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PGx Analysis in VarSeq: A User’s
Perspective
June 19, 2024
Presented by Solomon Reinman, Technical Field Application Scientist and
Darby Kammeraad, Director of Customer Success
2
PGx Analysis in VarSeq: A User’s
Perspective
June 19, 2024
Presented by Solomon Reinman, Technical Field Application Scientist and
Darby Kammeraad, Director of Customer Success
Today’s Presenters
4
PGx Analysis in VarSeq: A User’s Perspective
Solomon Reinman
Technical Field Application
Scientist
Darby Kammeraad
Director of Customer Success
NIH Grant Funding Acknowledgments
5
• 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
o 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.
Golden Helix at-a-Glace
6
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
7
Confidential |
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
ISO Certification 13485:2016
8
• ISO 13485:2016 from TÜV SÜD
• ISO 13485:2016 is an international standard that specifies requirements for
a quality management system (QMS) for organizations involved in the
design, development, production, and servicing of medical devices.
o maintain a quality management system
o demonstrate sufficient risk management
o show consistent tracking of customer satisfaction and safety in the
market
o demonstrate continued improvement efforts on the product and
system level.
• ISO 13485:2016 is designed to objectively document that we are holding
ourselves to the highest quality standards as we are providing innovative
solutions to hospitals, testing labs, and research institutions globally.
Overview
9
Recap on PGx feature release in VarSeq 2.6.0
Recent webcasts: https://www.goldenhelix.com/resources/webcasts/index.html
• VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis
• Introducing VSPGx: Pharmacogenomics Testing in VarSeq
Users Perspective with PGx
• PGx diplotype calling and star alleles: Options for genotyping with NGS or array
• VarSeq Workflow design options: PGx stand-alone or Diagnostic + PGx reporting
• Options for report customization
• Deployment and Validation considerations
• Automation options
• Investigating PGx markers
Clinical Pharmacogenomic Implementation Consortium (CPIC)
10
• CPIC has developed best practice guidelines for
pharmacogenomic tests
o Includes standardized grading of evidence
linking genotypes to phenotypes
o Assigning phenotypes to genotypes and
diplotypes
o Prescribing recommendations based on
diplotype and phenotypes
CYP2D6 Diplotype Metabolizer Phenotype
CYP2D6 *1/*1 Normal metabolizer
CYP2D6 *2/*122 Intermediate metabolizer
CYP2D6 *3/*3 Poor Metabolizer
CYP2D6 *1/*1x2 Ultrarapid metabolizer
CYP2D6 *5/*5 Poor metabolizer
Secondary options: NGS genotyping
11
Secondary options: Conversion of array data
12
PGx Variant Detection and Recommendations Algorithm
13
• Algorithm Function (In VarSeq)
• Diplotype caller
• Phenotype and drug recommendation
annotation
• Algorithm Requirements:
• Call variants at all required positions for
PGx genes
• Required annotations
• Optional Customization
• Customize annotation sources used
by the algorithm
• Recommendations can also be
provided for structural variant data
• Variant calling (Prior to VarSeq)
• 1. Array data converted to vcf for
VarSeq import
• 2. Utilize NGS pipeline (ex. Sentieon)
• Call alternate calls along with
must call positions
• GVCF calling hard filtered to PGx
markers in import
Pharmacogenomic Report
14
• What’s in the PGx Report from VarSeq?
• Current Patient Medications and Recommendations
• Gene-Drug Interactions
• Prescribing Recommendations
• Phenotype Associations
• Tested Alleles
• Word-based reports are fully customizable
• Reports can be rendered for a single sample or a batch of
samples
15
• How to deploy both workflows in one
template
• Filter 1: PGx diplotypes
• Filter 2: Diagnostic workflow
driven by sample phenotype
PGx + Diagnostics
Demo
16
• Genotyping: Review of NGS calling and array conversion script
examples
• gVCF subset on VarSeq import
• Usecase 1: PGx standalone
• Usecase 2: PGx + Diagnostic analysis
17
Product Demo
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
o 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.
19
eBook Library
20
• Prenatal Genetics – Learn the Following
o Existing approaches to prenatal WES, along with clinical
indications for its use
o How VarSeq and VSClinical can be utilized for its use
o A few interesting cases of variants and their classifications
• Pharmacogenetics – Learn the Following
o Foundations of Pharmacogenomics
o Genetic variability and drug response
o Pharmacogenomic test reporting nomenclature and
terminology
o The Pharmacogenomic eco-system
o VSPGx - A pharmacogenomics application
Secured CE Mark for EU
21
• VarSeq Dx
• 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
• 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.
• User Certification
• Tiered certification option to ensure training and proper usage
of the various VarSeq Suite modules. User Proficiency
Certificate upon successful completion of evaluation.
22

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PGx Analysis in VarSeq: A User’s Perspective

  • 1. PGx Analysis in VarSeq: A User’s Perspective June 19, 2024 Presented by Solomon Reinman, Technical Field Application Scientist and Darby Kammeraad, Director of Customer Success
  • 2. 2
  • 3. PGx Analysis in VarSeq: A User’s Perspective June 19, 2024 Presented by Solomon Reinman, Technical Field Application Scientist and Darby Kammeraad, Director of Customer Success
  • 4. Today’s Presenters 4 PGx Analysis in VarSeq: A User’s Perspective Solomon Reinman Technical Field Application Scientist Darby Kammeraad Director of Customer Success
  • 5. NIH Grant Funding Acknowledgments 5 • 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 o 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.
  • 6. Golden Helix at-a-Glace 6 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
  • 7. 7 Confidential | 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
  • 8. ISO Certification 13485:2016 8 • ISO 13485:2016 from TÜV SÜD • ISO 13485:2016 is an international standard that specifies requirements for a quality management system (QMS) for organizations involved in the design, development, production, and servicing of medical devices. o maintain a quality management system o demonstrate sufficient risk management o show consistent tracking of customer satisfaction and safety in the market o demonstrate continued improvement efforts on the product and system level. • ISO 13485:2016 is designed to objectively document that we are holding ourselves to the highest quality standards as we are providing innovative solutions to hospitals, testing labs, and research institutions globally.
  • 9. Overview 9 Recap on PGx feature release in VarSeq 2.6.0 Recent webcasts: https://www.goldenhelix.com/resources/webcasts/index.html • VarSeq 2.6.0: Advancing Pharmacogenomics and Genomic Analysis • Introducing VSPGx: Pharmacogenomics Testing in VarSeq Users Perspective with PGx • PGx diplotype calling and star alleles: Options for genotyping with NGS or array • VarSeq Workflow design options: PGx stand-alone or Diagnostic + PGx reporting • Options for report customization • Deployment and Validation considerations • Automation options • Investigating PGx markers
  • 10. Clinical Pharmacogenomic Implementation Consortium (CPIC) 10 • CPIC has developed best practice guidelines for pharmacogenomic tests o Includes standardized grading of evidence linking genotypes to phenotypes o Assigning phenotypes to genotypes and diplotypes o Prescribing recommendations based on diplotype and phenotypes CYP2D6 Diplotype Metabolizer Phenotype CYP2D6 *1/*1 Normal metabolizer CYP2D6 *2/*122 Intermediate metabolizer CYP2D6 *3/*3 Poor Metabolizer CYP2D6 *1/*1x2 Ultrarapid metabolizer CYP2D6 *5/*5 Poor metabolizer
  • 11. Secondary options: NGS genotyping 11
  • 12. Secondary options: Conversion of array data 12
  • 13. PGx Variant Detection and Recommendations Algorithm 13 • Algorithm Function (In VarSeq) • Diplotype caller • Phenotype and drug recommendation annotation • Algorithm Requirements: • Call variants at all required positions for PGx genes • Required annotations • Optional Customization • Customize annotation sources used by the algorithm • Recommendations can also be provided for structural variant data • Variant calling (Prior to VarSeq) • 1. Array data converted to vcf for VarSeq import • 2. Utilize NGS pipeline (ex. Sentieon) • Call alternate calls along with must call positions • GVCF calling hard filtered to PGx markers in import
  • 14. Pharmacogenomic Report 14 • What’s in the PGx Report from VarSeq? • Current Patient Medications and Recommendations • Gene-Drug Interactions • Prescribing Recommendations • Phenotype Associations • Tested Alleles • Word-based reports are fully customizable • Reports can be rendered for a single sample or a batch of samples
  • 15. 15 • How to deploy both workflows in one template • Filter 1: PGx diplotypes • Filter 2: Diagnostic workflow driven by sample phenotype PGx + Diagnostics
  • 16. Demo 16 • Genotyping: Review of NGS calling and array conversion script examples • gVCF subset on VarSeq import • Usecase 1: PGx standalone • Usecase 2: PGx + Diagnostic analysis
  • 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 o 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.
  • 19. 19
  • 20. eBook Library 20 • Prenatal Genetics – Learn the Following o Existing approaches to prenatal WES, along with clinical indications for its use o How VarSeq and VSClinical can be utilized for its use o A few interesting cases of variants and their classifications • Pharmacogenetics – Learn the Following o Foundations of Pharmacogenomics o Genetic variability and drug response o Pharmacogenomic test reporting nomenclature and terminology o The Pharmacogenomic eco-system o VSPGx - A pharmacogenomics application
  • 21. Secured CE Mark for EU 21 • VarSeq Dx • 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 • 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. • User Certification • Tiered certification option to ensure training and proper usage of the various VarSeq Suite modules. User Proficiency Certificate upon successful completion of evaluation.
  • 22. 22

Editor's Notes

  1. Casey’s intro
  2. Casey reminding them to input questions
  3. Darby Intro
  4. So with the recent release of VarSeqs pharmacogenomics capability, Solomon and I have gotten some feedback from our users on workflow topics when setting up your PGx analysis in our software. We wanted to provide some more exposure to key components of the PGx pipeline that will assist you when moving through the validation process.
  5. 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. We are also grateful to have received 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, Before diving into today's topic, I'd like to offer some background and context on what Golden Helix brings to the table as a company
  6. Golden Helix as a company has been around over 25 years now and established itself as a premier tertiary platform for both next gene sequencing and array data. Our primary mission to develop high quality general purpose bioinformatic software with a key focus on facilitating routine clinical applications. Our software solutions are highly scalable for everything from panels to genomes but are highly automatable when processing a large number of samples in your lab. This combined with our subscription based business model, allows users to process as many samples as needed, without us chipping away at your revenue stream with most per sample applications on the market. The assays designed in our software are built by the user and span a wide spectrum of uses, including somatic workflow, hereditary cancer, rare diseases, prenatal testing and family based analysis, and of course our recent addition of Pharmacogenomics. Our customer base is also wide spread with users in government and testing labs, hospitals, universities, and many research and pharmaceutical labs.
  7. Lets review where our tools fit into the bigger picture of an NGS pipeline. The Golden Helix software is in tertiary analysis stage following output from your preferred secondary analysis solution. You can see here we have a partnership with Sentieon to provide the secondary solution for labs who may need it, but overall, our VarSeq software is agnostic to the variant caller being used. Moreover, we are also agnostic to the sequencer and have had a number of demonstrations on VarSeqs’ capability of processing long read data as well. With VarSeq, users will be able to import any scale of data from panels to genomes, for both short and long read data, from any sequencer to quickly annotate and filter variants to evaluate and report on the clinically relevant findings. And recently we’ve announced our medical device certification of our VarSeq software suite
  8. For European labs or any lab processing European samples, we’re happy to announce our recent ISO13485 certification as the result of our diligence in creating a thorough quality management system coupled with our manufacturing process. In the near future, labs developing in house tests will need to adhere to the IVD regulations, and can rely on streamlining integration of our software having the certification already in place. When implementing our tools, our support staff is also ready to guide you through our own user onboarding and certification process bringing your users up to speed as we move through the workflow validation process together. Now let’s get to todays topic with Pharmacogenomics
  9. If you are a regular at our webcasts, you may have seen the recent presentations on the release of the PGx capabilities in VarSeq. Th
  10. I encourage you to go back and watch the earlier webcasts as they go into deeper detail on the nature of our PGx solution. The star alleles we’ve integrated thus far are based on the Clinical Pharmacogenomic Implementation Consortium or CPIC database. CPIC is an international consortium dedicated to facilitating the use of pharmacogenetic tests for patient care. Their goal is to create clinical best-practice guidelines for pharmacogenomic testing so that clinicians, health care providers and vendors can leverage genetic laboratory results into actionable prescribing recommendations. CPIC provides this publicly available database that links phenotypes to specific allele combinations and provides prescribing recommendations based on this phenotypic information, with each recommendation being ranked based on the level of supporting evidence. This database has been indispensable in the development of our own pharmacogenomic solution.
  11. Let's take a moment to break down the inputs to the PGx algorithm. As Darby just elucidated, star alleles are at the core of our PGx workflow, which makes pharmacogenomics unique in the NGS space in that we're just as concerned with reference calls as we are with variant calls. This requires special treatment during the secondary analysis phase. Ultimately, our goal is to produce a VCF containing both variant and reference calls, or calls with a 0/0 genotype, for specific loci defined by the CPIC database. As Darby mentioned, flexibility and the ability to easily integrate with existing tools are priorities when our team develops new workflows in VarSeq. Hence, we have a few different solutions for getting NGS data into VarSeq. We have developed a Sentieon pipeline to implement forced calling of CPIC variants that is available to our Sentieon customers, but we also provide support for gVCF inputs, array data conversion, and other secondary analysis pipelines capable of implementing forced calls.  Let's dissect the two routes for producing PGx input with NGS data. The first is using a given VCF with must-call variants, derived from the CPIC database. We have implemented this workflow with Sentieon, but it can just as easily be replicated in other secondary analysis tools. Fundamentally, this just means performing standard alignment and variant-calling steps and providing a list of variants where the caller must evaluate a variant or reference call. We'll take a deeper look at this during our demonstration of the software in just a bit. Alternatively, we can handle the reference call inference during the VarSeq import step with a gVCF as input. A gVCF contains a list of intervals where no variants were detected, and hence can be used to infer reference calls that overlap with these intervals.  In either case, both variant and reference calls are subject to the coverage of your NGS sample. We can only make calls where there is coverage, and this is reflected in the PGx diplotype calling algorithm as well as the report, which Darby will show off shortly. This means that you can be confident the PGx workflow is only working with the genes you are including in your assay. This is also true for array data, which we're happy to support as well. 
  12. Array data is still common for PGx testing. We can handle this data in VarSeq by converting from a text file source into a VCF and importing into VarSeq. Just like with NGS data, this will ensure that the PGx analysis is subject only to the variants of interest for your workflow. We've seen a plethora of text outputs from PGx array data, but a common theme is a list of RSIDs and associated alleles. We can cross-reference these with our PGx must-call VCF in a conversion script and produce something similar to what the NGS approach would yield. So, regardless of where your data is coming from, we have a solution to get it into VarSeq and run it through the PGx diplotype caller. I'm going to hand things back to Darby here to show off what that process looks like.
  13. Thank you Solomon for providing a simple overview of the genotyping options that are supported. As Solomon had mentioned, if you are working with array data, we’ve had numerous iterations of helping our users convert this data to VCF so to import into VarSeq. Now let’s review what happens next once the data is in the software.
  14. After running the PGx Variant Detection and Recommendations algorithm, a clinical report can be generated using VarSeq’s customizable reporting system. Clinical reports are generated using an easy-to-modify Microsoft Word report template and VarSeq comes shipped with an initial PGx report template that serves as an excellent starting point for creating custom reports. Information included in this report includes Implications for Current Patient Medications, Gene-Drug Interactions, Prescribing Recommendations, Phenotype Associations, and a description of all tested alleles. The calling of diplotypes, annotation of phenotypes, and reporting of recommendations is performed by VS-PGx in just a few simple steps with minimal user involvement. While the annotations and report templates can be customized, the annotation tracks and report templates provided by VarSeq have everything you need to start annotating and reporting all alleles defined in the CPIC database.
  15. After running the PGx Variant Detection and Recommendations algorithm, a clinical report can be generated using VarSeq’s customizable reporting system. Clinical reports are generated using an easy-to-modify Microsoft Word report template and VarSeq comes shipped with an initial PGx report template that serves as an excellent starting point for creating custom reports. Information included in this report includes Implications for Current Patient Medications, Gene-Drug Interactions, Prescribing Recommendations, Phenotype Associations, and a description of all tested alleles. The calling of diplotypes, annotation of phenotypes, and reporting of recommendations is performed by VS-PGx in just a few simple steps with minimal user involvement. While the annotations and report templates can be customized, the annotation tracks and report templates provided by VarSeq have everything you need to start annotating and reporting all alleles defined in the CPIC database.
  16. After running the PGx Variant Detection and Recommendations algorithm, a clinical report can be generated using VarSeq’s customizable reporting system. Clinical reports are generated using an easy-to-modify Microsoft Word report template and VarSeq comes shipped with an initial PGx report template that serves as an excellent starting point for creating custom reports. Information included in this report includes Implications for Current Patient Medications, Gene-Drug Interactions, Prescribing Recommendations, Phenotype Associations, and a description of all tested alleles. The calling of diplotypes, annotation of phenotypes, and reporting of recommendations is performed by VS-PGx in just a few simple steps with minimal user involvement. While the annotations and report templates can be customized, the annotation tracks and report templates provided by VarSeq have everything you need to start annotating and reporting all alleles defined in the CPIC database.
  17. 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. We are also grateful to have received 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, Before diving into today's topic, I'd like to offer some background and context on what Golden Helix brings to the table as a company