Next-Gen Sequencing at Scale: Transforming Per-Sample Variant Outcomes into Institutional Knowledge with VSWarehouse.pptx

Learn how VSWarehouse transforms per-sample analyses into scalable institutional knowledge—streamlining workflows and enhancing genomic insight across your organization.

1. Next-Gen Sequencing at Scale: Transforming Per-Sample Variant Outcomes into Institutional Knowledge with VSWarehouse October 22, 2025 Presented by : Darby Kammeraad, Director of Customer Success

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3. Next-Gen Sequencing at Scale: Transforming Per-Sample Variant Outcomes into Institutional Knowledge with VSWarehouse October 22, 2025 Presented by : Darby Kammeraad, Director of Customer Success

4. NIH Grant Funding Acknowledgments 4 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 NIH SBIR Grant 1R43HG013456-01  NIH SBIR Grant 2R44HG013456-02 – Pharmacogenomics Workflow: Identifying Biomarkers and Treatment Options PI is Dr. Andreas Scherer, CEO of 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. Golden Helix at-a-Glance 5 Golden Helix is a SaaS bioinformatics solution provider specializing in next-gen sequencing (“NGS”) data analysis  The Company’s software enables automated workflows and variant analysis for gene panels, exomes, and whole genomes  Key Clinical Applications Prenatal testing Hereditary disease testing Reproductive testing Oncology Marquee Global Clients Golden Helix’s solutions allow clients to increase throughput, ensure consistent quality, maximize revenue, and save time  1998 Company Founded Bozeman, Montana Headquarters Recognitions Government Research Pharmaceuticals Testing Labs Human Genetics Research Hospitals Publications Content & Resources Pharmacogenetics testing

6. NGS Clinical Workflow 6 DNA Extraction in Wet Lab and Sequence Generation Interpretation and Result Reporting Primary Read Processing and Quality Filtering Alignment and Variant Calling Secondary *Golden Helix provides Secondary Analysis through a reseller agreement Tertiary Golden Helix’s software and primary focus Comprehensive secondary and tertiary analysis solutions for primary data aggregated by all commercially available sequencers Type Size Gene Panel Small (100MB) Whole Exome Medium (1GB) Whole Genome Large (100GB) Cancer use case Hereditary use case Process Analysis …and scales across multiple data set sizes for cancer, hereditary diseases, and pharmacogenomics use cases. Filtering and Annotation Data Warehousing Workflow Automation Golden Helix works with all major NGS platforms…

7. Recent news: 7 Golden Helix + Genomenon Strategic Partnership Integration of the Mastermind and Cancer Knowledgebase (CKB) into VarSeq for high-confidence genomic interpretations Seamless access to expertly curated germline and somatic content directly within VarSeq and VSClinical . More accurate and accelerated clinical decision-making from fully curated literature and variant classifications Golden Helix receives the NIH SBIR Phase 2 grant for Pharmacogenomics workflow: Identifying Biomarkers and Treatment options.

8. On Premises | Cloud Deployment 8 Configured to meet your business needs.

9. Recent Webcasts: 9 Secondary NGS Workflow Automation in VSWarehouse Automation of the FASTQ -> Clinical Report Automating Pharmacogenomics Workflows with VSWarehouse 3 From Variants Clinical Reports VSWarehouse 3: Secondary Analysis Platform Overview Simplified Installation and deployment of the secondary and tertiary tools VSWarehouse 3: Enterprise-Grade Genomic Analysis Across Cloud and On-Premise Environments

10. VSWarehouse Diagnostic Pipeline 10 Expert Automated Raw Seq Data FASTQ BAM VCF Target Coverage Annotate & Filter CNV Calling Autoclassifier CNV Interpret ACMG/AMP Evaluation Report Review & Sign-Off Lab Director Process User Experience Product Sentieon/WDL/Other VSPipeline Secondary Tertiary: VarSeq VSClinical VSWarehouse Docker Genomenon Mastermind + CKB

11. Deployment: NGS Automation and Orchestration 11 Secondary -> Tertiary Fully automated, end-to-end analysis process from raw (FASTQ) data to report with minimal manual intervention. Predefined workflows for both short and long read data Other useful Bioinformatic tools Cohort allele frequency calculator IGV Data portals: Cloud-based and local storage AWS S3/Azure Archer Basespace DNANexus Secondary Analysis Tertiary Analysis Expert Review

12. VSWarehouse : Admin Utilities and User Access 12 System oversight Extensive logs of user activity Comprehensive resource performance (RAM/CPU/IO) User Access to VSWarehouse Web access Workspace isolation Single sign-on support Observer -> Member-> Admin Notification system User Notification system Admin Dashboard

13. Scalability with VSWarehouse 13 Challenge: Rapid growth of WGS sequencing demands dynamic, scalable infrastructure Solution: VSWarehouse dynamically allocates compute for parallel processing on-prem or in cloud Automated system utilization in real-time to prevent overconsumption of resources Cloud storage utilized  to store large secondary analysis files Simple web interface and API connectivity Elimination of manual scripting while enabling scalable storage and compute

14. Denmark: A Countrywide Implementation 14

15. Breakdown of VSWarehouse Benefits 15 Workflow aspects VarSeq desktop app VSWarehouse Description Import all variant types Yes Yes Flexibility in workflow design Yes Yes Comprehensive annotation/filter Yes Yes Guideline based variant interpretation Yes Yes Removing variant artifacts Yes Yes, and improved Calculate frequency of common variants across all sequenced samples Visualization Yes Yes, and improved Supports other apps like IGV Customized reports Yes Yes, and improved Full API support for report pipeline Cataloging variants Yes Yes, and improved Expanded capability for querying across sample and variant catalogs Secondary analysis No Yes Easy to download complete short and long read callers (prebuilt workflows) Automate NGS pipeline No Yes FASTQ -> Clinical report or prioritized variants Dynamic scaling of compute No Yes Automated allocation on demand for automated workflows and analysis. Streamlined multi-user access Dynamic storage No Yes Mount any local or cloud-based storage (AWS, Azure, DNANexus , BaseSpace ) NGS pipeline customizability No Yes Freedom to install any other bioinformatics tools not part of the GHI software stack Cloud or On-prem On-prem Cloud or On-prem Web-based access to remove requirement for remote access and user permissions managed by install. Also supports single sign on

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17. Assessment Catalogs Overview 17 In addition to creating a variant report, assessment catalogs are also part of the VarSeq workflow to store evaluated variants. Assessment Catalogs have a wide range of uses across all projects. Some examples include: Frequency catalogs to store all variant counts and filter out common variants. Small variants, CNVs, SVs Variant evaluations storing evidence, classifications, interpretations, and treatments. Variant artifacts. Gene level data such as dosage sensitivity. Sample information : demographics, phenotypes, ethnicity, etc.

18. Added Catalog functionality with VSWarehouse 18 Assessment catalogs enable aggregating per-sample information into catalogs and cohort databases so you have long-term learning and improvement . Capturing this cataloged data becomes easier with automation of saved exports removing manual steps to move data from projects to catalogs If you have multiple users or scale to a lot of samples , you need VSWarehouse to be the platform for storing/accessing cataloged data VSWarehouse simplifies in tegration of catalogs into other systems and adds query functions to review cataloged data outside a VarSeq project VSWarehouse catalog browser

19. 19 Product Demo

20. NIH Grant Funding Acknowledgments 20 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 NIH SBIR Grant 1R43HG013456-01  NIH SBIR Grant 2R44HG013456-02 – Pharmacogenomics Workflow: Identifying Biomarkers and Treatment Options PI is Dr. Andreas Scherer, CEO of 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.

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