Summary

With the release of Genotyper 2.0, several new features and improvements have been implemented. Genotyper 2.0 is more performant and developed in such a way that more functionality can be added easily in future releases.
In General, this release consists of three important topics: Platform Integration, Algorithm 2.0 and Data Intelligence. We have the vision for Genotyper to evolve to an agnostic application that does not only automate your cluster calling with AI, but also has the capability to leverage Data Intelligence to create even more insights in your genotyping lab.

General

Platform Integration

• Genotyper 2.0 is integrated in the FastFinder Platform, Genotyper Users can thus benefit from other platform applications such as Fastfinder Workflow.
• The Kraken FastAgent connection is replaced with Fastfinder Drive. To link your Genotyper environment with Kraken, FastFinder Drive should be installed on your on-premise Kraken server.

Algorithm 2.0

• The new algorithm will allow for better generalization over different instruments and data quality. The algorithm does not have to be tuned for every separate instrument type and thus allows more flexibility in using different instrument types.
• Concept of history is implemented and used in a different way
  • History is no aggregate of all passed results as before, but will model evolution of an assay
  • History will be insensitive for shifting of assay results
  • History will be insensitive for wrongly called outliers
  • The history model is managed by the algorithm, no responsibility lies on the User
• Due to the characteristics of the history, visualization is different compared with Genotyper 1.X.
• Certain warnings will be shown in case the algorithm detects an issue during the processing of input data. These warnings will be visualized per read on the results screen. In total, eleven warnings can be shown, each for one of the following warning types:
  • Preprocessing warnings
  • Algorithm failure warnings
  • Incomplete history warnings
  • History training warnings
• A User will have the possibility to tune the algorithm manually with parameters. In this way, Users can tailor the algorithm to their needs and wishes. More parameters can be included in the future. The parameters that are available today are:
  • Deconvolution parameters
  • Background correction parameters
  • Normalization
  • Aggressiveness

Data Intelligence

• Multiple dashboards created with Power BI are added to Genotyper under the tab BI insights. ‘Basic dashboards’ are generally made available, ‘Pro dasboards’ are available upon additional payment. Custom dashboards can be built for clients upon additional payment.
  • Basic dashboards:
    • Order overview
    • Sample overview
    • Assay overview
  • Pro dashboards:
    • User overview
    • Sample result overview
    • Assay usage overview
    • Algorithm overview
  • Custom Dashboards

UI – UX

• UI was rebuilt based on FastDesign UI components. In this way, Genotyper has the same look and feel as other Fastfinder products.
• Several improvements were made to increase the overall User Experience
  • Settings
  • Instruments
  • AI Warnings

Feature changes and improvements

Technical Improvements

• Backend is upgraded to .NET6
• Frontend upgraded to Angular 14
• Extensive refactoring of back-end code for better performance and scalability

URL to enter Genotyper Application

• Test environment: https://tenantshortcode-test.fastfinder.app/genotyper
• Production environment: https://tenantshortcode-fastfinder.app/genotyper

Side Navigation

The side navigation bar will consist of a few new entries. The ‘Insights BI’ button will lead to an overview of all created dashboards, where users can track certain metrics on the usage of Genotyper. The ‘Instruments’ button will lead to an overview of all instruments known by Genotyper. The ‘Orders’ button replaces the ‘Analyze’ button that was used in Genotyper 1.X.

Settings

To become a more scalable and general software solution, Genotyper 2.0 will only show settings that are relevant for a specific user. For example, previously a tab ‘Kraken Settings’ was visible, also for users that did not use Kraken in their lab. In Genotyper 2.0, we want a more general solution for everyone. For this reason, the settings screen will be organized in a different way.

• ‘Kraken Settings’ will be removed as it is not necessary anymore because Kraken Fastagent is replaced with Fastfinder Drive
• ‘Arraytape settings’ will be removed as these parameters will be configurable for every instrument in the instrument list.
• ‘Analysis settings’ and ‘Graph settings’ are still available but now as ‘General Settings’

The new Settings Screen will consist of a tab ‘General Settings’ and a tab ‘Statuses’. The ‘General Settings’ tab will consist of the following settings:

• Warnings: The User can enable/disable warnings and define a certain threshold above which the warnings will be shown. There will be three different warnings:
  • ‘Uncalled warnings’ to be shown when percentage of uncalled datapoints is above given threshold (percentage)
  • ‘Shortfall warnings’ to be shown when number of shortfall datapoints is above given threshold (absolute number)
  • ‘Failed NTC warnings’ to be shown when number of failed NTC is above given threshold (absolute number)
• ‘Graph Settings’ to configure how the axes of graphs in Genotyper are formatted
  • Uniform axes
  • Fit axes around data
  • Fit axes around data and history
• ‘Plate Settings’ to configure default behaviour for plates and plate selection
  • First plate selected
  • All plates selected
  • No plates selected

In the ‘Statuses’ tab, a user can map every Genotyper status with names that suit their needs better

• With the “plus” button, a User can add a mapping to the list
• In the dropdown, a User can select the Genotyper specific status to rename
• In the textfield, a User can enter a new name for this status

Instruments

• List with instruments accessed with the ‘Instruments’ button in the side navigation
  • Instruments can be added manually by the user
  • If Genotyper encounters an unknown instrument, it will automatically add this new instrument to the list
• For every instrument, certain parameters can be changed
  • Instrument ID: Unique ID of the instrument, should not be changed
  • Instrument shortfall cutoff
  • Instrument information: text field where user can add information regarding the instrument
  • Instrument deconvolution parameter X
  • Instrument deconvolution parameter Y
  • Instrument background correction X
  • Instrument background correction Y
  • Instrument normalisation
• Before uploading an array tape file, the user should create the reader in the instruments list

Audit Logging

Genotyper 2.0 will keep track of certain activities by users in the application. Genotyper sends information to be saved in the audit logs. In Genotyper 2.0 , these audit logs will not yet be accessible by users but can be requested via support. The following data will be saved in the audit logs, always with a timestamp and email address of User:

• Successfully logged in
• Change instrument settings
  • Added a new instrument
  • Updated instrument settings
• Change callings
  • Datapoints on plate … were called manually
• System migrated to new version
• Order authorized

Drilldown Functionality

• Drilldown functionality will still be used on a masterplate level
• Following ratio is calculated (# AssaySamples with status Called, Failed Control, Passed Control)/ (# AssaySamples with status Called, Uncalled, Shortfall, Failed Control, Passed Control)
• The user chooses a drilldown percentage and a master plate well is failed if the calculated ratio is lower than this percentage for the callings of this respective master plate well
• This calculation will now be done per read and samples are thus being set to bad per read
• If user decides to change the chosen read, the drilldown has to be performed again
• A reset button will allow to reset the Drilldown for all selected masterplates
• Bad samples (yellow color) will be visualized on the PCR plate as before but now also in the graph

File Import Screen

• To import new files into Genotyper, Users click on the ‘Create New Order” button in the right upper corner
• Users can upload files by drag&drop or by clicking the ‘upload new files’ button
• For every order, the User can select the ‘Aggresiveness’ to be used when calling the datapoints. This is done under the ‘Actions’ button.
• Once a file is uploaded, the file has a color depending on the next steps to take
  • White: file can be analyzed
  • Yellow: a reader needs to be assigned
  • Red: a problem occurred
• White files can be imported to Genotyper 2.0 as an order and analyzed

Order Table

• The order overview table will change and will be similar as the tables in other Fastfinder products
• Several filters allow users to search and filter the table more easily
• Custom filters can be created
• Users can configure the layout of the table
  • ‘ID’, ‘Reference’, ‘Name’ and ‘Status’ columns are always shown
  • ‘Assays’, ‘PCR plates’, ‘Master Plates’, ‘Created At’, ‘Created By’, ‘Last modified At’ and ‘Last Modified By’ columns can be hired
• Historic orders will still be shown with the status ‘legacy’, new orders will be added at the top of the table as before
• It is now possible to open new orders in a new browser tab by clicking on the ‘plus’ icon.

Order Overview Screen

• ‘Edit’ button will become ‘Actions’ dropdown

Result Screen

• If multiple reads are detected, the algorithm will select the best read. This will be indicated with the tekst ‘algo chosen’. If a user selects another read, this is indicated with the test ‘user chosen’
• Under the graph, a ‘Warnings’ icon is added. After clicking this icon, all warnings regarding this specific PCR plate and read will be shown.

Authorize Behaviour

• In Genotyper 2.0, it will only be possible to Authorize an order once. After authorizing, it will still be possible to view the results, but it will not be possible to change callings and authorize again.
• After submitting, the export files can be downloaded by clicking on the ‘Actions’ button and selecting the file that you want to download.