VSWarehouse 3: Enterprise-Grade Genomic Analysis Across Cloud and On-Premise Environments

Clinical laboratories and genomic research centers are increasingly seeking flexible deployment options that can seamlessly span both on-premises and cloud environments while maintaining enterprise-grade security and control. VSWarehouse 3's enterprise platform capabilities enable organizations to leverage their existing infrastructure while scaling into the cloud on their own terms. Join us to discover how VSWarehouse 3's cross-platform deployment model combines the security of on-premises installations with the scalability of cloud computing, all accessible through a streamlined browser interface. In this webcast, we will:

Demonstrate how VSWarehouse 3 enables deployments across on-premises servers and major cloud providers (AWS/Azure) through our Bring Your Own Cloud (BYOC) model.
Explore enterprise-grade security features including role-based access controls, Active Directory integration, and workspace isolation that enable secure multi-team collaboration.
Show how organizations can replace legacy remote access solutions with VSWarehouse 3's native browser-based platform, simplifying deployment while enhancing scalability.
Detail our comprehensive workflow automation capabilities, including integration with upstream providers and support for custom analysis pipelines.

This session will provide IT leaders and laboratory directors with practical insights into how VSWarehouse 3's enterprise platform can modernize their genomic analysis infrastructure while maintaining complete control over their data, security, and resource allocation. Whether you're looking to extend existing on-premises capabilities or implement a full cloud deployment, learn how VSWarehouse 3 can support your organization's growth and evolution.

1. VSWarehouse 3: Enterprise-Grade Genomic Analysis Across Cloud and On-Premise Environments February 26, 2024 Presented by : Gabe Rudy, VP of Product & Engineering

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3. VSWarehouse 3: Enterprise-Grade Genomic Analysis Across Cloud and On-Premise Environments February 26, 2024 Presented by : Gabe Rudy, VP of Product & Engineering

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  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-Glace 5 Company Snapshot: Leading SaaS provider of tertiary genomic analysis solutions for NGS labs 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 Agrigenomics Testing Labs Translational Labs Human Genetics Research Hospitals Academia Publications Content & Resources Pharmacogenetics testing

6. NGS Clinical Workflow Golden Helix provides comprehensive data analytics software that scales across gene panels, whole exomes, and whole genomes 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 and hereditary use cases Filtering and Annotation Data Warehousing Workflow Automation Golden Helix works with all major sequencers… Medical Device Certification

7. Secured CE Mark for EU 7 VarSeq Dx VarSeq Dx is designed with compliance and reliability for your clinical analysis. VarSeq Dx is our flagship software, VarSeq , that is CE marked to meet the European In Vitro Diagnostic Regulation (IVDR 2017/746) requirements. VarSeq Dx satisfies the IVDR requirements within the European Economic Area (EEA). Verification CE MARK ISO Certification Our customers will work with our Field Application Scientist to verify the installation and ensure proper usage of the software. This can be used for ISO QMS software validation documentation.

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9. Why Genomic Analysis Demands Flexibility 9 Genomic testing starts small: targeted analysis, limited samples Demand grows: automation and multi-computer power become essential Exomes and genomes require massive storage capacity VSWarehouse 3 adapts: Secure on-premises deployments Harnesses local compute clusters and storage Integrates with your preferred cloud (Azure/AWS) Scales seamlessly across environments Growth

10. Deploy Anywhere: On-Premises or Cloud 10 On-premises deployment: Secure, leverages local compute clusters and storage Cloud integration: Seamless support for Azure and AWS via Bring Your Own Cloud (BYOC) model Automated deployment processes: Simplify setup, no cloud expertise required Flexible scaling: Grow from single-server setups to multi-computer clusters or cloud elasticity Growth

11. Uncompromising Security for Genomic Data 11 Role-based access controls : Granular permissions for teams and users Active Directory/SAML integration : Seamless authentication with enterprise systems Workspace isolation : Secure multi-team collaboration without data overlap Robust user management : Centralized control over access and permissions Logs and Audit Support : Security logs, workflow activates tracks usage and access Clinical Workspace Research Workspace 3 Server Mark, Julia, Andrew Admin, Approver, Observer Custom Annotations, FASTQ, Projects VarSeq 3.0, BaseSpace Integration Signed Out Variants Dan, Roger, Julia Admin, Member, Observer Research Cohorts, Cloud Storage VarSeq 2.6.2, Custom WDL Pipeline Research Variants, Interesting CNVs Cloud Storage Cohort Project FASTQ BAM VCFs

12. Transform On-Premises with VSWarehouse 3 12 Replace solutions like Citrix/Windows Server with a streamlined platform Leverage local Linux server clusters for workflow and application runs Integrate cloud-mounted drives for long-term storage (Bring Your Own Bucket) Simplify deployment while maintaining security and scalability Linux Cluster 3 Server Catalogs Application Workflows Local Files Mounted/Cloud Storage (NAS) FASTQ, BAM, VCFs, Projects Firewall

13. 13 Prefers fewer large servers Target time limit of 24 hours to process 300 exomes (buffer time for re-run if failure) Windows server with Powershell scripts Analysis workflow includes: Coverage stats and QC VS-CNV calling Annotation and filtering Gene panel and phenotype automation Region Testing Lab Scaling Exomes

14. Pharma Services Scaling Genomes 14 Deliverables are locked down through versioned pipelines All steps inside read-only Docker containers VSPipeline + Annotations + Project Templates Local Linux cluster and cloud deployment scenarios Secure Cloud deployments in China with no outbound internet access Batch node job: Download docker containers [Cloud only] Download BAM, VCF from storage Docker run pipeline [Cloud only] Upload results to storage

15. Genome Center Scaling Genome Interpretation 15 Air-gapped environment with no direct internet Internally mirrored data and license servers Leverage Linux cluster for interactive analysis Segregated into groups Group level access to input/output files Group level permissions and sharing Group level VSWarehouse Aggregate and share across groups

16. Workflow Automation: Streamlined Genomic Pipelines 16 Secondary analysis pipeline automation: Efficiently process exomes, genomes, and more Integrations with BaseSpace , Archer Analytics, and Sentieon for seamless data flow Custom workflow support: Build and integrate any secondary, upstream, or downstream pipelines Comprehensive API documentation: Empower developers with flexible automation tools

17. Browser Access: Simple, Scalable, Secure 17 No local installation required: Access VarSeq and VSWarehouse 3 from any browser Multi-user environment: Enable collaboration across teams with ease Cloud resource optimization: Automatically scale resources based on usage Secure access: Integrated with enterprise-grade security features

18. Simplified Administration & Resource Monitoring 18 Distinct server admin roles: Manage accounts, security, and resources—separate from workspace users Review security activities: Monitor access and detect potential issues Dashboard insights: Track server resources, usage, and performance Access server logs: Maintain transparency and troubleshoot efficiently Configure server with institutional logos, messages and policies

19. Flexible Deployment & Licensing for Your Lab 19 Pay-per-sample pricing: match your business model Professional deployment support: Expert guidance for seamless setup, workflow automation, report customization Scalable infrastructure management: Adapt resources to your needs Usage monitoring and controls: Optimize usage with real-time insights

20. VSWarehouse 3 in Action: Whole Genome Orchestration 20 End-to-end whole genome analysis workflow on the Azure cloud Workflow automation using dynamic scaling of Azure VMs Storage on Azure Blob storage Trio analysis germline workflow with ACMG guidelines performed in VarSeq Filtered variants, CNVs, and report stored in VSWarehouse Downstream automation of output into EHR / FHIR WGS Tumor/Normal Workflow Illumina FASTQ BAM/VCF Project Download from BaseSpace Sentieon Tumor Normal VSPipeline Tumor/Normal Template WGS Trio Workflow PacBio FASTQ BAM/VCF Project Upload to “Bring Your Own Bucket ” PacBio WDL WGS Pipeline VSPipeline ACMG Trio Template

21. 21 Product Demo

22. VSWarehouse 3 Supports Cloud Deployment Flexible Deployment Deployable as Bring Your Own Cloud: Amazon, Azure or On-Premises Analysis Application Support Run VarSeq , VSClinical , GenomeBrowse , and other custom applications Workflow Automation Run VSPipeline , Sentieon , custom workflows, and other bioinformatics tools. Integrations with other cloud vendors and institutional stores File Management Built in file management system to easily upload, download, and preview files and directory management 22 VSWarehouse 3 our complete server platform for genomic analysis ( ( ( (

23. Modernize Your Genomic Analysis with VSWarehouse 3 23 Flexible deployment : On-premises or cloud, scaling to your needs Enterprise-grade security : Protect data with advanced controls Streamlined workflows : Automate pipelines for efficiency and growth Simplified access : Browser-based platform for all users Ready to transform your lab? Contact us today for a demo or trial!