Version 92 Updates

We are happy to introduce several enhancements and new features in our latest update:

Franklin now supports Manual Report Editing, allowing users to override the template-based Report and create a fully customized version, before signing:

With this capability, you can edit report content freely in a Word-like editor (no protected fields), save manual report versions with a required justification (tracked in case history), and export the saved manual report as Word and PDF. You can regenerate a template-based Report at any time before signing (which replaces the manual report).

Please note: manual report edits do not update case data, and future case updates will not be reflected in the manually edited report. Manual editing is intended as a last-resort workflow and should be used only when template-based reports cannot meet reporting needs. For full details, see the relevant Help Center article. To enable Manual Report Editing in your organization, please contact our support team ([email protected]).

In germline cases, you can now classify the SMN biomarker directly from the SMA tile (as already available for the UPD biomarker). Clicking the new classification button opens the interpretation popup for classifying the biomarker and adding interpretation and references, where SMA-specific snippets can be inserted (once they are set up).

The most recent user classification is displayed on the biomarker tile and in Report Preview. SMA classification and the interpretation fields can now be included in the Report.

Additionally, as available for variants, the biomarker interpretation popup of SMA and UPD now includes Discussion Topics:

Discussion Topics appear on the right side of the popup and allow you to create, view, edit, and delete topics and comments. The latest discussion message is displayed on the biomarker tile.

All of the Frequency filters in the Variants tab (SNP) are now grouped in organized, collapsible sub-sections. Each sub-section displays a blue dot badge when at least one of its filters has a value.
Example of the new sub-sections in germline and tumor (somatic) cases:

“Internal” sub-section includes the internal frequency and number of samples filters; “Franklin” includes Franklin’s aggregated frequency and community filters; “COSMIC” (somatic only) includes the Cosmic frequency filter; “gnomAD - Exome” and “gnomAD - Genome” include the respective frequency filters whereas “gnomAD - Other” includes the gnomAD max filter; finally, “Additional databases” includes the frequency filters related to 1000 Genomes, ESP, ExAC, and UK10K databases. Additionally, the somatic filter "Internal sample count" has been renamed to "Internal number of samples" to align with germline cases. This more compact and organized layout helps you find and manage filters more efficiently.

Franklin’s API now allows you to retrieve information on signed case reports based on specified criteria. You can query by signing date range, case ID, or report status (final, revision, etc). The retrieved information includes the signing date, case ID, report status, report signer, and the revision date and signer where applicable. The latest signed report per analysis is returned. This enhancement allows you to obtain a list of reports, e.g. recently signed reports, for downstream integrations or operations. Please note: fetching a very large number of reports in a single API call (e.g. all of the organization’s signed reports) is not supported. For more details, please visit Franklin API documentation.

You can now attach files to a variant. Files are managed via a sidebar interface, supporting common Office files, PDFs, CSVs, and images (PNG, JPEG), with a single-file size limit of 20 MB. Uploaded files are also displayed in the new Uploaded Files widget in the Variant Assessment tab, where users can view and download attachments.

This feature is available for all variant types in a case, the Knowledge Base, and Search - with all files securely stored as part of the organization’s curation data. Please note: attaching a file to a variant in one of the above mentioned locations will associate the attachment with the variant in the other locations, including in other cases.

We enhanced our support of Agilent CGH workflows under Franklin’s CMA solution category. You can now create cases that contain PDF files generated from CytoGenomics software and view them in Franklin. The case PDF files are available for download through Sample Files in Case Details. This enhancement enables easier access to essential CGH assay information, such as graphical reports - directly from Franklin.

HGMD data, available for users with an active HGMD Online license configured in Franklin, has been updated to reflect HGMD v2025.4, the latest available version.

COSMIC data for somatic variants (available for Franklin Premium users) has been updated to the latest COSMIC release version - v103.