM Morbid
genes.
 Level 2: ClinVar genes not covered in Level 1.
 Level 3: Other OMIM genes not identified as Level 1.
 Level 4: Other Ref Seq, UCSC, Ensembl genes, LOVD.

Recommended Loading XNCHP file(s)

workflow for 1. Click File → Open.
analyzing the 2. Select the XON-Level 1 Named Setting.
whole exome
The XON Region Segment Calls in genomic regions assigned as Level 1 are
shown.
3. Turn off any filters that are based on markers or size.
The XON gain/loss segments that are contained in/or overlap with Level 1 regions
will be exposed on the XON Region Segment Track. The data in the Level 1
regions (Log2 Ratio, Weighted Log2 Ratio, Smooth Signal, Allele Difference, B-
allele Frequency) will show in color (based on the sample color assignments in
the User Configuration). The data in the remaining Level 2-4 regions will remain
gray and no XON segments will be revealed.

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 Appendix H Recommended CytoScan XON array workflows
Whole exome analysis H

Figure 537 Example: Level 1 check only

4. Add the XON Region Level and Summarized Log 2 Ratio columns to the segment
table, then use the Segments Table to review the XON Region segment calls.
5. Optional: Annotate the XON Region segments as you normally would using the
Call and Interpretation columns, as described in "Adding annotations at the
sample (xxCHP) file level" on page 250.
6. Optional: Exon Region segment calls from other Levels can be displayed by
selecting the check box(es) in the Filters Tab.

Figure 538 Example: Level 1 and 2 checked

7. Optional: Publish the XNCHP file to the ChAS DB, as described in "Publishing
data to the database" on page 406.

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 Appendix H Recommended CytoScan XON array workflows
Whole exome analysis H
Targeted analysis When you have a specific set of genes that you want to search for XON Region
segment calls, a targeted analysis can be performed using CytoRegions for Targeted
XON analysis. Details on this feature can be found in "Assigning a CytoRegion for
targeted XON analysis" on page 277.
1. Create an AED file from your list of genes. See "Creating an AED File from a gene
list" on page 277. If you already have an AED/BED file containing your genes of
interest, go to step 2.
2. Click File → Open to load the AED/BED file.
3. Locate the file, then click Open.
4. Right-click on the loaded file, then select Set File as CytoRegion for Targeted
XON Analysis.
This assigns the file as a CytoRegions File, as well as automatically sets the
appropriate filters for Targeted XON analysis. The filters hide all segments in the
Genome region and colors all the data gray and turns on all levels in CytoRegions
to expose any XON Region segment call and colors the data the assigned sample
color.
Note: Only XON Regions calls within the CytoRegions are displayed in the views
and tables.
5. Optional: Annotate the XON segments as you normally would, as described in
"Adding annotations at the sample (xxCHP) file level" on page 250.
6. Optional: Publish the XNCHP file to the ChAS DB, as described in "Publishing
data to the database" on page 406.

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31 January 2023