In this webcast, we provide an overview of our complete end-to-end clinical stack. Initially, we walk through our powerful secondary analysis pipeline which allows you to call SNVs and CNVs. We then demonstrate how various types of CNVs are called and discuss metrics that express the confidence associated with each call. From there, we show you our powerful tertiary analysis capabilities for gene panels, exome, and whole genome data. We show how our users can move seamlessly from the variant interpretation stage to a clinical report. Lastly, we demonstrate how our genetic data warehouse, VSWarehouse, can be used in the clinic. We also demonstrate various use cases and show how a comprehensive assessment catalog can be utilized to ensure consistent analysis across multiple labs. We hope you enjoy our first presentation on Golden Helix's entire end-to-end solution for clinical labs!

1. Golden Helix’s End-to-End Solution for Clinical Labs
Steven Hystad - Field Application Scientist
Nathan Fortier – Senior Software Engineer
20 most promising
Biotech Technology
Providers
Top 10 Analytics
Solution Providers
Hype Cycle for
Life sciences

2. Use the Questions pane in your
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Questions during
the presentation

3. Golden Helix
Golden Helix is a global bioinformatics
company founded in 1998.
GWAS
Genomic Prediction
Large-N-Population Studies
RNA-Seq
Large-N CNV-Analysis
Variant Warehouse
Centralized Annotations
Hosted Reports
Sharing and Integration
Variant Calling
Filtering and Annotation
Clinical Reports
CNV Analysis
Pipeline: Run Workflows

4. Cited in over 1,100 peer-reviewed publications

5. Over 350 customers globally

6. Golden Helix – Who We Are
When you choose a Golden Helix solution, you get more than just software
 REPUTATION
 TRUST
 EXPERIENCE
 INDUSTRY FOCUS
 THOUGHT
LEADERSHIP
 COMMUNITY
 TRAINING
 SUPPORT
 RESPONSIVENESS
 INNOVATION and
SPEED
 CUSTOMIZATIONS

8. Secondary Analysis

9. Why Sentieon? – Pipeline Improvements
 Why Improve Broad’s GATK Haplotype Caller?
 GATK Haplotype Caller is the most accurate DNA analysis tool
 Problem: GATK Haplotype Caller is too Slow
 Solution
 Consistent: No down-sampling or thread dependency = no run-to-run differences = More accurate
 No Javascript: low level C
 More Robust: Can handle joint genotyping on over 100K samples simultaneously without needing a gVCF
 Software-only Solution: Easily deployable, easily scalable, and easily upgraded.
 Two Product Lines
 DNAseq – BWA-GATK Haplotype Caller
 Tnseq – MuTect and MuTec2

10. Performance: Sentieon vs Broad
DNAseq TNseq

11. Proven Accuracy – Precision FDA
 Consistency Challenge
- Processed single sample consistency
- Single biological sample x two library preps
- Top overall performance
- Highest reproducibility
 Truth Challenge
- Determine accuracy in Truth Set
- Highest indel precision
- Highest SNP recall

12. Proven Accuracy - ICGC-TCGA DREAM Mutation Calling Challenge
 Evaluates Somatic Variant Call Accuracy
SNV INDEL Structural Variants
Sentieon 98.57% Sentieon 98.14% Sentieon 100%
Bina/Roche 97.57% Bina/Roche 97.01% Genowis 99.82%
Genowis 96.92% OICR‐GSI 86.99% Gridss 99.63%
 Sentieon leads in all categories

13. Customizable secondary pipeline
Sequencer Sentieon
Linux
CNV caller
FASTQ
BAM
VCF -Annotate & filter
-Clinical reports

14. CNV and LoH Detection
 VarSeq Calls CNVs on
- Gene Panel Data
- Exome Data
- Whole Genome Data
 Faster than CMA and MLPA
 Utilizes existing coverage data
 Calls CNVs of every size
- Small Single Exon Events
- Large Cytogenetic Events

15. CNV Detection via NGS
 CNVs are called from coverage
data
 Challenges
- Coverage varies between samples
- Coverage fluctuates between targets
- Systematic biases impact coverage
 Solutions
- Data Normalization
- Reference Sample Comparison

16. CNV calling in VarSeq
 Reference samples used for normalization
 Metrics
- Z-score: number of standard deviations from reference
sample mean
- Ratio: sample coverage divided by reference sample
mean
- VAF: Variant Allele Frequency
 For Gene Panels and Exomes
- Probabilistic model used to call CNVs
- Segmentation identifies large cytogenetic events
 For Whole Genome Data
- Targets segmented using Z-scores
- Events called based on Z-score and Ratio thresholds

17. VarSeq Full Clinical Stack

18. VarSeq Suite
 Variant annotation, filtering,
and interpretation
 Rich visualizations with
GenomeBrowse built-in
 Powerful GUI and
command-line interfaces
 Repeatable workflows
VarSeq
Simple
Flexible
Scalable

19. Example Workflows
 Illumina TruSight Cancer Sequencing Panel
- Oncogenes & Tumor Suppressor Genes
- Drug Targeting Information & Ongoing Clinical Trials
 Exome Trio Workflow
- Casual Variants Associated with Phenotype
- Incidental Findings
 Hereditary Risk Sequencing Panel
- Comprehensive coverage of 175 genes with known associations to inherited cardiac
conditions, cancers, and other inherited diseases.

20. Sample Data for Cancer Gene Panels
 Illumina TruSight Cancer Sequencing Panel
- Comprehensive coverage of 154 genes designed to target exons of key tumor
suppressor genes and frequently cited oncogenes.
- BAM and VCF files for each replicate are available
VSReports

21. VarSeq Demonstration

22. Sample Data for Exome Trio Workflows
 NA1278 17-year old Caucasian Women
- Admitted for Symptoms of Acute Gastroenteritis.
- Serum testing revealed elevated pancreatic enzymes.
- Genetic testing revealed Heterozygosity for CFTR gene mutation Δ F508
 Incidental Findings
NA12891NA12892
NA12878

23. VarSeq Demonstration

24. VSWarehouse – Variant Warehouse Server
 A place to archive full VCFs of every
sequenced sample
 Centralized genomic data hosting,
integration with other systems
 Ask the Variant Warehouse:
- Have I ever seen this variant in my
previous test samples?
- At what frequency? (counts as well)
- Does this gene contain other rare variants
in my cohort?
- Did I provide a pathogenicity assessment
for this variant? Has that changed?
- Has ClinVar changed since that
assessment was initially made?
- Have I put this variant into a clinical report
for any previous samples?

25. Integration with VarSeq
 VarSeq can “Export to Warehouse”
- Create a new Project
- Current project template is used
- Add Variants to Existing (data only)
 Annotate with Warehouse Counts
- Allele / Genotype counts computed on
warehouse variants (or other sources in
template).
 Remote Assessment Catalogs
- Customize databases of variant classifications
or internal flags like false-positives.
 Remote Reports
- Central versioning of report
- Queryable database of all saved reports, with
all data in form ready for EMR/LIMS
integration

26. VSWarehouse – Centralized Collaboration
Project A
Project B
VSWarehouse Server
Group A Group B Collaborators

27. VSWarehouse – Centralized Collaboration

28. VarSeq Full Clinical Stack

29. Questions or
more info:
 Email
info@goldenhelix.com
 Request an evaluation of
the software at
www.goldenhelix.com