We are happy to introduce several enhancements and new features in our latest update:
Change the Affected Status of Family Members
You can now change the Affected status of family members in a family case, after the case was created. This enhancement allows you to update the disease status in a family based on clinical information that was not known or was not available when the case was created.
Changing the Affected status of family members can be done from the Case Details popup:
Upon changing an Affected status, a family analysis rerun is triggered, recalculating variant inheritance models and applying the assay’s latest Filter Decision Trees. This process will hence update variant annotations and accordingly update the case’s workbench and filtering results.
Affected status changes are also reflected in the Family Pedigree visual, and are logged in the Case History tab.
Support for DRAGEN roh.bed Files
Franklin now supports DRAGEN’s roh.bed files. When configured in an assay, these files are parsed and used to populate both the ROH widget and the ROH filter in the Variants tab.
If the DRAGEN option is enabled in an assay but no file is provided for a specific case, ROH data will not be displayed. Additionally, please note that the data from DRAGEN does not affect Franklin’s UPD detection algorithm.
By default, Franklin uses its own algorithm to calculate ROH. If you’d like to switch your assay to use DRAGEN’s ROH output, please contact our support team ([email protected]).
Support Manta-Detected Breakend Variants in the Report
With the recent addition of Manta-detected Breakend variants in Franklin, you can now streamline your workflow by including Breakend variants directly in your report.
Export All Variant Submissions from the Knowledge Base
Until now, export of variant information from the Knowledge Base has been limited to only the latest submission per variant. The Knowledge Base can now be configured to export all variant submissions. Please contact our support team ([email protected]) to set this configuration for your Knowledge Base.
Display SMN Copy Numbers when Negative to SMA
The Workbench SMA biomarker can now display the copy numbers of SMN1 and SMN2 genes when the case is negative to SMA.
Bug Fixes:
Tumor Cases: Replacing Auto-Filled Cancer Type in Somatic Classification
In tumor (somatic) cases, fixed an issue where the auto-filled (case’s) cancer type could not be replaced and persisted in the Variant Interpretation popup. Submitting a somatic classification with no cancer type or a cancer type different than the case’s is now fully supported.
Tumor Cases: Manually Added Variants Export Failed
In tumor (somatic) cases, fixed an issue where the workbench export failed when including manually added variants.