We are happy to introduce several enhancements and new features in our latest update:
Missing Phenotype Categories in Variant Highlight
In germline cases, we enhanced the genotype-phenotype variant highlight feature. When hovering over matching case phenotypes, you will now see a new section in the displayed tooltip, labeled “Main categories absent from case”:
This section lists the main phenotype categories associated with conditions linked to the gene, if non of these categories are present among the case’s phenotypes. The absence of the main categories can affect the gene-phenotype scoring, providing better transparency as to why a score may be lower than expected. This capability allows you to better understand which important phenotypic categories are missing from a diagnostic case. Note that for genes which have more than one main phenotype category, the score will be affected only if the case’s phenotypes do not match any of the main categories
Tumor Cases: Quality Score Displayed for CNV
In tumor (somatic) cases, the expanded tile of CNV in the Workbench or Variants tab now shows the Quality score under the Confidence section.
Tumor Cases: Display STAR-Fusion Quality Annotations
In tumor (somatic) cases, fusion variants can now display on the expanded tile quality annotations from STAR-fusion calling pipeline, such as junction read count and large anchor support. This information is displayed under the Extra VCF Annotations section, and does not change Franklin’s Confidence calculation for the variant. To enable this for your assay, please contact our support team ([email protected]).
Tumor Cases: Configuration for Clinical Trial Inclusion/Exclusion in Report
We recently introduced a Clinical Trials section in the Case Summary tab of the Workbench in tumor (somatic) cases, allowing you to select clinical trials to include in your report. It is now possible to configure whether clinical trials are included or excluded in the Report (by default they are included). Contact our support team ([email protected]) to have this configuration changed for your organization.
Tumor Cases: Variant Type Update in Workbench Export
In tumor (somatic) cases, the Workbench (WB) export file’s “Variant Type" column now displays "SV" instead of "CNV" for all structural variants. The “Variant Subtype” column continues to show a more specific SV type, such as deletion, duplication, or fusion.
Bug Fixes:
Cytoband Displayed instead of Gene Name in Breakend Variants
Resolved an issue in Breakend variants from Manta caller output, where the cytoband was displayed on the tile instead of the gene name.