Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
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The document presents the VarSeq Suite, an automated bioinformatics solution by Golden Helix designed to streamline the process from FASTQ files to clinical reports. It outlines the capabilities of the system, including flexibility, automation, and support for various genomic analyses, while emphasizing the importance of profitability and quality in NGS (Next Generation Sequencing) testing. Additionally, it details NIH grant acknowledgments, upcoming innovation awards, and conference participation.
Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
- 1. Automated FASTQ to Reports with VarSeq Suite: A Fast, Flexible Solution February 8, 2023 Presented by Gabe Rudy, VP of Product & Engineering, and Solomon Reinman, Technical Field Application Scientist
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- 3. Automated FASTQ to Reports with VarSeq Suite: A Fast, Flexible Solution February 8, 2023 Presented by Gabe Rudy, VP of Product & Engineering, and Solomon Reinman, Technical Field Application Scientist
- 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: o Award Number R43GM128485-01 o Award Number R43GM128485-02 o Award Number 2R44 GM125432-01 o Award Number 2R44 GM125432-02 o Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 • 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. Who Are We? 5 Golden Helix is a global bioinformatics company founded in 1998 Filtering and Annotation ACMG & AMP Guidelines Clinical Reports CNV Analysis CNV Analysis GWAS | Genomic Prediction Large-N Population Studies RNA-Seq Large-N CNV-Analysis Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration Pipeline: Run Workflows
- 6. Cited in 1,000s of Peer-Reviewed Publications 6
- 7. Over 400 Customers Globally 7
- 8. The Golden Helix Difference 8 FLEXIBLE DEPLOYMENT On premise or in a private cloud BUSINESS MODEL Annual fee for software, training and support CLIENT CENTRIC Unlimited support from the very beginning SINGLE SOLUTION Comprehensive cancer and germline diagnostics SCALABILITY Gene panels to whole exomes or genomes THROUGHPUT Automated pipeline capabilities QUALITY Clinical reports correct the first time
- 9. Today’s Agenda 9 Solomon Reinman Technical Field Application Scientist Gabe Rudy VP of Product & Engineering Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution
- 10. Content Overview 10 Demonstration 1) FASTQ to report example automation 2) VSClinical AMP demonstration Automation Support for Workflow Analysis for NGS tests and the use of automation to tackle complexity and improve quality NGS Cancer Testing Workflow Overview of the process and variety of NGS tests for precision medicine
- 11. Keys to Profitability: Capability, flexibility, automation 11 The core tenets of long-term success Ability to create new tests quickly according to market demand Bottom line-oriented business partners enabling your lab Scalable solutions and a high degree of automation
- 12. 12 • Local-first algorithm and data strategy • Building from-scratch algorithms and integrated data storage strategies • FASTQ to clinical reporting in one solution, with training and support • Industry standard guidelines: o ACMG: Germline interpretation for diagnosis and hereditary disease risk o AMP: Somatic interpretation for targeted molecular therapy and cancer prognostics • Automation and customization of lab-specific needs • Long term data storage and knowledgebase management with VSWarehouse Bottom Line-Oriented Partners Enabling your Lab Golden Helix Clinical Suite
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- 14. Pipelines of Cancer Workflow 14 • Vendor bundles: o Archer fusion kit and caller o TSO500 and bioinformatics o Ion Torrent variant caller • Lab-developed tools: • TMB / MSI caller • Histochemistry or other tests • Specialized tools • SV callers LUMPY, DELLY, Manta • RNA-based exon-skipping callers • Integration analysis o Inputs from various sources o Holistic interpretation of by lab expert o Store and leverage findings over time Seq CNVs SVs (RNA) Variant Annotate Reads Alignment Annotate Annotate Filter Filter Filter Interpret Warehouse Report Cohort Analysis Re-Analysis Specialized Pipelines Integrated Analysis Longitudinal Findings
- 15. The challenges of NGS testing 15 Automation bridges the gap between profitability and quality • Pipelines require validation o Confirm performance against reference samples o Explainable and transparent to review and audit • High-complexity problem o Without automation, a lab will struggle with bandwidth and consistency o Low turnaround leads to low profitability Profitability Automation Validation, Clarity, Reproducibility
- 16. VarSeq Suite: Automate Inputs and Outputs 16 • VarSeq built for flexibility and automation • A modular set of capabilities at the disposal • Support all records in VCF 4.3 • Custom pipelines support built-in: • TMB/MSI caller outputs • Cancer assessments and histochemistry • Sample or patient info • Flexible export and endpoints • Reduction or elimination of custom work
- 17. 17 Workflow Templates • Cancer Gene Panel • Tumor-Normal Workflow • Comprehensive Cancer Template Report Templates • Report on TMB/MSI • Include new genomic signatures • Structural variants • Negative findings Annotation Library • Common population frequency catalogs, gene annotations, functional predictions, and more • Updated monthly • Golden Helix CancerKB Advanced starting points for taking tests to production
- 18. TSO-500 genes Interpretation for all 523 genes included in TSO-500 kit Updates to Golden Helix CancerKB 18 Copy Number Base Substitutions Expanded Interpretations Increased Tier 1 and 2 interpretations Genomic Signatures 17 new Genomic Signatures Drug descriptions 147 new drug descriptions with indications Combination biomarkers Report on combinations of biomarkers including negative findings and biomarker impacts Tumor Specific FDA therapies 82 new interpretations for FDA approved therapies at tumor type level
- 19. 19 Automation in Review Powerful, modular NGS testing Secondary Analysis Tertiary Analysis Interpretation • Strong Starting points with Sentieon • Ability to import results of any secondary pipeline • Reliance on validated, reproducible VarSeq templates • Thorough automation options with VSPipeline • Automatically pull from vast, expert- review repositories like CancerKB • Interface with VSWarehouse to track assessments across your institution
- 20. 20 Product Demo
- 21. Wrapping up 21 A snapshot of the vast capabilities of automation • VarSeq Suite can accommodate automation from the straightforward to the complex • Overall reduction in work and human error, while retaining expert input • We invite you to give our software a try!
- 22. NIH Grant Funding Acknowledgments 22 • Research reported in this publication was supported by the National Institute Of General Medical Sciences of the National Institutes of Health under: o Award Number R43GM128485-01 o Award Number R43GM128485-02 o Award Number 2R44 GM125432-01 o Award Number 2R44 GM125432-02 o Montana SMIR/STTR Matching Funds Program Grant Agreement Number 19-51-RCSBIR-005 • 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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- 24. eBook Update: Clinical Variant Analysis for Cancer 24 Want a free copy? Request one in the questions or chat panel and our team will follow up with you!
- 25. Innovation Awards 25 The 2023 Golden Helix Innovation Awards will run from Dec. 1st, 2022 - Feb. 28th, 2023 • We want to see how YOU are using our tools to the best of their ability. • Anyone using Golden Helix Software tools is eligible to submit for entry, and no prior publication of research is required. • Submissions can be for clinical or hospital laboratory work, academic research, government, or commercial, we just want to see great examples of your workflows. • 3 winners, each receiving 1 user license for either SVS or VarSeq, and first place receiving in addition a Dell Latitude 5000 series laptop. • All winners will receive the opportunity to present their research via webcast. Goldenhelix.com/events/Innovation_Awards
- 26. Awards 26
- 27. Conferences 27 Annual Clinical Genetics Meeting, Booth #507 • March 14 – March 18, 2023 • Exhibitor Theater Talk: Achieving Economic Success as an NGS Lab: Strategy and Implementation Bio-IT World Conference, Boston • May 16 – 18, 2023 • Andreas Scherer, CEO, presenting: Achieving Economic Success as an NGS Labs: Strategy and Implementation European Human Genetics Conference, Booth #566 • June 10 – 13, 2023 • Glasgow, UK Association for Molecular Pathology • June 18 – 20, 2023 • Milan, Italy
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