Webcast Follow-Up: Powering Genomic Workflows with Upgraded Catalogs in VSWarehouse and VarSeq 3

Thank you to everyone who joined our recent webcast, “Powering Genomic Workflows with Upgraded Catalogs in VSWarehouse and VarSeq 3,” presented by Gabe Rudy on April 23rd, 2025. We appreciate the engagement and interest in the latest advancements to our platform.

For those who missed it or need a recap, the session focused on the pivotal role Catalogs play as the backbone of clinical genomic workflows. Catalogs are essential for building institutional knowledge by storing curated interpretations, decisions, and critical workflow artifacts, supporting everything from variants to clinical metadata.  

What’s New with Upgraded Catalogs?

The webcast highlighted significant upgrades designed to enhance scalability, security, and automation:

• Flexible Data Storage Architecture: A modernized backend provides greater flexibility in how your genomic and clinical data (variants, CNVs, breakends, interpretations, sample info) is managed and structured. You can customize fields and add validation rules to ensure data quality.  
• Enterprise-Grade Security and Governance: We’ve introduced robust features including role-based access controls, a structured Draft → Approve → Publish workflow (with options for multiple approvers), comprehensive audit trails, and integration with Active Directory. Workspace isolation is also available for multi-team environments.  
• Automation via REST APIs and Saved Exports: Streamline your processes with new automation capabilities. This includes automating imports/exports using REST APIs, utilizing a database approach for sample attributes (replacing text manifests), and saving exports directly to Catalogs. A dedicated query and export interface enhances your ability to leverage this warehouse of knowledge.  

Demo Highlights: Catalogs in Action

The live demo provided a practical look at how these upgraded Catalogs enhance a typical cancer workflow within VarSeq 3 and VSWarehouse 3, using a project analyzing variants, fusions, and CNVs:

1. Centralized Sample Information: Instead of relying on separate text manifests, the demo showcased pulling sample information (like BAM path, tumor type, sex) directly from a Sample Manifest Catalog when creating a new VarSeq project. This ensures consistency and centralizes data management.  
2. Dynamic Filtering & Knowledge Recall: Catalogs were used dynamically within the VarSeq project. Artifact or Whitelist catalogs allowed specific variants to be automatically excluded or included in filters. Furthermore, catalogs storing all previously seen somatic variants or classified variants provided instant context within the variant table, showing how often a variant was seen or previously classified.  
3. Streamlined Interpretation in VSClinical: When moving to VSClinical, the sample’s tumor type was automatically populated from the catalog. Crucially, custom interpretations associated with specific variants or biomarkers were stored and recalled from Catalogs, saving customizations to the rich source of report-ready language from Golden Helix CancerKB. The system also leveraged catalogs to show which variants had been previously classified in other samples.  
4. Workflow Tracking: A dedicated Sample Tracking Catalog was used to monitor and update the status of samples (e.g., moving from “Interpretation” to “Ready for Sign Out”), demonstrating a simple, integrated way to manage workflow steps directly within the platform.
5. Enterprise Management & Approvals: Switching to the VSWarehouse interface (as a different user), the demo showed how catalogs can be centrally managed, queried, and updated. It highlighted the approval workflow, where a variant added to the Whitelist Catalog required a second user to approve it before it was published and active in subsequent analyses.  
6. Automation with VSPipeline: The demo concluded by running an automated VSPipeline task. This task automatically created a new project for a different sample, pulled necessary information from the Sample Manifest Catalog, processed the data using a standard template, and crucially, used “Saved Exports” to automatically update relevant catalogs (like the Somatic Variants catalog) with the results from the new sample. This highlighted how the entire process, from sample import to catalog update, can be automated, leaving only the necessary review steps for the analyst.  

These real-world examples demonstrate how Upgraded Catalogs provide tangible benefits in efficiency, consistency, security, collaboration, and automation for genomic workflows.

Looking Ahead

The upgraded Catalogs in VSWarehouse and VarSeq 3 represent a significant step forward in providing a secure, scalable, and efficient platform for modern genomic laboratories. VSWarehouse is required to utilize the full suite of enterprise features, such as approval workflows and advanced automation capabilities.  

If you have more questions or would like a personalized demo to see how these features can be implemented in your specific workflows, please feel free to reach out to our team.

P.S. Planning to attend ESHG 2025 in Milan? Visit us at booth #510 to discuss these updates and see live demos!