We are happy to introduce several enhancements and new features in our latest update:
“Closest Exon” Displayed on Open Variant Tile and Popup
SNP transcript information in germline and tumor (somatic) cases, indicating the closest exon number for variants in non-exonic regions, is now displayed on the open variant tile and variant popup, completing the display on the closed variant tile (and table row).
Organization Variant Filters in CNV Region Viewer
In the Organization Variants track, located in the Region Viewer of CNVs, we have added the ability to filter variants based on their confidence, overlap with the evaluated variant, and the submitted organization classification. This should help you find the relevant variants when comparing a variant to your organization's previously submitted variants.
Tumor Cases: Frame Interpretation for RNA Fusions
In tumor (somatic) cases, you can now view reading-frame retention status for RNA fusions directly in the fusion variant tile:
In this enhancement, if the breakpoints occur in the CDS or 5’ UTR, the number of bases upstream of each breakpoint within the codon is counted. The frame is then annotated accordingly, having three possible values - 0, 1 or 2. If both fusion genes have the same frame annotation (e.g. both have frame 1), the overall fusion frame is considered “Retained”. If the frame annotations differ, the overall frame annotation is considered “Disrupted”. Finally, if the frame cannot be calculated (e.g. because a breakpoint falls outside a CDS or 5’ UTR) the status is considered “N/A”. For example, in the above image of the BRD4::NUTM1 fusion, the breakpoint in BRD4 exon 11 is located one base into the codon (frame 1) and the breakpoint in NUTM1 exon 3 is also located at frame 1, so the fusion is marked Retained, indicating an uninterrupted open reading frame, typically associated with the production of a functional chimeric protein.
Please note that the calculation is available for, and is based on, the canonical transcript only. Additionally, if multiple transcripts or genes overlap, only the severest model is annotated. Finally, frame retention is determined solely based on breakpoint positions, without consideration of any potential insertion at the fusion junction.
Undo Actions in Filter Tree Builder
You can now undo actions while editing filter trees, either by clicking the new Undo button or using Ctrl+Z / Cmd+Z keyboard shortcuts. Following an undo, you can also redo the action, by clicking the new Redo button or using Ctrl+Y / Cmd+Shift+Z keyboard shortcuts.
This allows you to quickly revert recent changes or mistakes, with support for multiple consecutive undos, enhancing flexibility when working with complex filter logic.
Tooltips for Custom QC Metric Results
Any QC metric customized for your organization can now be configured to include an explanatory tooltip. The tooltip will be available when hovering over the results of the QC metrics in the Quality Control tab of the Workbench, similar to what is already available for Franklin’s standard QC metrics. This enhancement makes it easier to interpret custom QC metrics directly within your workflows. To configure tooltips for your custom QC metrics, please contact our support team ([email protected]).