The document describes funding that supported research conducted by Golden Helix. It lists several National Institute of General Medical Sciences grant numbers that supported the work. The principal investigator for the grants is named as Dr. Andreas Scherer, CEO of Golden Helix. It is noted that the content of any research supported by this funding is solely the responsibility of the authors and does not necessarily represent the views of the National Institutes of Health.

1. 1

2. NIH Grant Funding Acknowledgments
2
• 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.

3. Who Are We?
3
Golden Helix is a global bioinformatics company founded in 1998

4. Cited in 1,000s of Peer-Reviewed Publications
4

5. Over 400 Customers Globally
5

6. When you choose Golden Helix, you receive
more than just the software
6
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

7. VS-CNV: Power of NGS CNV Detection
• One single testing paradigm
• True simplification of clinical workflow
• Saves time and money – all on site
Small: 150bp+ Medium: 1 – 10Kb Large: 10Kb+ Gene Panel Whole Exome Whole Genome
MLPA ✓ ✓
CMA ✓ ✓
VS-CNV ✓ ✓ ✓ ✓ ✓ ✓
7
Detectable Events Supported Data Types
7

8. VS-CNV: 225+ Users and 15+ Publications
8
• Journals
o Atherosclerosis
o Journal of Clinical Lipidology
o American Journal of Medical Genetics
o BMC Medical Genomics
o Medicine
• Analysis Topics
o Hypercholesterolemia
o Retinal dystrophy
o Pituitary hormone deficiency
o Rare Mendelian disorders
• Lacocca et al.
o Whole exome CNV detection comparison
o 100% concordance between MLPA and VSCNV
o Improves resources, cost, analysis time

9. 9

10. New ACMG and ClinGen Guidelines
10
For the Interpretation of Copy Number Variants
• Provides much needed framework for evaluation of small CNVs
detected in gene panels
• High level overview of CNV scoring system
o Complex, 5 pages table with ~80 distinct criteria codes
o Scoring system with criteria broken down into 5 sections
• We designed a comprehensive workflow to score, classify,
interpret and report CNVs following these guidelines
Riggs ER, Andersen EF, Cherry AM, et al. Technical standards for the interpretation
and reporting of constitutional copy-number variants: a joint consensus
recommendation of the American College of Medical Genetics and Genomics
(ACMG) and the Clinical Genome Resource (ClinGen). Genet Med. 2020;22(2):245-257.
doi:10.1038/s41436-019-0686-8
https://clinicalgenome.org/

11. CNV Guidelines Components
11
1 Genomic content of the gene: overlap protein coding genes
2 Overlaps known haploinsufficient genes or triplosensitive regions: ClinGen
3 Assigns points to CNVs overlapping a large number of genes
Five Sections of the scoring system
4
5 Patient disorder and inheritance alignment to what is known for the gene
Peer-reviewed publications and/or internal data; Phenotype and
Inheritance

12. 12
Have you ever had to interpret a gene with limited evidence of
pathogenicity: a gene without dosage sensitivity information or
uncertain significance?
Audience Poll

13. CNV Guidelines Components
13
Phenotype Specificity
• Specificity of the patient’s phenotype and association with gene of interest
• Generic phenotypes do not offer strong evidence
• Important for novel genes

14. Section 4: Literature Consideration
14
• Individual/family evidence or case-control data
• CNV deletion~LOF variants
• Is the Phenotype consistent with what is expected for
the gene?
• Is the inheritance status known?
o De novo or inherited (confirmed or assumed)
• Confirmed Parental Relationships?
• Segregation (Section 4F-H)
o Proband is only affected individual or variant segregates; OR
o Variant is absent in another affected individual and does not
segregate
• Phenotype specificity (highly specific or not)

15. Example: 12:27715514-29628122x1
15
• Shortening of the digits, mainly in the metacarpals
(III-V) and metatarsals
• Brachydactyly Type E yields 4 results (rare)
• Given the limited heterogeneity, this is classified as “a
highly specific, but not necessarily unique
“phenotype
• Overlaps 10 genes, PTHLH shows low evidence for
dosage sensitivity
PTHLH and Autosomal Dominant Brachydactyly Type E (BDE)
David et al. (2015). Diagnostic and Interventional Imaging 96(5):443-448

16. Example: De Novo Variant
16
• PMID: 26640227
• c.101+3delAAGT
• Influences donor splice site predicted to lead to
premature stop codon
• Female proband with no reported family history
• Parental relationships were not confirmed
• Highly specific but not necessarily unique phenotype
represents moderate level of evidence (4B)

17. Example: Variants of Unknown Inheritance
17
• PMID: 20170896
• One individual with heterozygous nonsense variant
(p.K120X)
• Located more than 50bp away from the 3’ boundary
of the second-to-last exon, expected to undergo
NMD
• Individual presented with Barchydactyly type
• Affected sister and nephew,, unclear if tested
• Parental testing was not performed

18. Example: Segregation Among Family Members
18
• PMID: 26763883
• p.N87Tfs*18
• Female proband with BDE
• Sister and father were also reported to be affected
• Tested positive for same mutation
• Mother and paternal aunt unaffected
• Segregations counted= 2

19. Example: Project Demonstration
19
• Start with Clinical Notes to identify phenotypes and
disorders
• Create a list of genes relevant for testing
• Determine evidence for Section 2 and 3
• Move into Section 4 to incorporate literature
publications
• De novo variant
• Variant of unknown inheritance
• Segregation
• Use this information to determine final classification
• Render ACMG CNV clinical report

20. 20
VarSeq Demonstration

21. 21
Inc 5000 Recognition
Golden Helix was named to the 2020 Inc 5000 List
of Fastest-Growing Private Companies
• Second year in a row receiving this award
• Thank you to our customers and partners for our
sustained success

22. COVID-19 Publications & Articles
22
Investigating the Global Spread of SARS-CoV-2 Leveraging
Next-Gen Sequencing and Principal Component Analysis
European Journal of Clinical and Biomedical Sciences
Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer
Diagnosing and Tracking COVID-19 Infections Leveraging
Next-Gen Sequencing
The Journal of Precision Medicine Feature | July 8, 2020
Golden Helix: Enabling Precision Medicine with Cutting-
Edge NGS Technologies
Clinical OMICs Feature | July 15, 2020
Leveraging Next-Generation Sequencing Technology in the
Fight Against COVID-19
Clinical Lab Manager Feature | May 4, 2020
SARS-CoV-2 Global Spreading Investigation using Principal
Component Analysis of Sequence Variants
Journal of Genetics and Genome Research
Christiane Scherer, James Grover, Darby Kammeraad, Gabe Rudy, Andreas Scherer

23. 23
ClinGen Requirements
Genomic Analysis Software Platforms

24. 24
Any Questions?
Interested in a free trial of what you saw today? Let us know in the questions tab and we will follow up
after this webcast is finished with details to get you started!