church dm grc_workshop
DESCRIPTION
Using the genome by Deanna ChurchTRANSCRIPT
© 2014 Personalis, Inc. All rights reserved.
Pioneering Genome-Guided Medicine
A view from the trenches
Deanna M. Church
Senior Director of Genomics and Content
Real world challenges to using GRCh38
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Acknowledgements
PersonalisJason Harris
Sarah Garcia
Jeanie Tirch
Gabor Bartha
Mark Pratt
Scott Kirk
Michael Clark
Rich Chen
John West
Genome Reference Consortium
NCBIValerie Schneider
Nathan Bouk
Terence Murphy
Alex Astashyn
Donna Maglott
Melissa Landrum
Wendy Rubinstein
Jennifer Lee
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Who we are
Inherited
Disease
Diagnostics
Cancer
Services
ACE Platform
Research
Services
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Accuracy is key to what we do
Case courtesy of Geisinger Health System
• Both affected children– Macrocephaly
– Low muscle tone, hypotonia
– Delay in early milestones
– Dysphagia
– Esotropia
• Affected Male (3 yr)– Intellectual disability
– Mild hearing loss
– High arched palate
– Small cyst near eye
• Affected Female (15 mo)– Sleep apnea
– Failure to thrive
– Laryngomalacia
– Anisocoria
– Small optic nervesNovel 2bp deletion in GATAD2B
Called by GATK as paternally inherited
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Accuracy is key to what we do
Sample GATK-
determined
Genotype
Ref Alt Depth Allele
Freq.
Father 0/1 108 11 121 0.09
Mother 0/0 111 0 112 0.00
Brother 0/1 63 44 109 0.40
Sister 0/1 64 52 119 0.44
Case courtesy of Geisinger Health System
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Excitement about GRCh38
GGAACGCAGGGAACACAG
DPYD
R->C
Alt loci
Model Centromere Sequences
Miga et al., 2014
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Medical content not on chromosome sequences
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Medical content not on chromosome sequences
NT_113939: chr19 unlocalized contigGRCh37
GRCh38
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Medical content not on chromosome sequences
NT_167246.2: MHC alternate locus
No SNP annotationSparse SNP
annotation
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By any other name
chr19 vs 19
GenBank: CM00681.2
RefSeq: NC_000019.10
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By any other name
chr19_KI270938v1_alt
CHR_HSCHR19KIR_G248_BA2_HAP_CTG3_1
GenBank: KI270886.1
RefSeq: NT_187640.1
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Unflattening the data MICB
Reporting formats (GFF, VCF, etc) don’t
manage multiple locations easily
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NW_003871068.1
NC_000006.12 BestRefSeq gene 31494881 31511124 . + . ID=gene13336;Name=MICB;Dbxref=GeneID:4277
NT_167244.2 BestRefSeq gene 2827449 2843674 . + . ID=gene42005;Name=MICB;Dbxref=GeneID:4277
NT_113891.3 BestRefSeq gene 2972222 2988464 . + . ID=gene43669;Name=MICB;Dbxref=GeneID:4277
NT_167245.2 BestRefSeq gene 2742492 2758910 . + . ID=gene44377;Name=MICB;Dbxref=GeneID:4277
NT_167246.2 BestRefSeq gene 2810648 2816200 . + . ID=gene44827;Name=MICB;Dbxref=GeneID:4277
NT_167247.2 BestRefSeq gene 2836836 2853071 . + . ID=gene45127;Name=MICB;Dbxref=GeneID:4277
ID=gene13336;Name=MICB;Dbxref=GeneID:4277
ID=gene42005;Name=MICB;Dbxref=GeneID:4277
ID=gene43669;Name=MICB;Dbxref=GeneID:4277
ID=gene44377;Name=MICB;Dbxref=GeneID:4277
ID=gene44827;Name=MICB;Dbxref=GeneID:4277
ID=gene45127;Name=MICB;Dbxref=GeneID:4277
Building snpEFF
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Incremental steps: using fix patches
SHANK2
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Using Fix patches to improve alignments
Incremental steps: using fix patches
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Migrating to GRCh38: using Fix patches
hs37d5
Fix patch
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Migrating to GRCh38: using Fix patches
hs37d5
Fix patch
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Migrating to GRCh38: using Fix patches
GRCh37 vs. Fix Patch
GRCh38
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GRCh37.p13 Improved alignments outside of fix patch regions
Regions outside of fix patches
Jason Harris
hs37d5
GRCh37.p13
hs37d5GRCh37.p13
378 Ten kb windows that don’t
overlap fix patches with >10 SNV
call differences
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GRCh37.p13 Improved alignments outside of fix patch regionsJason Harris
hs37d5
GRCh37.p13
hs37d5
GRCh37.p13
hs37d5
GRCh37.p13
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Using Fix patches
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Aligning GRCh37 and GRCh38
Seq in
assembly 1
Seq in
assembly 2
A A
B
B’
B
Unique well aligned
region in both assemblies.
First Pass (FP) alignments
Second Pass (SP) alignments
SP only
Expansion
Assembly 1
SP + FP
Collapse
Assembly 2
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Aligning GRCh37 and GRCh38
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Mapping to GRCh38
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Mapping to GRCh38
Dataset Starting
loci
Failure Unique to
Primary
Unique to
Alts
Collapse
in
GRCh37
Collapse
in
GRCh38
GWAS
catalog
7,991 0 7,827 0 14 0
ClinVar* 88,343 3 86,549 5 278 4
GO-ESP
6500
1,982,177 180 1,920,864 339 5,792 324
GIAB 2,915,713 274 2,874,786 47 1,662 4
*clinvar_20140902.vcf
NCBI assembly-assembly alignments from:
Sept 20, 2014, software version 1.7
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Remap vs. liftOver
liftOver-dbSNP remap
rs141109950chr7
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Remap vs. liftOver
rs267602252
remap liftOver
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First Pass remap Second Pass remap
Migrating to GRCh38
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Migrating to GRCh38
New PRODH paralog
Sequence is unlocalized on chr22.
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Using GRCh38 to improve GRCh37 annotationKCNE1
Alignment to new paralog added in GRCh38
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Getting the most out of the reference
Still challenging because tools and
data structures expect a flat assembly
Remap/liftOver not the final answer for
moving variation
Even modest changes (via fix patches)
are promsing