This document summarizes a presentation about visualizing genomic variants and annotations for accurate interpretation. It discusses the speaker's background working on genetic association software and tools for analyzing single nucleotide polymorphisms, copy number variants, and next-generation sequencing data. It emphasizes the importance of visualizing variants in genomic context, alignment evidence from BAM files, representing variants and annotations consistently, and left-aligning data to facilitate comparison. Examples are provided of visualizing the speaker's own variants and those of family members identified through consumer genomics testing.

1. Visualizing Genomic
Variants and Annotations
is Vital for Accurate
Interpretation
April 23, 2015
Gabe Rudy
@gabeinformatics
VP Product Management and Engineering
Golden Helix

2. My Background
 Golden Helix
- Founded in 1998
- Genetic association software
- Analytic services
- Thousands of users worldwide
- Over 800 customer citations in journals
 Products I Build with My Team
- SNP & Variation Suite (SVS)
- SNP, CNV, NGS tertiary analysis
- Import and deal with all flavors of upstream data
- VarSeq
- Annotate and filter variants in gene panels, exomes and
genomes for clinical labs and researchers.
- GenomeBrowse (Free!)
- Visualization of everything with genomic coordinates.
All standardized file formats.

3. Visualization of Variants to Aid Interpretation
 Variants + Genomic Context
- Where it is in gene
- Annotations that match, don’t match
- Other variants in cohort
- Nearby variants in cohort/population
 Alignment Evidence
- BAM files provide more than is in VCF
 Variant Representation
- Multi-Allelic Sites
- Allelic Primitives
- Left-Alignment
- Combination!

4. My Exome Variants

5. My OTC Variant

6. X:38226614 - G/A
• Novel in all Population Catalogs but ExAC’s ~60K exomes

7. X:38226614 - G/A
• Recent Addition to ClinVar:
• 2013-05-09 G/A - Untested with Disease Unspecified
• 2014-03-03 G/A - Pathogenic with not_provided
citing:

8. X:38226614 - G/A
• Cited PubMed article was on ResearchGate, Hiroki Morizono contacted
• Provided full text and lots of interesting backstory on OTC
• “If you are able to eat all the steak you want, you may have the mutation; it would
appear to be a hypomorphic allele (and a very mild one at that)”
• “Is possible that the late onset case that [was] identified may have been someone
who was having a very bad day, and several things went poorly for them.”
• “The R40H mutation, there was a grandfather or granduncle who was affected who
ate whatever he wanted, and seemed unaffected while the proband had several
episodes.”

9. X:38226614 - G/A
• Most likely partial penetrance, with potential risk of triggering with shock event
• The Glycine is conserved down to Opossum (Platypus, Zebafish has a Alanine)

10. The Reference Sequence

11. Splice Mutation

15. Transcripts

16. Reference Sequence Versus Gene Sequence
EMG1 on GRCh37
 “Gap” of the mRNA coding sequence versus reference seq:
 Handled differently by 3 different “gene alignments”

17. Reference Sequence Versus Gene Sequence
EMG1 on GRCh38
 Reference sequence patched, no gap
 Alignments agree

19. Left-Align

21. Left-Align Delta F508 to Make it Match

22. Left-Align Annotations
 Using a Smith-
Waterman
algorithm to left-
align variants
from public
databases show
non-obvious
differences
 NGS alignment
and variant
calling always
left-aligned
 Left-align your
database so they
can be annotated

23. Allelic Primitives

24. My Son’s de Novo

25. Exome Sequencing in Consumer Genomics
 Exomes done as part of Pilot
Program
 80x coverage
 Raw data with no interpretation
Erin
JIA
Gabe
(me)
Ethan

26.  asdf

29. NM_002626.4:c.1877G>C in PFKL
 NP_002617.3:p.Arg626Pro missense mutation
 Predicted damaging by 4/5 functional predictions
 VEST3: 0.948, GERP++: 4.59
 ExAC and 1kG have a G>A, but G>C is novel
 Variants in region are extremely rare (G>C ExAC 4 of 122,364 alleles) – 0.003%
 No ClinVar variants for gene
 OMIM entry has no known disease association
 PubMed search shows few recent articles: Most recent 1998 paper showed
- phosphofructokinase (PFKL) overexpressed in Down syndrome (DS)
- Transgenic PFKL mice had an abnormal glucose metabolism with reduced clearance
rate from blood and enhanced metabolic rate in brain.

30.  d

31.  d
35 LoF Variants, None Homozygous

32. Thank you
 Heidi Rehm – Chief Laboratory Director at
Laboratory for Molecular Medicine,
PCPGM
 Hiroki Morizono – Children’s National
 Reece Hart – Computational Biologist,
Invitae (now 23andMe)
 Greta Linse Peterson – Director of Product
Management and Quality, Golden Helix

33. Questions?