Version 90 Updates

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

Users with an active HGMD Online license configured in Franklin can now access the latest HGMD data (v2025.3). If you already have an HGMD Online account and have previously contacted us to configure it in Franklin - no action is needed, your configuration will be updated automatically within the next few days. If you have not yet requested configuration, please reach out to our support team ([email protected]) for assistance. For more details about HGMD in Franklin, please visit the relevant Help Center article.

COSMIC widget, available in the variant popup and replacing the Somatic Frequency widget, will reflect COSMIC release v102 (latest to date). The COSMIC widget now includes a grouping feature that organizes cancer types by tissue and displays the top five tissues by occurrence. Each tissue group can be expanded to view specific cancer types, with the number of cancer types shown per group. Bar charts now represent the number of samples and are dynamically sorted from highest to lowest. COSMIC linkouts are conveniently available at the top of the widget. Please note that COSMIC data is available for Franklin Premium users only.
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Franklin’s Shared Knowledge Base feature allows an organization, when configured to belong to a Group of Organizations, to view and add Knowledge Base variant submissions in a Knowledge Base shared between all members of the Group of Organizations.

The present update of Franklin’s Shared Knowledge Base feature introduces two enhancements: when viewing somatic submissions from other organizations, the submitting organization’s name now appears in both the Source and Submitter fields, allowing you to easily identify the origin of the somatic submission:
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Furthermore, previous submissions from other organizations in the Group of Organizations (i.e. from non-self organizations in relation to the submitting user), now include the latest submission per condition, and not only the latest submission globally - ensuring a more complete and up-to-date view of submitted variant interpretations across the Group of Organizations. To configure a Shared Knowledge Base for a group of organizations, please contact our support team ([email protected]).

Your assay can now be configured to support variant calling from UMI-trimmed FASTQs, which contain the UMIs in the read names. When configured, the Franklin pipeline will skip the UMI trimming step and only perform UMI grouping and collapsing. Other trimming steps (such as adapter trimming) remain unaffected. This configuration therefore supports workflows where UMIs have already been trimmed and embedded in the read names by upstream analysis software.

Variant import to the Knowledge Base now support inheritance information - an Inheritance column in the imported variant file is now supported with the following values: Autosomal Dominant, AD, Autosomal Recessive, AR, X Linked Dominant, X-Linked Dominant, XD, X Linked Recessive, X-Linked Recessive, XR. Following import, this information will be displayed within the variant submission in the Knowledge Base. For more information on importing variants and the updated templates, please visit the following Franklin Help Center article.

Variant export from the Knowledge Base now uses semicolons (";") as separators in the Conditions column, ensuring better alignment between the Knowledge Base import and export formats.

In cases where FreeBayes is used for calling, handling of multiallelic variant has been improved to ensure accurate determination of allele depth fields.

Resolved an issue where exporting somatic submissions from the Knowledge Base, when configured for latest-only export (latest per condition rather than all submissions per condition), incorrectly included information from the latest germline submission.