Advanced VSClinical Reports with Scripting and Custom Integrations
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Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines for the evaluation of variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since VSClinical was introduced, we have provided a powerful Word-based templating system that allows labs to customize reports to include their specific content and branding. Although powerful, this capability has been limited to customizing the contents of a Word file. Sometimes, the next logical step for the VSClinical analysis result is not a Word file, but some other file or target system: A database, LIMS, EMR, or even just a custom structured text file. Join us in this webinar, as we discuss the next version of VarSeq, which will introduce a powerful scripting and custom integration engine built into VSClinical Reports. We will cover: Capabilities and outputs of the workflows of VSClinical ACMG and Cancer Content of VSClinical reports, including sample-QC, coverage statistics, custom gene panels, and data providence The shipped report templates that range from gene panels to exome trios and comprehensive cancer testing The new custom script-based reports and example workflows it enables The tools enabling a powerful developer experience when building custom outputs and integrations The VarSeq Suite holds customization and extendibility as core values, allowing the powerful capabilities of variant analysis to be truly customized to the needs of a specific laboratory and NGS test. The new scripting and integration capabilities build on this tradition for the VSClinical workflows. We hope you can join us as we explore this topic in-depth in this webinar.
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Advanced VSClinical Reports with Scripting and Custom Integrations
- 1. Advanced VSClinical Reports with Scripting and Custom Integrations October 6, 2021 Presented by Gabe Rudy, V.P. of Product and Engineering
- 3. Advanced VSClinical Reports with Scripting and Custom Integrations October 6, 2021 Presented by Gabe Rudy, V.P. of Product and 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: 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
- 9. 10
- 10. Content Overview 11 Demonstration 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
- 11. VSClinical Report Content • Sample, Family, Patient Information • Coverage stats summary and per-gene • Custom gene panels • Variants & CNVs with evaluation results • Biomarkers, Drugs, Trials (cancer) • Data providence (version of tracks) 12
- 12. VSClinical Shipped Report Templates • ACMG Workflow: • Gene Panel Template • Mendelian Disorder Template • Trio Report Template • AMP Workflow: • Cancer Report Template • Cancer Drugs and Trials Template 13
- 13. Next Steps After Variant Evaluation 14 • Creation of Customized Clinical Report • Push structured data to LIMS/EMR • Append or integrate with other lab tests • Export report data as JSON/XML/VCF
- 14. Enhancements to Word-Based Template Reporting 15 • Integrate other test results (TMB/MSI/HRD) • All sample fields now available • Pull in non-standard VCF fields • Add lab-specific custom annotations • Report custom coverage statistic thresholds • Support more than one configured report
- 15. Addition of Custom Script Reporting 16 • JavaScript (ES6) runtime based reports • Configured once in project template • Can include extra files (logos etc) • Also defines inputs and outputs • Example outputs: • Structured XML, JSON, VCF • HTML • PDF • Outputs can be chained, run automatically when out of date • Integrated Preview of output
- 16. Developer-Friendly Customization Experience 17 • First-class developer experience (debugging, logging) from VSCode • Capabilities (such as REST API) through web standards • Upload/download binary data with FormData API • Extendable with Javascript ES6 modules • Modern Javascript run in secure sandbox
- 17. Example Use Cases Supported 18 • Convert report data to structure text for LIMS • Grab additional project table data into report • Pull in sample details from LIMS (REST API) • Push final report data + rendered DOCX to API • In-house DOCX to PDF converter • Create PhenoPackets GA4GH Compliant Output • Create ClinVar ready submission data • Integrate with a consortium data repository • Things we have not enough thought of!
- 18. 19 Product Demo
- 19. 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: 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.
- 20. 21 Inc 5000 Recognition Golden Helix was named to the 2021 Inc 5000 List of Fastest-Growing Private Companies • Third year in a row receiving this award • Thank you to our customers and partners for our sustained success
- 21. 22 Special Pricing Through 2021 • 2-Seat VSClinical Package - $19,995: Includes VSClinical, VS-CNV, Sentieon Tier 1 • 3 packages remaining • 2-Seat VSClinical AMP License - $29,995: Includes VSClinical + AMP, VS-CNV, Sentieon Tier 1 • 3 packages remaining • 2-Seat Small Warehouse License - $47,995: Includes VSClinical + AMP, VS-CNV, VSReports, VSPipeline, Sentieon Tier 1 • 2 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.
Editor's Notes
- Before we start diving into the subject, I wanted mention our appreciation for our grant funding from NIH. The research reported in this publication was supported by the National institute of general medical sciences of the national institutes of health under the listed awards. Additionally we are also grateful for receiving local grant funding from the state of Montana. Our PI is Dr. Andreas Scherer who is also the CEO at Golden Helix and the content described today is the responsibility of the authors and does not officially represent the views of the NIH. So with that covered, lets take just a few minutes to talk a little bit about our company Golden Helix.
- Golden Helix was founded back in 1998, and we are one of the few bioinformatic companies that can say we have 20 years of experience building NGS solutions in the research and clinical space. These solutions have a very broad range of capabilities, including VarSeq and the clinical products that are part of the VarSeq clinical suite, such as VS-CNV and VSClinical. Given the focused topic of this webcast, we won’t have time to even the full scope of our ACMG and AMP workflows that are part of the VSClinical clinical suite, but you are interested in any of these, please check the archive of previous webcasts and tutorials on our website.
- We have been cited in thousands of peer reviewed publications, and we are always happy to celebrate the success of our customers in performing their research with our tools. We even have a regular posting to our blog highlighting these publications!
- We serve over 400 customers globally, and these customers span many different industries, from academic institutions, to research hospitals, to commercial testing labs and government institutions.
- And that large customer base is really an asset that is hard to match. We can deliver a very high quality product, that meets the very diverse needs of this market because we work so closely with our customer base. As a business, we want to be aligned with the success of our customers. To that end, we use a simple per-user subscription model that comes with unlimited training and support, and is not based on the number of samples you run. So lets move on now, and start today’s discussion with an overview of the VarSeq product suite, and how our topic today builds off of its capabilities.
- The Golden Helix stack provides the capability to start with an initial FASTQ file all the way down to a clinical report. This is achievable through our partnership with Sentieon providing the alignment and variant calling steps to produce the VCF and BAM files. This output serves as the basis for CNV detection and import data for your tertiary analysis in VarSeq. If you are performing NGS based CNV analysis, Golden Helix is the market leader; supported by studies like Robarts Research Institute showing 100% concordance with MLPA. Additionally, the imported variants in your VarSeq project can be run through VSClinical’s automated ACMG and AMP guidelines. After completing secondary and tertiary processing, all analysis can be rendered into a clinical report which can be stored in VSWarehouse providing researchers and clinicians with access to this information and to view previous findings.
- The general clinical testing workflow requires taking an enormous amount of raw genomic variants, whether they are small variants or copy number variants, and determining which ones are high quality, and through a standardized interpretation process, which ones should be put on a individualized clinical report. VarSeq is the base platform that supports variant annotation and QC analysis. Our VSClinical package implements industry standard guidelines such as ACMG for germline variants and AMP for somatic variants found in cancers to evaluate, score and interpret variants in a systematic and repeatable manner. And finally, a clinical report can contain the supporting information and resulting work of this entire process.
- Today, our topic is going to start with a discussion of the current VSClinical reporting capabilities, their flexibility within the context of generating Word-based reports and the existing templates we provide. Then, we will go into some of the specific improvements that were made to CNV calling and how these changes can be worked into a VS_CNV best practice workflow. We will spend most of our time discussing the new enhanced capabilities for reporting available in the next VarSeq release. This includes APIs and capabilities to enhance the existing Word-based reporting model to do things not currently possible. And then further explore the possibilities of an fully-featured scripting environment embedded into VarSeq to drive the report generation process. Finally we will demonstrate these concepts in a couple VarSeq analysis projects. The first will be featuring the VSClinical ACMG workflow and demonstrate some examples of the type of custom output formats we can now support. The second will be based on the AMP workflow and explore how the scripting environment can pull and push things from outside the existing VSClinical evaluation.
- How can we enhance what we have, and then add even more use cases beyond word-template based reports
- Full (EcmaScript6) javascript with all the power and conveniences of the latest standard. Includes things like the spread operator and arrow functions. But this is delivered in a secure sandbox.
- Inputs enhanced, previously limited in the Word reporting to what could be done with existing data. Now we can stack inputs.
- RD Batch 30 (sample fields in table) - VSClinical, add some variants, add some CNVs, get to a report – go through report (10 min) - Create Custom Script from Scratch HTML - XML - JSON Advanced Example - Custom Sample Fields - Augment CN field - Debugging of API - Custom PDF Convert
- First and foremost, we recently received grant funding from NIH which we are incredibly grateful for. The research reported in this publication was supported by the National institute of general medical sciences of the national institutes of health under the listed awards. Additionally we are also grateful for receiving local grant funding from the state of Montana. Our PI is Dr. Andreas Scherer who is also the CEO at Golden Helix and the content described today is the responsibility of the authors and does not officially represent the views of the NIH. Again, we are thankful of grants such as this which provides huge momentum in developing the quality software we provide. Now let’s learn more Golden Helix as a company.
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