Instructions for Use FastFinder Genotyper

Updated NOV 3, 2022, Genotyper Release V2.0

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Introduction to FastFinder Genotyper

FastFinder Genotyper genotyping platform

FastFinder Genotyper is a cloud platform on which UgenTec supports you in analyzing and
interpreting endpoint PCR data. The combination with an integrated algorithm, allows the
generic FastFinder Genotyper platform to turn into a system for automating PCR analysis
interpretation for a specific assay. This assay-specific algorithm is trained to differentiate
cluster calling and converts the raw PCR data into end-results. Overall, the result is an analysis
workflow that begins with the import of raw PCR data and ends with a sample result.

The FastFinder Genotyper environment

FastFinder Genotyper is designed to feel as familiar and intuitive as your internet browser
with all your analyses and plates displayed as hyperlinks accessible with a single click. From
your homepage, you access all available orders and in the side navigation on the left, separate
FastFinder Genotyper modules are devoted to Orders, Assays, Insights, Instruments, Settings and
Support. Y ou can open multiple browser tabs, enabling multiple orders to be processed at
the same time.

Key concepts:

Algorithm: The data analysis component of the platform: it is trained on representative data to
differentiate clusters and to provide a calling for each well on a PCR plate. The calling is the result
determined by the algorithm.

Order: Associated group of assays and plates that are analyzed together.

Laboratory environment: the shared workspace for all FastFinder Genotyper users in your
laboratory, pertaining to a single database and a set of users managed centrally from the admin
module.

The following symbols are used in FastFinder Genotyper

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 Zoom

Open Order/Assay in new browser tab

Area zoom

History grid visualization in graph

No warnings

Selection lasso-tool

Redirect to assay information in assay module

Flagged assay – Unflagged assay

Save history grid for this assay – Do not save history grid

Assay contains a comment in the assay module

PCR plate has user edits

Locked History Grid

Order information

Show plot legend

Reset plot scaling

Table overview

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 Plate view

Help module

Settings module

Home page

Minimum system requirements

Hardware requirements:

• Processor: 2 GHz, 2 GB RAM

• Disk space: none

• Broadband internet connection (*.ugentec.app, port 443)

• Screen resolution: min. 1280 x 960 pixels

Supported browsers:

• Microsoft edge

• Firefox

• Google Chrome

UgenTec customer support

For technical support in setting up and operating your FastFinder Genotyper laboratory
environment,please contact [email protected]

Setting up your FastFinder Genotyper laboratory environment

FastFinder Genotyper is browser based and is accessed via https://tenantshortcode-
fastfinder.app/genotyper for the production environment and https://tenantshortcode-
test.fastfinder.app/genotyper for the test environment.

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Credentials are provided by your contact person at UgenTec or via [email protected]

Input data to FastFinder Genotyper

There are two methods of creating ‘orders’ in FastFinder Genotyper.

For Kraken users (LGC), connection to the Kraken database will be made after installing
Fastfinder Drive. After installation, Kraken orders with the correct predefined status are
automatically uploaded and analyzed within Genotyper and automatically submitted back to the
Kraken database. To install Fastfinder Drive, an installation file is required and an installation manual
where every important step is explained.

For users of other platforms, data import can go via file based import. UgenTec foresees several
formats of the shelve, but for specific formats, please contact [email protected]. Custom
made parsers can be developed for your specific data usage.

FastFinder Genotyper modules

The FastFinder Genotyper platform consists of five main modules which can be selected in
the side navigation:

• Orders module, where the result interpretation takes place

• Assay module, which provides an overview of the configured assays
• Insights module, which can provide an overview of data insight dashboards
• Instruments module, which provides an overview of all instruments and specifications
• Settings module, which allows you to configure your laboratory preferences
• Support module, that contains product documentation and Support contact details

In this IFU, an overview is given from the modules and functionalities.

For a training which provides more in depth details, please reach out to your UgenTec contact
person.
Settings
In the Settings module you can configure General settings and map sample statuses that will be
applicable for all analyses.

General Settings

In General Settings, the user can configure warnings, graph settings and plate settings.

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A user can enable or disable ‘Uncalled warnings’, ‘Shortfall warnings’ and ‘Failed NTC warnings’. For
every warning, a user can define a threshold above which the Genotyper system will show the
respective warning. During analysis of a specific order, these settings can be changed for that specific
order via the ‘Actions’ button.

Under Graph Settings, a user can choose how the graphs will be visualized. Uniform Axes will result in
a graph with the same length for the X-axis and the Y-axis. Fit around data will automatically create
an X-axis and Y-axis that fit the data and fit around data and history will create an X-axis and Y-axis
that fith both the data and the history.

Under Plate Settings, a user can choose the default behavior for plate selection when selecting an
assay in the matrix screen of an order. First plate selected will result in the first plate being selected
in the plate table on the results screen. All plates selected will result in all plates being selected in the
plate table. No plates selected will result in no plates being selected in the plate table.

Changes to the General Settings will be saved automatically.

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Sample Statuses

In the sample statuses (i.e. call names) tab, a user can configure the sample statuses to be used
within the application. Genotyper uses a default set of statuses, but every sample status can be
renamed.

For Example, by pushing the ‘plus’ button, a new mapping entry is added to the ‘Status Mappings’
list. The user can then select a default status from the dropdown. In this case, status ‘Shortfall’ is
selected. For the selected status, a user can now enter a text to rename this status. This same action
can be performed for every default status that is known to the Genotyper system.

Instruments
In Genotyper 2.0, every known instrument will be shown in the instruments list. A User can enter this
list from the ‘Instruments’ button in the side navigation. After doing this, the user will be redirected
to the following screen:

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On the left side, a list with known instruments is shown. A user can add instruments manually or
instruments are automatically included in this list when the Genotyper system detects a new
instrument in the import files.
For every instrument, a user can change instrument specific parameters as can be seen on the right
of this screenshot. Important to understand, is that these parameters influence the algorithm and
thus the callings of datapoints.

User Roles
FastFinder Genotyper offers 3 user role types to its users.

Regular user (no role)

A regular user can import files/data, can edit graphs, can change calls. The regular user has no
rights to submit the order.
The regular user can watch history grids. The regular user can also not change any settings.
The regular user is often used for trainees, interns, or temporary users of the platform.

Authorizer role

The authorizer can import files/data,can edit the graphs,can change calls. The authorizer can
submit orders. The authorizer can watch history grids and reset them.
The authorizer cannot change settings.
The authorizer role is used for most users who need full control of the software, but not of the
settings.

Admin role

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The admin can do everything possible in the platform, and on top of the authorizer role, he can
change settings. The admin role is mostly given to the champion user or to IT who need to set
certain settings.

Changing roles goes via a request to [email protected]

Performing an automated analysis

FastFinder Genotyper: a brief overview

Given sufficient configuration of your FastFinder Genotyper environment described above, only
four actions are required to complete an analysis:

• Import new orders

o For Kraken users this is done automatically via Fastfinder Drive
o Other users can import files manually

• Choose an order in the Orders module

• Check the plots with analysis warnings, and if necessary, correct the calling of the data
points

• Submit your results back to Kraken or export a file

All of the above steps take place within the Orders module of FastFinder Genotyper following an
analysis workflow of order import, algorithm analysis, and result submission.

Getting Started
In the Orders module you can select the orders you want to process by filtering on the header
columns.

There are two possibilities for new orders to be imported in Genotyper: via Kraken, or by
uploading files manually.

Kraken

Kraken orders will be imported and analyzed automatically. This will be possible after installation and
configuration of Fastfinder Drive. After configuration, Fastfinder Drive knows the Kraken status for
orders that need to be imported into Genotyper. When the Kraken user sets the status of an order to
this specific status, Fastfinder drive will automatically import these files into Genotyper. When the
import of new orders is finished, these orders will automatically be analyzed.

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Manual import

It is also possible to import files manually, for which no Kraken database is required. To do this,
the user clicks on ‘create new order’ in the upper right part of the home screen, after which the
import screen is shown.
A user can then drag and drop files in this screen, or click on the ‘upload new files’ button to open
the file explorer.

After upload, the files are shown in the upload table. After selection of the reader to be used (only
for array tape files), the files can be analyzed by clicking ‘analyze selected’. The import screen should
be closed manually by the user.

Every order that is imported into genotyper will be in a certain order status. This status informs you
about the progress of the analysis.

• Status ‘Importing’: the data is being imported into FastFinder Genotyper

• Status ‘Imported’: the data is imported into FastFinder Genotyper

• Status ‘Analysis pending’: analysis of this order has not yet been completed

• Status ‘Analyzed’: the algorithm is finished analyzing the data

• Status 'Authorized’: the analyzed data is submitted back to Kraken Clicking on the home icon

returns you to the list of orders

Clicking on the plus icon in the order table will open this order in a new browser tab. Clicking
elsewhere in the row of an order will open the order in the current browser tab.

TIPS:

A user can filter the orders table with the filters shown above the table. Additional filters can be
created by clicking the ‘add filter’ button. A user can sort the table on ID, reference, name, … by
clicking on the respective column header.

A user can configure the orders table by clicking on the settings icon on the upper right part of the
table

Order Overview

Upon selecting an order, you are directed to the order matrix which gives an overview of all
assays (left column) and PCR plates (matrix on the right of the assay column). Based on the

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warning level settings, assays/plates are either acceptable (checkmark) or flagged for review.
Warnings (in orange for assays with uncalled points or yellow for assays with shortfalls) are
indicated per plate. A sum of all warnings is shown next to the assay, and these are sorted
descending. Assays are sorted either alphabetically , or by warnings .

At the top right corner, you can choose to:

Authorize the results back to Kraken or export a file with the call results

Edit the results:

Change the Analysis settings for this particular order.

Apply a Drill down factor to set master plates to bad. The Drill down functionality allows users to
determine if a sample on a master plate is bad by calculating a Drill down factor. The Drill down
factor is the percentage of all called wells (not shortfall or uncalled) of all results related to a
sample on a masterplate. Uncalled means that the data was not clear enough to determine a
result and shortfall means that the ROX fluorescence did not pass the threshold. The user can
set the Drill down factor to a certain percentage and all wells below this factor will be indicated
as failed.

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Assay Results
Upon selecting an assay, you are directed to the assay results. The left column contains the
assays, you can navigate through the assays with the ‘left’ and ‘right’ arrows.

Each assay will be represented in (a) PCR plate(s). Navigating through the PCR plates can happen
with the ‘up’ and ‘down’ arrows.

Above the PCR plates, there is an order summary which contains the overall statistics of
shortfalls, uncalled/called samples or failed NTC’s.

Next to the assay name there are icons representing information on the assay:

redirects you to the assay in the assay module

there is a comment about this assay in the assay module. Hovering over this icon also shows
you this comment

Flagging of the assay. Flagging an assay is done when an assay always needs to be reviewed
and will end up on top of the assay result list

PCR plate actions

In the plate overview, specific PCR, DNA or master plates can be selected via the dropdown filters.

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On top of the plate, there are plate sample selection tools available.

Options available are:

• Sample selection: you select 1 sample, or you can drag your mouse over the plate and
select a region
• Column selection
• Row selection
• Quadrant selection
• Select all samples
• Deselect all samples

Tip: Hovering over a sample will show you the sample information.
Selecting one or multiple plates, allows for the user to perform batch actions on the PCR plates

Undo user edits for selection: on the selected plates, the edits manually done by users will be
erased.
Do not authorize selection: The plate/selected plates will not be authorized(no calls will be made)
when the order is exported/authorized (only for Kraken)
Authorize selection as failed: The plate/selected plates will be authorized as failed when the
order is exported/authorized (only for Kraken)
Mark selection as unread: the selected plates will appear unread again
Mark selection as read: the selected plates will appear read

On one plate specifically, you can also perform actions by clicking the 3 dots. An action you can
do here is authorizing a certain read of choice.

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 Scoring an assay
The graph shows how the samples are grouped on a specific plate for an assay.
The algorithm has tried to score as much as possible automatically, but there are tools
available for manual scoring of the groups/samples. Under the graph, you can see
which read the algorithm has chosen for scoring the algorithm. As a user, you can
select the read of choice with the slider and by saving the chosen read.

With the lasso tool, , samples/clouds can be selected and when clicking on the according
call, the call will be assigned. There are also shortcuts available:
• 1: red (homozygous YY)
• 2: green (heterozygous)
• 3: blue (homozygous XX)
• 5: no call
A legend for all used colors in the graph is shown in the upper left part of the graph.
History grid visualization: A history grid is built up per reader and per assay, as each reader can
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have different calibrations. The history model will be visualized with contour plots, as can be seen
in the example.

The icons in the graph mean: Open color selection dropdown, move graph area, zoom to area, lasso
tool, reset graph zoom, automatic graph zoom.

Submitting the order

Go back to the ‘Order overview’ and click the ‘Authorize’ button

Click Authorize.

You will see a double arrow appearing next to the assays that have been submitted. After
submitting, a user can still access the order, but it will not be possible to change information and
submit again.

For Kraken users, the order will be written back to the Kraken database. For file based orders, a
csv file will be downloaded with the called results.

Assay Module

The assay module can be seen as a library of the assays that were used/imported in Genotyper.
The library is built up automatically by importing files/orders in Genotyper.
By clicking the ‘+’ sign, assays will be opened in a new browser tab. In the table overview you can
flag an assay.
When you need to perform these actions on all assays simultaneously, you can perform batch
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actions by the Actions menu in the right upper corner.

Flag: flag all assays/unflag all assays

Import assay alleles: this is for users of Array Tape files where Genotyper does not get input of
the assay alleles via the input files. A csv file with the assay name; X-label, Y-label can be imported
like this and then these allele labels will be used.

When an assay is opened (clicking on the assay or opening by the + sign in a new tab), the ‘history
model’ of the assay can be inspected. These are a collection of scores of several PCR plates.
History grid is always saved per reader as readers can have small calibration differences.

Assay comments can be added to the assay record:

Here you can add important information about an assay. A comment can be edited or deleted
afterwards by the user who as written the comment.

(Assays with a comment will get a comment icon to indicate this, next to the assay name in
the assay order overview.)

This summarizes all features of Genotyper, for all questions, please reach out to
[email protected].

Thank you!

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The UgenTec FastFinder Genotyper Team

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