Exploring next-generation sequence data requires an iterative process whereby a researcher can find a "needle in the haystack" that contributes to a particular disease or other phenotype. Once that needle has been found, a workflow can be established for analyzing other samples or to create a repeatable, time-effective process for clinical usage. Yet, repeating a workflow that involves several different quality control, filtering, and analysis steps is burdensome and error-prone. To solve this problem, we introduce custom workflow automation in SVS, which allows you to collapse dozens of steps into a few run-specific options. This click-and-go process saves an exponential amount of time while eliminating the inevitable user error that happens with tedious repetition and ensures that the exact same protocol is followed with each run, a critical requirement for use in the clinic.

1. Autumn Laughbaum, Biostatistician
with introduction by Dr. Andreas Scherer,
President & CEO
Making NGS Data Analysis Clinically Practical:
Repeatable and Time-Effective Workflows

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3. Introduction
ClinicianResearcher

4. Hands-on Time Savings
2 weeks
2 minutes
2 hours
1 trio using Excel 100 trios
using SVS
Unlimited trios
using automated
workflow

5. Today’s Agenda
Status Quo
Example Workflow: Ogden Syndrome
Example Workflow: Trio Analysis
Discussion
1
2
3
4
Moving from Excel > SVS > Automated Workflows
General sequencing workflow

6. Analyzing Data from a secondary analysis pipeline:
Using Excel

7. Analyzing Data from a secondary analysis pipeline: Using SVS

8. Analyzing Data from a secondary analysis pipeline:
Automated Workflow

9. Analyzing Sequencing Data
Filter to coding regions
Non-
synonmyous
variants
 2 variants
Filter based on
population frequencies
Functional
prediction
 10,000
 30,000
 35,000
 40,000
Data from
secondary analysis
pipeline (VCF) –
2 million variants
Inheritance
pattern
Filter on read depth & quality
score
 3,000

10. WORKFLOW EXAMPLE – TRIO
ANALYSIS
Workflow Example – Ogden
Syndrome

11. Pedigree
Ref_Alt
Ref_Alt Ref
Ref Alt Affected
Male
Female
Deceased
Sequenced

12. SVS Demo

13. Ogden Syndrome
Filter based
on VCF
quality
metrics
Filter based
on
population
frequencies
Annotate
based on
functional
predictions
Filter based
on variant
classification
Filter based
on
inheritance
pattern
5 Samples
107,000 variants
1 damaging
variant
Ref_Alt
Alt

14. WORKFLOW EXAMPLE – TRIO
ANALYSIS
Workflow Example – Trio Analysis

15. Trio Analysis – 3 Distinct Mutation types
• de Novo Mutations
• Rare Recessive
Mutations
• Compound
Heterozygous
Mutations
Import variant
data (VCF)
Exon Regions
Filter on VCF
Quality Metrics
Damaging
Variants
Variant
Classification
(remove synon)
Find de Novo
Variants
Filter on Variant
Frequencies
Heterozyous
Child
Compound
Heterozygous
Genes
Rare Recessive
Mutations
AdditionalAnnotations

16. de Novo Mutation
Ref_Ref
Ref_AltChild
Ref_Ref
Father Mother

17. Rare Recessive Mutation
Ref_Alt
Alt_AltChild
Ref_Alt
Father Mother

18. Compound Heterozygous Mutation
Ref_Ref
Re
Ref_Alt
Ref_Alt
Within a Gene
Ref_AltRef_Ref
Ref_Alt

19. Trio Analysis – Automated Workflow

20. Trio Analysis – Automated Workflow

21. Trio Analysis – Automated Workflow

22. Trio Analysis – Automated Workflow
2.3 Million
38K
36K
30K
10K
de Novo: 2 5K
3K
Compound
Heterozygous:
85
Rare Recessive:
12

23. Automated Workflow - Results

24. Automated Workflow Results

25. Additional Annotations

26. WORKFLOW EXAMPLE – TRIO
ANALYSIS
Example in GenomeBrowse

27. WORKFLOW EXAMPLE – TRIO
ANALYSIS
Discussion

28. Clinicians vs. Researchers
Clinicians
 Running well-defined
workflow on additional
samples
 Minimum user-interface
knowledge
 Small learning curve
 Limited hands-on time
Researchers
 Building and testing workflows
 More complex but intuitive
interface
 Larger learning curve
 Power to investigate and
manipulate data

29. Conclusion – The GHI Approach
Work closely
with clients to
learn about
needs and
develop
workflow
specification
Create document
and workflow
diagram outlining
specifications
and
requirements
Build automated-
workflow
prototype
Thorough
internal testing
and complete
documentation
Finished product
works seamlessly
within SVS

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