Introduction to Microarray

Technology
Presenter: Wayne Xu, PhD
Computational Genomics Consultant
Supercomputing Institute
Email: [email protected]
Phone: (612) 624-1447
Help: [email protected]
(612) 626-0802
 Outline
• Introduction
• Array chips
– cDNA array
– Affymetrix array
• Microarray experiment and data
acquisition
• Data analysis
Introduction
What is microarray?
 Microarray
– A high throughput technology that
allows detection of thousands of genes
simultaneously
– Principle: base-pairing hybridization
– Much rely on computer aids
– Central platform for functional genomics
 Features
– Parallelism
• Thousands of genes simultaneously
– Miniaturization
• Small chip size
– Multiplexing
• Multiple samples at the same time
– Automation
• Chip manufacturing
• Reagents
What circumstances brought
out this technology?
– Fact: biological processes are
complicated with many molecules
working together. Biologists are eager
to obtain the “whole picture”
– Genome sequences availability
– Computer aids
What problems can it solve?
– Differing expression of genes over
time, between tissues, and disease
states
– Identification of complex genetic
diseases
– Drug discovery and toxicology studies
– Mutation/polymorphism detection
(SNP’s)
– Pathogen analysis
 What is its pitfall?
– Detect transcription mRNA level, not translation
protein level
– Many factors (variations) can affect the result
• Chip and probe design
• Experiment design
• Sample preparation
• Image acquisition
• Data normalization
• Data analysis
• ….
– Success crucial:
• You know both the biology problem and the computer
aids (software, statistics).
 Principle
• Similar to Northern
– Base-Pairing, hybridization between nucleic
acids
• Major differences from Northern
– Detects thousands of genes simultaneously
/individual
– Probes fixation on glass slide / nylon membrane
– Target samples labeling with
fluorescent/radioactive dNTP
 Principle
• Base-pairing
– DNA: A-T and G-C
– RNA: A-U and G-C
Principle
 Northern Blotting
Northern measures relative expression
levels of mRNA

– mRNA isolation and purification

– electrophoreses on a gel
– The gel is probed by hybridizing with a
labeled clone for the gene under study.
Northern Blotting
 Microarray Steps
• Experiment and Data Acquisition
– Chip manufacturing
– Sampling and labeling
– Hybridization
– Image scaling
– Data acquisition
• Data normalization
• Data analysis
• Biological interpretation
Array Chips
Introduction
 Array Chip Types
1. cDNA chip (DNA microarray, two-channel
array):
– Probe cDNA (500~5,000 bases long) is
immobilized to a solid surface such as
glass
– Using robot spotting
– Traditionally called DNA microarray
– Firstly developed at Stanford University.
 Array Chips
2. Gene chip (DNA chip, Affymetrix chip):
– Oligonucleotide (20~80-mer oligos) is
synthesized either in situ (on-chip) or by
conventional synthesis followed by on-chip
immobilization
– Historically called DNA chips
– Developed at Affymetrix, Inc. , under the
GeneChip® trademark
– Many companies are manufacturing
oligonucleotide based chips using
alternative technologies
 Affymetrix Chip
• Each gene has 16 – 20 pairs of probes
synthesized on the chip
• Each pairs of probes have two
oligonucleotides
–Perfect match (PM, reference seq) ATG…C…TGC (20-25
bases)
–Mismatch (MM, one base change) ATG…T…TGC

• The scanned result for a given gene is the

average differences between PM and MM
signals, over probes
–(MAS5 algorithm)
Introduction
Introduction
Principle
 The photolithgraphic method
1. Treat substrate with chemically protected
“linker” molecules, creating rectangular
array
• Site size = appro. 10x10 um
2. Selectively expose array sites to light
• Light deprotects exposed molecules, activating
further synthesis
3. Flush chip surface with solution of
protected A,C,G,T
• Binding occurs at previously deprotected sites
4. Repeat steps 2&3 until desired probes are
synthesized
Introduction
Introduction
 Manufacture cDNA Array
• Start with individual genes, e.g. the
~6,200 genes of the yeast genome
• Amplify all of them using polymerase
chain reaction (PCR)
• “Spot” them on a medium, e.g. an
ordinary glass microscope slide
• Each spot is about 100 µm in diameter
• Spotting is done by a robot
Introduction
Introduction
 Contact Printing
• pins
– Uptake 0.25 ul
– Dispense 0.6 nl
– (approximately 1-10ng
per spot)
– 100 um feature size
 Non Contact Printing
• Piezoelectric
• Ink jet
• Higher reproductivity
• 1 drop = 100 picolitres
Experiment & Data
Acquisition
 Example
• Extract mRNA
• Convert mRNA into colored cDNA
(fluorescently labeled)
• Mix labeled cDNA together
• Hybridize cDNA with array
• Each cDNA sequence hybridizes specifically
with the corresponding gene sequence in the
array
• Wash unhybridized cDNA off
• Read array with laser
• Analyze images
 Affymetrix Microarray
Experiment
1. Sample RNA labeling
– First-strand cDNA synthesis
• Reverse transcriptase
– Second-strand synthesis
• DNA polymerase
– cDNA purification
– In Vitro transcription to synthesize
biotin-labeled RNA
• T7 enzyme
2. Fragmentation
– Use heat and Mg++
– Reduce RNA to 25-200 bp
fragment
– Facilitate efficient and
reproducible hybridization
3. Hybridization
– Preheat hybrid mix solution (99 C)
– Affy chip in hybrid solution 5min
– Add probe and hybridization for 16
hours
4. Wash and Stain
– Wash buffer
– Stain with a fluorescent molecule
(streptavidin-phycoerythrin) that
binds to biotin
– A signal amplification step that
employs anti-Streptavidin
antibody (goat) and biotinylated
goat IgG antibody
5. Scan
– Affymetrix scanner and follow
the menu
– .dat image file
– .cel tab delimited file
– .CHP data file
 Data Acquisition

• Affymetrix Microarray Suite

• GCOS (Genechip Operating System)

• Need chip description file (CDF)

– For probe location
Introduction
 .Cel file
X Y Mean STDV NPixels
0 0 166 30.8 16
1 0 13135 1216.2 16
2 0 165.3 25.5 16
3 0 13706 1305.2 16
4 0 95 24.9 16
5 0 155.8 21.8 16
6 0 11675.8 1296.9 16
7 0 184 24.3 16
8 0 11465.5 1533.1 16
.. .. .. .. ..
 .CHP text file

ID Signal Det P-value Desc

AFFX-CreX-5_at 1200.5 P 0.0007 X03453
AFFX-CreX-3_at 235.8 P 0.0005 L38424
AFFX-CreX-9_at 15 A 0.5 K01391
.. .. .. .. ..
 cDNA Microarray
Experiment
1. Array fabrication
– DNA clones
• Unigene
• EST clustering
– PCR amplification of clones
– Array printing
Overview of Example

Brown & Botstein, 1999

2. Probe preparation
– RNA extraction (control, test)
– RNA labeling
• Incorporate fluorescently labeled
deoxyribonucleotides
• First strand cDNA
• Cyanine5 labels Test sample RNA
• Cyanine3 labels Control sample RNA
– Mix the labeled two RNAs
3. Hybridization
– Prehybridize slide 42C 45 min
– Hybridize preheated probes 16-20
hours
4. Slide scaning
– C3 16-bit TIFF image file
– C5 16-bit TIFF image file
 Data Acquisition
• GenePix
• Quantarray

• Need chip description file (CDF)

– For probe location
Introduction
 Raw Data

Name ch2/ch1 Ratio

Control_M12 2.953803
PPSL_25A09 1.206626
PPSL_25C09 2.389387
PPSL_25E09 2.24675
….. ….
Data Normalization
and Data Analysis
 Data Normalization
• Why?
– Reliability
• Remove non-biological variation
– Comparability
• Scale (multiplicative factor)
 Data Analysis and
Visualization

• Use microarray software

• Address biological questions
 Address Biological Questions
• What genes are involved in a particular
biological process?
• What genes are turned-on?
• What genes are turned-off?
• What genes are the key elements in a
biological process?
• Similar clinic samples share similar
gene expression profile?
– Sample classification
 Address Biological Questions
• What genes have similar profile?
• What are the features for the similar
profile genes?
– Gene classification
• Functional annotation
• Pathways
• What is the functional behavior of a
particular gene?
– Functional screening
 Software Tools
• GeneSpring (SiliconGenetics)
• Expressionist (GeneData)
• GeneTraffic (Iobion)
• Spotfire (Spotfire)
• Cluster and TreeView (free)
• …..
Gene Lists
Introduction
Clustering of entire yeast genome

Campbell & Heyer, 2003