Version 93.1 Updates

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

We are launching the Franklin Community Forum - a space for genomics professionals to connect, share knowledge, and discuss variants, guidelines, and workflows together with the Franklin team.
If you would like to be a Beta user of the forum, allowing you to get early access to shape the community, connect with peers facing the same challenges, and have a direct line to the Franklin team as we build this together - please fill out this form and we will be in touch soon. Please note that Beta access is limited to a small number of participants.
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Franklin now offers a guided ACMG variant classification workflow - the Variant Curation Interface (VCI). VCI introduces two key changes to how you classify variants. The first key change is a guided, section-by-section curation - ACMG criteria are organized into sections, each curated independently with Met / Unmet / N/A, Strength, and free-text curator notes; the Suggested Classification updates according to your work, in real time. The second key change is per-condition classification - the same variant can be classified independently for multiple conditions, each with its own curation, notes, and status.

This approach is aligned with the ClinGen variant curation process, supporting a structured, evidence-based classification workflow consistent with community guidelines.
VCI is currently in Beta, to join the Beta please contact our support team ([email protected]); please note that Beta access is limited to a small number of participants. For more information on VCI, please visit the following help center article.

Franklin now supports Case Groups, allowing you to organize related cases together under a named group - for example, cases belonging to the same patient, family, or clinical order. With Case Groups, you can view cases grouped together on the My Cases page “View as”:

Additionally, you can navigate between cases in a group directly from the case header, without returning to My Cases:

Finally, you can see all cases in a group from the Group Details widget in the Case Details tab, and search by group name from both the Groups view and the standard Cases view.
Groups are assigned during case creation - presently available when creating cases using a sample sheet or via the case creation API. To enable Case Groups for your organization, please contact our support team ([email protected]). For more information on Case Groups, please visit the following article.

The Profile Details tab of the Settings page now displays your organizational role (admin or member). If user roles are configured for your organization, your user role (e.g. Director) will also be visible.

Both fields are read-only - assigning organizational and user roles can be done by admins from Members tab. For more information on roles in Franklin, please visit the following help center article.

You now receive an email after uploading of variants to the Knowledge Base completes. The email provides counts of successful, duplicate, and error variants. All variants that produced errors or identified as duplicates are provided in a downloadable spreadsheet similar to the uploaded file, with an additional column that details the encountered issue. You can fix issues directly in the file and upload it as needed. This enhancement allows you to better monitor and review variant uploads to the Knowledge Base. For more information on importing variants to the Knowledge Base, please visit the following help center article.

In germline cases created in Franklin using GATK pipeline, the Quality Control tab of the Workbench can now display the AT Dropout and GC Dropout metrics - indicating the percentage of misaligned reads that correlate with low (%GC < 50%) or high (%GC > 50%) GC content, respectively. The thresholds (percentage of misaligned reads) for triggering a warning can be configured separately for each metric. This enhancement helps you monitor sample-level data quality and identify sequencing bias related to AT- and GC-rich regions. To configure the AT Dropout and/or GC Dropout QC metric for your assay, please contact our support team ([email protected]).

When adding phenotypes in New Case or Case Details popups, duplicate phenotypes are now better processed as a single instance in both copy-paste and auto-complete entries. Additionally, when copying phenotypes to the clipboard from the Case Details popup, phenotypes are now copied as a semicolon-separated list, matching the input format.

In tumor (somatic) cases, custom annotations can now be configured for SV, as previously supported for SNP. To configure custom annotations in your assay, please contact our support team ([email protected]).