Visualizing Genomic Variants and Annotations

is Vital for Accurate Interpretation

April 23, 2015

Gabe Rudy

@gabeinformatics

VP Product Management and Engineering

Golden Helix

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.

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!

My Exome Variants

My OTC Variant

X:38226614 - G/A

• Novel in all Population Catalogs but ExAC’s ~60K exomes

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:

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.”

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)

The Reference Sequence

Splice Mutation

Transcripts

Reference Sequence Versus Gene Sequence

EMG1 on GRCh37

“Gap” of the mRNA coding sequence versus reference seq:

Handled differently by 3 different “gene alignments”

Reference Sequence Versus Gene Sequence

EMG1 on GRCh38

Reference sequence patched, no gap

Alignments agree

Left-Align

Left-Align Delta F508 to Make it Match

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

Allelic Primitives

My Son’s de Novo

Exome Sequencing in Consumer Genomics

Exomes done as part of Pilot Program

80x coverage

Raw data with no interpretation

ErinJIA

Gabe(me)

Ethan

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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.

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35 LoF Variants, None Homozygous

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

Questions?