We are happy to introduce several enhancements and new features in our latest update:
HBA Biomarker from DRAGEN Caller Output
As part of the DRAGEN/Franklin ongoing compatibility enhancements, Franklin now includes HBA biomarker information derived from the DRAGEN HBA caller in WGS analyses.
The HBA caller genotypes HBA1 and HBA2 genes. Those genes, which encode α-hemoglobin, are located back-to-back with high homology. In noncarrier individuals, there are typically four functional copies (two of each gene), while the severity of symptoms in affected individuals is influenced by the number of nonfunctional copies.
With this update, you will now see the HBA caller output in Franklin. If four functional copies are detected, it will be indicated as a "Normal copy number". However, if nonfunctional copies are detected or small variants appear in the HBA1 and HBA2 regions, Franklin will display the total HBA copy number, genotype, interpretation, and details of any small variants present in those regions:
The HBA biomarker will be displayed in the Workbench under “Additional Information” section.
Tumor Cases: Copy Number Calculation Corrected for Tumor Purity
In tumor (somatic) cases, the copy number calculation can be configured to be corrected for tumor purity when calling CNVs using our propriety caller Rainbow. The calculation considers the sample sex, tumor purity, and raw variant copy number. Applying this configuration will allow you to view, filter (using the Estimated Copy Number filter) and report purity-corrected copy numbers. The variant tile will show the corrected copy number in the Copy Number field, and the raw copy number in the Raw CN field as well as the Confidence section:
Contact our support team ([email protected]) to enable this configuration for your organization.
Tumor Cases: Enhanced Variant Filtering with Status Tags
Tumor (somatic) cases can be configured to support tumor mutational burden (TMB) information from DRAGEN TMB output. This enhancement allows for viewing and filtering on the variant’s germline status (appearing in a germline database, calculated as germline by proximity, or only somatic). This information can be displayed on the Custom Annotation section of the expanded variant tile, and is filterable via the Custom Annotation filter. Please contact our support team ([email protected]) to enable this configuration for your organization.
Long-Read Sequencing: Support for Sniffles2 Caller Output
Franklin now supports case creation from the VCF output of Sniffles2 long-read sequencing caller. Upload of VCFs is supported from sample sheet or API, for both SNP and SV caller outputs. Please contact our support team ([email protected]) to enable this workflow for your organization.
Bug fixes:
Cancellation Popup Appears After Successful Case Creation
Resolved an issue where the case creation cancellation popup (“Are you sure…”) appeared following successful case creation if the Assay input field was active when clicking Next to create the case.