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.

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?
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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
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7. Over 400 Customers Globally
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8. When you choose Golden Helix, you receive
more than just the software
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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
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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

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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
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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

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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

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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)

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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

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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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News & Publications

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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.

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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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