Mendelian violations in the CEU and YRI Pilot 2 Trios

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1 Mendelian violations in the CEU and YRI Pilot 2 Trios Mark DePristo and Mark Daly Manager, Medical and Population Genetics Analysis Medical and Population Genetics Program Broad Institute of Harvard and MIT March 8, 2010

2 Summary Multi-sample (but trio-unaware) calls made with GATK Unified Genotyper for each Pilot 2 trio Part of the official release intersected with UMich calls This presentation focuses on Mendelian violations in general Next presentation will analyze highly-validated classic de novo mutations (novel het where parents are hom-ref) Violations fall into three distinct classes described in more detail here: True de novo mutations Cryptic copy number variation Many likely due to cell line degeneration but many segregating too FP due to sequencing artifacts

3 The Broad Unified Genotyper SNP caller was applied to all three wings of the project Sample-associated reads Individual 1 Genotype likelihoods Allele frequency Individual 2 Joint estimate across samples SNPs Individual N Genotype frequencies This approach allows us to combine weak single sample calls to discover variation among samples with high confidence See h%p:// for more informa3on

4 Pilot 2 yielded ~2.7B genotyped sites, discovering ~4-5M variants in each trio CEU trio YRI trio All variants SNPs 3.6M dbsnp % 89% Ti/Tv 2.07 All variants SNPs 4.5M dbsnp % 77% Ti/Tv 2.09 Novel variants 409K SNPs Ti/Tv = 2.04 Novel variants 1.05M SNPs Ti/Tv = 2.08

5 Mendelian violations identify germ-line and somatic de novo mutations Algorithm to identify putative Mendelian violations Autosomal Mendel violations in the CEU and CEU trios 1 De novo SNP or 2 somatic parent CNV Genotyping error or somatic parent CNV Genotype (A is ref, B is alt, * is either) CEU Trio YRI Trio A/A A/A B/B B/B Child Parents A/B A/B 1 2 A/B A/A and A/A 1, A/B B/B and B/B 1, Segregating CNV* A/A */* B/B */* 3 3 A/A B/B and */* B/B A/A and */* Total 3,769 2,174 B/B *Equivalent violations for mom A/A Initial validation suggests high validation rate for the de novo SNPs, but 80+% are non-inherited somatic events

6 Mendelian violations by known/novel Mendelian by genotype (A is ref, B is alt, * is either) CEU YRI Known Novel Known Novel Child genotype Parent genotypes A/B A/A and A/A A/B B/B and B/B A/A B/B and */* B/B A/A and */* Total Consistent with classic de novo SNP Autosomal Mendelian viola3ons where GQ >Q30 for all three individuals

7 Mom Dad No evidence in parents 454 Child SLX Consistent in all three technologies SOLid Work of Andrew Kernytsky Validated as a true de novo mutation

8 Many of the lost homozygous variant alleles in the parents are clustered For example, the 10 sites in 8Kb at 1: Consistent with somatic deletions in the parent (in this case Mom) Overlaps CNV discovered in pilot 1

9 Log10 of inter- SNP distance Clustering of violations on YRI chr1 Colored clustered have distance < 10Kb Cluster of violations marks 10 Mb deletion of chromosome arm Rare, randomly occurring de novo SNPs Inter-SNP distance for regular variation Distribu3on from all SNPs Histogram of log10 of inter-snp distances

10 Genome-wide perspective for YRI Top level junctions are among chromosomes CNVs are common and clear Signature of CNVs

11 Opposite homozygous SNPs are cluster on the chromosome whereas hets are not Opposite homozygote violations are the most clustered Consistent with cryptic copy number variation Few clusters of violations where the child is heterozygous Almost no SNP clusters Kid is heterozygous, parents are homozygous reference Mostly clustered No SNP clusters Kid and one parent are opposite homozygotes Kid is heterozygous, parents are homozygous variant

12 CEU cell line are apparently degrading with large somatic deletions throughout the genome Opposite homozygote Mendelian violations YRI trio CEU trio YRI samples prepared more recently, fewer cell line passages CEU samples prepared less recently, more cell line passages Older, more passaged CEU samples exhibit more and larger apparently somatic cell line artifacts

13 Many Mendelian violations overlap CNVs Overlaps Pilot1-only CNV Overlaps Pilot CNV Overlaps Pilot2-only CNV Not in CNV Overlaps Pilot1-only CNV Overlaps Pilot CNV Overlaps Pilot2-only CNV Not in CNV OppositeHoms CNV false negatives? Chromosome KidHet_ParentsHomRef 0.6 Freq Freq 0.8 Real de novo SNPs, mostly somatic False negative in pilot 1 calls? Likely all real CNVs Somatic CNVs in parents Violation index on chromosome KidHet_ParentsHomRef OppositeHoms CNVs from validated list of deletions in mastervalidationtables_pilot1_pilot2_

14 Violations where child is A/B and parents are B/B are homopolymer-induced genotyping errors 1200 in CEU and 400 in YRI of which ~95% are in dbsnp, suggesting they are real variant sites Consistent with somatic deletions, but do not cluster Visual inspection shows that these are true homozygous non-reference sites All neighboring long homopolymer runs Genotyping failure due to misaligned 454 and miscalled SOLiD reads SOLiD recalibration partially fixes reference bias in this area Difficult-to-fix failure mode for 454; even fixable?

15 Example

16 How reliable are NA12878 chr1 calls? Comparison to Complete Genomics sequencing for NA12878 CEU Chromosome 1 violations only Mendelian viola@ons by genotype (A is ref, B is alt, * is either) CEU % in CG Known Novel Known Novel Child genotype Parent genotypes A/B A/A and A/A A/B B/B and B/B Child and parent are opposite homozygotes NA NA Total CG: 60x genome-wide Complete Genomics sequence, called with CG analysis software

17 Conclusions Violations fall into three distinct classes described in more detail here: True de novo mutations which look excellent, also observed in CG data Cryptic copy number variation Many opposite homozygotes overlap with CNVs Class of FP sequencing artifacts Mendelian violations in trios May provide false negatives for SV calls evaluation Some CNV calls may be be somatic not segregating One value of trio sequencing is to differentiate between segregating and somatic variation

18 Appendix

19 Example 1

20 Mendelian violations consistent with cryptic copy number variation and rare de novo mutations Most clustered violations are from opposite homozygotes