Anyone handling NGS data understands the constant issue of not only storing all the variant data but also the difficulties in querying through a massive dataset. VarSeq has grown an excellent reputation for being a powerful filtration and annotation engine for NGS data. Tightly coupled with VarSeq is our genomic repository solution, VSWarehouse. VSWarehouse provides a means of storing all variant cohort data as well as rapid querying capabilities to quickly navigate through the, potentially, millions of variants you may amass over time. Just as important is the ability to store this data; users can find relief that VSWarehouse is designed to be installed behind a private network to ensure the protection of all genomic data. Join us in this webcast as we explore the key value points, usability, and direct scalability of VSWarehouse. What will you learn in this webcast? From VSWarehouse, how to access the browser to investigate: -Querying updated clinical evidence against an existing variant cohort -Filtering through stored projects for all relevant variant data -Accessing the administrator-level permissions management site From VarSeq, how to leverage variant data in VSWarehouse to: -Filter out common variants in the store cohort -Annotate and plot VSWarehouse content in the VarSeq project -Utilize congruent assessment catalogs for storing variant classifications uniformly for all users

1. VSWarehouse;
a scalable, rapid genomic repository solution
Darby Kammeraad
Field Application Scientist Manager
20 Most Promising Biotech
Technology Providers
Top 10 Analytics
Solution Providers
Hype Cycle for Life sciences

2. Questions & Answers

3. VSWarehouse;
a scalable, rapid genomic repository solution
Darby Kammeraad
Field Application Scientist Manager
20 Most Promising Biotech
Technology Providers
Top 10 Analytics
Solution Providers
Hype Cycle for Life sciences

4. NIH Grant Funding Acknowledgments
• Research reported in this publication was supported by the National Institute Of General Medical
Sciences of the National Institutes of Health under:
• Award Number R43GM128485-01
• Award Number R43GM128485-02
• Award Number 2R44 GM125432-01
• Award Number 2R44 GM125432-02
• Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
• PI is Dr. Andreas Scherer, CEO Golden Helix.
• The content is solely the responsibility of the authors and does not necessarily represent the official
views of the National Institutes of Health.

5. Who Are We?
Golden Helix is a global bioinformatics company founded in 1998
Filtering and Annotation
ACMG Guidelines
Clinical Reports
CNV Analysis
Pipeline: Run Workflows
Variant Warehouse
Centralized Annotations
Hosted Reports
Sharing and Integration
CNV Analysis
GWAS | Genomic Prediction
Large-N Population Studies
RNA-Seq
Large-N CNV-Analysis

6. Cited in 1,000s of Peer-Reviewed Publications

7. Over 400 Customers Globally

8. SIMPLE, SUBSCRIPTION-
BASED BUSINESS MODEL
o Yearly fee
o Unlimited training & support
SOFTWARE IS VETTED
o 20,000+ users at 400+ organizations
o Quality & feedback
DEEPLY ENGRAINED IN
SCIENTIFIC COMMUNITY
o Give back to the community
o Contribute content and support
INNOVATIVE SOFTWARE SOLUTIONS
o Cited in 1,000s of publications
When you choose Golden Helix,
you receive more than just the software

10. VarSeq Suite
Simple Flexible Scalable
Variant annotation
filtering, and interpretation
Powerful GUI with
rich visualizations
Repeatable
workflows

11. • Archive full VCFs for Sample Cohort
o Optimized repository infrastructure for rapid queried through millions of
variants
• Centralized Genomic Data Hosting
o Integrated with other systems
• Query Variant Warehouse
o Have I seen this variant in my cohort?
o Has the classification changed with new evidence in ClinVar?
o How do I ensure consistency of CNV/variant interpretations across all
users?
VSWarehouse - Variant Warehouse Server

12. • From VarSeq to VSWarehouse
 Upload full cohort data
 Upload variant classification/interpretations
 Upload clinical reports
• From VSWarehouse to VarSeq
 Annotate with cohort data
o Variant frequencies
 Annotate with classified variants
 Access congruent Assessment Catalogs & Reports
• VSWarehouse Browser
 Query all genomic data
o Reports, catalogs, projects
 Evidence updates with ClinVar
 Manage access permissions
Integration with VarSeq

13. VSWarehouse – Centralized Collaboration
Project A
Project B
VSWarehouse Server
Group A Group B Collaborators

14. • Part I – Exploring VSWarehouse Browser
o General variant search
o Filtering/query
o Classification changes in ClinVar
• Part II – VarSeq & VSWarehouse
o Filtering out common variants
Example Project

15. Scalable Variant Warehouse for VarSeq
Project Demonstration >

16. NIH Grant Funding Acknowledgments
• Research reported in this publication was supported by the National Institute Of General Medical
Sciences of the National Institutes of Health under:
• Award Number R43GM128485-01
• Award Number R43GM128485-02
• Award Number 2R44 GM125432-01
• Award Number 2R44 GM125432-02
• Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005
• PI is Dr. Andreas Scherer, CEO Golden Helix.
• The content is solely the responsibility of the authors and does not necessarily represent the official
views of the National Institutes of Health.

17. Questions & Answers

18. Visit Golden Helix in booth 46!

19. Questions & Answers