Advanced Report Customization via VSClinical
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This document provides a summary of a presentation about advanced customization capabilities for clinical reports using VSClinical software: - VSClinical allows customization of clinical reports through custom HTML, XML, JSON templates and scripts to enhance Word reports and integrate with REST APIs. - Templates are provided for germline and somatic variant analysis that include ACMG/AMP guidelines and can be further customized. - Reports can include additional data such as gene impact analysis, drug/trial information, and machine-readable outputs like JSON can be generated. - A product demo was given to showcase report customization features.
Advanced Report Customization via VSClinical
- 1. Advanced Report Customization via VSClinical Dec 8, 2021 Presented by Rana Smalling, Ph.D, Field Application Scientist & Jennifer Dankoff, Field Application Scientist
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- 3. Advanced Report Customization via VSClinical Dec 8, 2021 Presented by Rana Smalling, Ph.D, Field Application Scientist & Jennifer Dankoff, 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 Pipeline: Run Workflows CNV Analysis GWAS | Genomic Prediction Large-N Population Studies RNA-Seq Large-N CNV-Analysis Variant Warehouse Centralized Annotations Hosted Reports Sharing and Integration
- 6. Cited in 1,000s of Peer-Reviewed Publications 6
- 7. Over 400 Customers Globally 7
- 8. When you choose Golden Helix, you receive more than just the software 8 Software is Vetted • 20,000+ users at 400+ organizations • Quality & feedback Simple, Subscription- Based Business Model • Yearly fee • Unlimited training & support Deeply Engrained in Scientific Community • Give back to the community • Contribute content and support Innovative Software Solutions • Cited in 1,000s of publications • Recipient of numerous NIH grant and other funding bodies
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- 11. Content Overview 11 1) Custom HTML, XML, JSON report 2) Enhance Word report data, REST APIs Enhanced custom reporting Scripts with APIs to enhance Word reporting, create new outputs or integrate with REST APIs VSClinical Workflow Results Use cases and current Word-template based reporting at end of analysis workflow
- 12. 12 VSClinical – AMP and ACMG Guidelines: One Suite • Increased lab throughput • Consistent results • Shorten learning curve • Staying abreast of new developments Germline Somatic
- 13. CNV Impact on Gene 13 CNV Guidelines Components • Simple for whole gene deletions/duplications • Use protein level in-silico analysis to evaluate partial gene impact • Partial gene duplications often act like Loss of Function variants
- 14. 14 VSClinical – Shipped Germline Templates • 3 Different Templates • Trio • Mendelian Germline • Hereditary Panel • Value • Consistent report standards (according to ACMG) • Faster reporting • Customization • Simple configurable options examples • Lab logo and contact info • Methodology • Test Descriptions • In depth customization examples • Custom fields from sample and project/VCF data • Tweaking panel tables
- 15. 15 VSClinical – Shipped Somatic Templates • Default Template includes Drugs & Clinical Trials - Automated population of the clinical report-based workflow outcome - For somatic variants, GHI provides predefined clinical assessments via our CancerKB catalog *Watch previous webcast for more details!* • Included Content - Biomarker Oncogenicity - AMP Tier Classification - Relevant Treatments - Prognostic, Diagnostic, Drug Sensitivity & Resistances - Clinical Trials - Search for nearest trials - All relevant inclusion/exclusion criteria • Additional Example Sample Inputs - Microsatellite Instability (MSI) - Tumor Mutation Burden (TMB)
- 16. 16 VSClinical Reports – Machine Readable Outputs • Additionally Reporting Options - Custom Scripts - Render in PDF - Export VCF on manually entered variants - Compatibility with API EHR/LIMS systems - JSON formats output in project folder
- 17. 17 Product Demo
- 18. NIH Grant Funding Acknowledgments 18 • 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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- 21. 21 Special Pricing Through 2021 • 2-Seat VSClinical Package - $19,995: Includes VSClinical, VS-CNV, Sentieon Tier 1 • 2 packages remaining • 2-Seat VSClinical AMP License - $29,995: Includes VSClinical + AMP, VS-CNV, Sentieon Tier 1 • 1 packages remaining • 2-Seat Small Warehouse License - $47,995: Includes VSClinical + AMP, VS-CNV, VSReports, VSPipeline, Sentieon Tier 1 • 1 packages remaining For any of the above bundle we give you the option to purchase 2 years upfront to receive a 3rd year for free.
- 22. 22 Abstract Competition The 2022 Golden Helix Innovation Awards will run from Dec. 1st, 2021 - Feb. 28th, 2022 • 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
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