We are happy to introduce several enhancements and new features in our latest update:
CMA Case Creation from IDAT Files
Franklin now supports CMA single case creation from Illumina Infinium Global Screening Array (GSA) IDAT files. The created cases support CNV and LOH similar to other CMA cases in Franklin. Creating CMA cases from IDAT files is available via sample sheet upload. To access a relevant assay, please contact our support team ([email protected]).
Improved File Downloads from the Case Menu
The case menu now directly shows the number of sample files available for download:
A file can be downloaded by clicking its download icon in the following popup, ensuring access without link expiry issues:
As a part of this update, it is now possible to download all available VCFs from the case menu in CMA cases (not only the CNV VCF). The update does not impact file download from the Case Details tab.
Exact Time Available for the Report
The Report can now be configured to include an exact report time (e.g. “10:29:56 AM”), in addition to the report date. Exact time is now also available for the report signatures. To configure this for your report, please contact our support team ([email protected]).
Tumor Cases: Classification Tags Displayed on Variant Tiles
In tumor (somatic) cases, classification tags are now visible on the variant tiles for all variant types:
When a variant is classified under multiple classification systems (e.g. somatic and oncogenic), only the tags for the currently displayed classification are shown. Similar to classification tags in germline cases, clicking a tag opens the Variant Interpretation popup, and updates to tags in the popup are immediately reflected on the tile. For more information on classification tags, please visit the following Help Center article.
Tumor Cases: Tumor Purity Supported in Create Case Implicit API
In Franklin API V1 and V2, the Create Case Implicit API (Shell Case API) request can now include tumor purity when creating tumor (somatic) cases. Similar to when specifying tumor purity in a sample sheet, the expected value is a number, e.g. “48.5” for a tumor purity of 48.5%, and the created case will display this value in Sample Details. For more information on Franklin API, please visit the Franklin API documentation (https://api-docs.genoox.com/).
Bug Fixes:
Incorrect Number of Coding Exons Displayed in a Gene Search Page
Resolved an issue in a gene search page, where the Coding Exons column in the Gene Structure tab considered both coding and non-coding exons. The column now displays the correct number of coding exons.