Version 13.13.0 of VarSome, VarSome API, and VarSome Clinical will be released on 13 December 2025.

Summary of Key New Features

• Major expansion of COSMIC variant card with transcript-level and sample-level tables
• Introduction of Group-based Roles & Permissions (granular access control)
• Enhanced Family Trio Recessive filter
• Optional ML-based Sentieon variant-calling pipeline available upon request
• Spreadsheet export now preserves the Variant Table ordering
  
  

New Features

Expanded COSMIC Card: Alternative Transcripts & Sample-Level Metadata

The COSMIC card in VarSome Clinical now includes two new data-rich sections:

1. Alternative Transcript Table

Displayed at the top of the COSMIC card, this table lists all alternative transcripts associated with the variant. Columns include:

• Transcript ID (clickable, linking to Ensembl)
• Coding notation
• HGVS protein notation

Each transcript is shown as a dedicated row, enabling clearer cross-transcript interpretation.

2. Sample-Level Metadata Table

Below the transcript table, users can now explore detailed COSMIC sample occurrences, with one row per sample. Fields include:

• Sample name
• Transcript
• Primary tissue & subtype
• Primary histology & subtype
• Somatic status 
• Zygosity 
• PubMed ID 

Users can filter by somatic status and zygosity, and search across tissue and histology fields. These additions provide richer biological context and streamline variant assessment by combining transcript-level and sample-level COSMIC evidence directly within the workflow, allowing faster, more confident somatic variant interpretation.

Group-Based Roles & Permissions

A new granular permission system is now available for groups, introducing four default roles:

• Group Admin
• Analyst
• Clinical Curator
• Report Writer

Each role comes with predefined permissions specifying:

• Access to samples
• Ability to upload files
• Ability to launch analyses
• Rights to manage users

Default roles can be adjusted by enabling or disabling specific permissions, and organizations may also create custom roles with any combination of permissions, custom names, and the ability to edit or delete them as needed.

The Group Supervisor retains full permissions across the platform, including complete control over role creation, modification, and assignment. Group Supervisor and Group Admin can assign roles and manage users via a new User Management page.  This feature provides:

• Clear and auditable access responsibilities
• Strict least-privilege principles (aligned with GDPR & IVDR)
• Reduced risk of unauthorized access
• Stronger access governance for sensitive clinical data

Minor Fixes and Additions

Enhanced Family Trio Recessive Filter

The Family Trio Recessive filter has been expanded to support the review of likely benign and benign variants, and it now accommodates analyses that include three or more samples. These enhancements offer a more complete view of recessive inheritance patterns and contribute to smoother, more efficient case-resolution workflows.

Optional ML-Based Sentieon Variant-Calling Branch

A refined Machine Learning (ML) version of the Sentieon variant-calling pipeline is now available upon request. This ML branch remains optional and operates separately from the standard pipeline, offering improved false-positive reduction for users who choose to enable it. 

At this stage, the ML version only works with germline single sample analyses, and we are actively working on extending coverage to additional pipelines.

The standard Sentieon pipeline continues to be the default for all customers and has also been upgraded to its latest version following full internal validation, without introducing any functional changes for end users.

Variant Table Order Added to Spreadsheet Export

When exporting selected variants to a spreadsheet, users will now see a new column: Variant Table Order. Sorting by this column reproduces the exact ordering seen in the analysis tab. This is also supported in VarSome Picks exports.

Support

We hope you find these improvements helpful. We would love to hear any feedback and suggestions you may have. Support is available as usual from support@varsome.com.

The VarSome Team.