1000g pilot 3 progress (in silico analysis and comparison to experimental validation) amit indap,...

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1000G Pilot 3 Progress

(in silico analysis and comparison to experimental validation)

Amit Indap, Wen-Fung Leong Gabor Marth (Boston College) Chris Hartl and Kiran Garimella (Broad Institute)

1000 Genomes Project Analysis GroupFebruary 2, 2010

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Acknowledgements

BaylorMatthew BainbridgeFuli YuDonna MuznyRichard Gibbs

BroadChris HartlKiran GarimellaCarrie SougnezMark DePristo

Wash. U.Dan KoboldtBob Fulton

SangerAarno Palotie

Boston CollegeAmit IndapWen Fung LeongGabor Marth

CornellAndy Clark

StanfordSimon GravelCarlos Bustamante

MichiganTom Blackwell

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Data

CEU TSI CHB CHD JPT LWK YRI

Number of samples 90 66 109 107 105 108 112

Sequencing technology SLX+454 SLX SLX+454 SLX+454 SLX+454 454 SLX+454

Per-sample coverage1 67X 64X 42X 59X 49X 30X 56X

• Capture technologies:– Nimblegen solid phase– Agilent liquid phase

• Sequencing technologies:– SLX– 454

• Data producers:– BCM– BI– WTSI– WUGSC

• Capture targets:– Started with ~1,000 genes / ~10,000 exons / 2.3Mb– 1.43Mb of total target length shared between 4 data

centers used for this analysis

• Samples:– 697 total samples– 7 populations

• Sequence coverage:– Goal was deep per-sample coverage– Effective coverage somewhat reduced by fragment

duplications

1. Mean of coverage medians per sample and population

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PipelinesProcessing step BC BI

Read mapping SW MOSAIK MAQ (SLX)SSAHA2 (454)

Duplicate filtering SW Picard MarkDuplicates (SLX)BCMMarkduplicates (454)

Picard MarkDuplicates (SLX) Picard MarkDuplicates (454)

Base quality recalibration SW

GATK (SLX)None (454)

GATK (SLX)GATK (454)

SNP calling SW GigaBayes (BamBayes) UnifiedGenotyper

CEU

TSI

CHB

CHD

JPT

LWK

YRI

Union of all called sites in all 697 samples

CEU

TSI

CHB

CHD

JPT

LWK

YRI

Segregating sites in each population sample

All 697 samples

All 697 samples

SNP calling

SNP statistics

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BC and BI call sets are convergingComparison # BC call

versionBC total calls

BC unique calls

BC & BI(intersection)

BC || BI(union)

BI unique calls

BI total calls BI call version

1 2009/11/20 11,580(55.96%)

733(3.54%)

10,847(54.34%)

20,695(100%)

9,115(44.04%)

19,962(96.46%)

v2

2 2009/11/20 11,580(65.75%)

1,480(8.40%)

10,100(62.60%)

17,613(100%)

6,033(34.25%)

16,133(91.60%)

v3

3 2010/01/20 14,502(79.35%)

2,144(11.73%)

12,358(76.60%)

18,277(100%)

3,775(20.65%)

16,133(88.27%)

v3

4 2010/01/20 14,502(72.91%)

1,741(8.75%)

12,761(64.16%)

19,890(100%)

5,388(27.01%)

18,149(91.25%)

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Comparison # CEU TSI CHB CHD JPT LWK YRI

1 3,354 (73.87%) 3,168 (65.88%) 3,279 (66.23%) 3,226 (68.42%) 2,942 (47.79%) 4,922 (70.56%) 4,917 (72.08%)

2 3,036 (70.62%) 2,893 (69.34%) 2,938 (62,23%) 2,783 (60.58%) 2,545 (55.64%) 4,486 (65.33%) 4,253 (66.30%)

3 3,333 (74.63%) 3,155 (73.15%) 3,294 (66.80%) 3,201 (66.69%) 2,795 (58.40%) 5,165 (73.18%) 4,728 (71.29%)

4 3,489 (78.78%) 3,281 (69.32) 3,415 (69.74%) 3,431 (72.81%) 2,900 (50.86%) 5,459 (78.55%) 5,175 (78.59%)

All called sites

Called sites per population (BC/BI intersection)

Intersection (% of union)

Number of sites(% of union)

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SNP calls (per population)CEU TSI CHB CHD JPT LWK YRI

samples 90 66 109 107 105 108 112

90 66 109 107 105 108 112

called SNPs 4,102 3,729 4,340 4,262 3,883 6,039 5,891

3,816 4,285 3,972 3,881 4,719 6,370 5,869

dbSNPs 2,422 2,257 2,042 1,924 1,950 2,872 2,897

2,352 2,200 1,827 1,753 1,710 2,825 2,856

% dbSNP 59.04 60.53 47.05 45.14 50.22 47.56 49.18

61.64 51.34 46.00 45.17 36.24 44.35 48.66

Ts/Tv (called SNPs) 2.73 2.78 2.82 3.06 2.85 3.45 2.92

3.14 2.38 3.15 3.16 1.83 3.17 3.15

novel SNPs 1,680 1,472 2,298 2,338 1,933 3,167 2,994

1,464 2,085 2,145 2,128 3,009 3,545 3,013

Ts/Tv (novel SNPs) 2.05 2.10 2.44 2.81 2.43 3.44 2.56

2.92 1.72 3.03 3.05 1.36 3.07 2.99

BCBI

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SNP calls (all samples)

BC BI

Samples 697 697

Called SNPs 14,502 18,149

dbSNPs 3,948 4,041

dbSNP fraction 27.22% 22.27%

5,388 SNPs172 dbSNPsdbSNP=3.19%

1,741 SNPs 79 dbSNPsdbSNP=4.54%

12,761 SNPs3,869 dbSNPs

dbSNP=30.32%

BC: 14,502 SNPs BI: 18,149 SNPs

BC U BI = 19,890

BC∩BI

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Genotype call accuracy relative to HapMap3

CEU TSI CHB CHD JPT LWK YRI

FDR of variant genotypes in HapMap3 (%) 0.96 0.23 2.61 1.42 3.60 0.47 0.57

1.41 0.45 2.99 1.82 3.56 0.66 1.25

Correct calls (%) 98.39 98.98 96.76 98.20 95.72 99.06 98.63

97.22 98.26 95.45 97.35 94.55 98.74 96.68

Accuracy of homozygote reference calls (%) 99.20 99.81 97.52 98.62 96.42 99.64 99.59

98.79 99.62 97.07 98.21 96.33 99.48 99.07

Accuracy of heterozygote calls (%) 97.50 97.72 97.98 99.12 96.81 98.37 96.53

94.49 95.43 94.19 97.37 92.30 97.89 90.81

Accuracy of homozygote non-reference calls (%) 97.31 98.44 93.27 95.78 92.69 98.21 98.45

96.77 98.76 93.26 95.16 93.43 97.67 97.46

BCBI

Data quality in CHB and JPT samples seems consistently lower

Statistics only include genotype calls at SNP sites in BC∩BI

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Genotype calls

All SNP sites considered Only SNP sites with >= 80% called genotypes

# SNP sites=3,075r=0.9979

# SNP sites=3,489r=0.9921

• Filtering:BC filters on genotype call qualityBI reports a genotype for any site where at least one read covers

• Nominally, BI makes more calls than BC, and has, on average, higher AF

The Broad caller does not filter on genotype quality

• Good allele frequency concordance between BC and BI• At genotype calls that passes BC filter, and BI also makes a call, no discordance was found

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1KG validation executive summary

• Evaluated BI and BC calls against validation– 1KG chip1

• 312/697 samples across 7 populations represented• ~300 sites (150 novel) overlap with Pilot 3 target region

• Concordance with 1KG chip is very high– Where covered (> 5 reads):

• 302/312 (97%) of samples have >90% variant sensitivity• 269/312 (86%) of samples have >90% genotype sensitivity

– Remaining disparities between 1KG chip and Pilot 3 calls can be explained by data quality issues• Later sequencing has far greater concordance with chip than earlier

sequencing1. Details in Appendix

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Variant PPV/Sensitivity to 1KG chip is reasonably high for most samples; discordant samples are poorly sequenced

0 50 100 150 200 250 300 3500.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV

% Variant Sensitivity

Sample (318 Pilot 3 samples overlapping with 1KG chip)

Spikes in Variant PPV are due to low-quality sequencing in JPT samples (see Appendix)

After filtering out sites with < 4 reads, nearly all samples in call-set overlap have high sensitivity and specificity

0 50 100 150 200 250 300 3500.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV


% Ignored Low-Coverage Bases

Sample (312 Pilot 3 samples after eliminating those with low-coverage)

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These 10 low-sensitivity samples have strange allele balances and are likely contaminated

All but one sample with low PPV (false-positive rate > 10%) are among the earliest-sequenced samples (JPT/CHB/CHD)

Concordance to chip tracks closely with submission-to-DCC date (proxy for sequencing date)

130 50 100 150 200 250 300 350

0.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV



Sample (312 Pilot 3 samples sorted by earliest DCC submission date)

Submitted: 12/08-7/09Median number of lanes: 2

Submitted: 8/08-10/08Median number of lanes: 3

The most recently sequenced samples have higher concordance to 1KG chip.

Increase in number of sites with < 4 reads corresponds with fewer lanes being run per sample.

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Mean sensitivity/PPV per population is good, and improves on more recently-sequenced populations

CEU CHB CHD JPT LWK TSI YRI0.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

Mean % PPV

Mean % Sensitivity

N Samples: 69 13 27 102 69 3 24

8/2008ILMN/454

All Ctrs

8/2008ILMN/454

All Ctrs

8/2008ILMN/454

BI/BCM

1/2009454BCM

8/2008ILMN/454

BI/BCM

10/2008ILMNBI/SC

2008/2009ILMN/454

All Ctrs

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Low-frequency / singleton validation: executive summary

• Low-frequency Sequenom assay1

– Chose 105 putative novel singletons from early Pilot 3 46-CEU-sample callsets (called in at least 2/4 callers)

– Validated sites in those 46 individuals• 89/105 are true singletons• 16/105 are false-positive singletons (hom-refs and two non-singletons)

• Concordance with low-frequency assay is very high– Callsets today (January 2010)

• In BI and BC overlap, recovered 71/89 (80%) of assayed singletons with 0 false-positives and 0 non-singletons

• In BI and BC union, recovered all 89 singletons with 3 false-positives and 0 non-singletons

1. Details in Appendix

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Call Set Loci Tested

Overlap with Test Set

TP (PPV) FP True, but not Singleton

BC ∩ BI 105 71 71 (100%) 0 0

BC BI∪ 105 92 89 (97%) 3 0

Callers are able to detect most singletons with very low false-positive rate

Assay Loci(after filtering1)

TP (PPV) FP True, but not Singleton

Whole Assay 105 89 (85%) 16 2

Assay Performance

Callset Performance

1. HWE violations, no-call rate > 5%

Callset union finds every singleton in the assay with few false-positives.

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Many sites shared between P3 and external projects; low overall FP rate

Calls (90 CEU samples)Loci in P1/P2 = 60%

Loci in other projects/databases = 71%1

FP Rate (sites on validation chips) =5.3%FN Rate (sites on validation chips) < 5%2

Calls (overall)FP Rate (sites on validation chips) =

9.1%3

FN Rate (sites on validation chips)< 5%3

1. Sites seen across all 91 Pilot 3 CEU individuals, occurring in dbSNP 129, Hapmap 3, Pilot 1, or Pilot 22. No per-locus FNs observed in overlapping set3. Includes FP and FN errors due to sample contamination/data quality

FP rate is likely a slight overestimate because a hom-ref site across the 69 CEU samples on the chip doesn’t preclude the possibility of a variant harbored in one of the other 21 samples not represented in the validation assay.

Some of these FPs are also due to sample contamination in older lanes.

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Conclusions / future directions

• Data quality has improved significantly over the life of the project

• Both BC and BI pipelines produce high-quality call sets– Good agreement between call sets– intersection highly concordant with experimental validation

data– Estimated FP rate below ~9%

• The current Pilot 3 release is the BC∩BI (intersection) call set

• We are proceeding with validations– Dual focus: accuracy and functional classes– Results will inform future releases

APPENDIX

Population spectrum of called SNPs

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Population-spectrum of called SNPs

CEU TSI CHB CHD JPT LWK YRI ALL

called SNPs 4,102 3,729 4,340 4,262 3,883 6,039 5,891 14,502

3,816 4,285 3,972 3,881 4,719 6,370 5,869 18,149

BCBI

• Observation: BC call more SNPs on the population level, but less SNP sites overall

• Reason: BC tends to call the same site in more populations…

BC/BI SNP calls per population (more detail)

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SNP calls (per population)CEU TSI CHB CHD JPT LWK YRI

samples 90 66 109 107 105 108 112

90 66 109 107 105 108 112

called SNPs 4,102 3,729 4,340 4,262 3,883 6,039 5,891

3,816 4,285 3,972 3,881 4,719 6,370 5,869

dbSNPs 2,422 2,257 2,042 1,924 1,950 2,872 2,897

2,352 2,200 1,827 1,753 1,710 2,825 2,856

% dbSNP 59.04 60.53 47.05 45.14 50.22 47.56 49.18

61.64 51.34 46.00 45.17 36.24 44.35 48.66

Ts/Tv (called SNPs) 2.73 2.78 2.82 3.06 2.85 3.45 2.92

3.14 2.38 3.15 3.16 1.83 3.17 3.15

novel SNPs 1,680 1,472 2,298 2,338 1,933 3,167 2,994

1,464 2,085 2,145 2,128 3,009 3,545 3,013

Ts/Tv (novel SNPs) 2.05 2.10 2.44 2.81 2.43 3.44 2.56

2.92 1.72 3.03 3.05 1.36 3.07 2.99

singletons 1,378 1,264 1,654 1,686 1,284 1,430 1,457

1,240 1,911 1,555 1,500 2,347 1,692 1,489

Ts/Tv (singletons) 2.72 3.36 3.33 3.39 3.09 4.68 3.04

2.84 1.72 2.81 3.03 1.11 3.26 2.73

BCBI

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Broad & BC calls: CEUPopulation: CEU (90 samples) BC Broad

# SNPs called (Ts/Tv) 4,102 (2.73) 3,816 (3.14)

#dbSNP (Ts/Tv) 2,422 (3.40) 2,352(3.28)

# novel SNPs (Ts/Tv) 1,680 (2.05) 1,464 (2.92)

# Singleton (Ts/Tv) 1,378 (2.72) 1,240 (2.84)

32752(15.90%)

1.32

BC613

122(19.90%)0.92

3,4892,300(65.92%)

3.47

SNP#dBSnp(%)Ts/Tv

Broad

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Broad & BC calls: CHBPopulation: CHB (109 samples) BC Broad

# SNPs called (Ts/Tv) 4,340 (2.82) 3,972 (3.15)

#dbSNP (Ts/Tv) 2,042 (3.37) 1,827 (3.30)

# novel SNPs (Ts/Tv) 2,298 (2.44) 2,145 (3.03)

# Singleton (Ts/Tv) 1,654 (3.33) 1,555 (2.81)

55732(5.75%)

1.37

BC925

247(26.70%)1.23

3,4151,795(52.56%)

3.74

Broad

SNP#dBSnp(%)Ts/Tv

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Broad & BC calls: CHDPopulation: CHD (107 samples) BC Broad

# SNPs called (Ts/Tv) 4,262 (3.06) 3,881 (3.16)

#dbSNP (Ts/Tv) 1,924 (3.40) 1,753 (3.30)

# novel SNPs (Ts/Tv) 2,338 (2.81) 2,128 (3.05)

# Singleton (Ts/Tv) 1,686 (3.39) 1,500 (3.03)

45031(6.44%)

1.33

BC

831200(24.07%)

1.68

34311,724(50.25%)

3.64

Broad

SNP#dBSnp(%)Ts/Tv

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Broad & BC calls: JPTPopulation: JPT (105 samples) BC Broad

# SNPs called (Ts/Tv) 3,883 (2.85) 4,719 (1.83)

#dbSNP (Ts/Tv) 1,950 (3.39) 1,710 (3.31)

# novel SNPs (Ts/Tv) 1,933 (2.43) 3,009 (1.36)

# Singleton (Ts/Tv) 1,284 (3.09) 2,347 (1.11)

983271(27.57%)

1.54

BC1819

31(1.70%)0.74

2,9001,679 (57.90%)

3.67

Broad

SNP#dBSnp(%)Ts/Tv

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Broad & BC calls: LWKPopulation: LWK (108 samples) BC Broad

# SNPs called (Ts/Tv) 6,039 (3.45) 6,370 (3.17)

#dbSNP (Ts/Tv) 2,872 (3.46) 2,825 (3.31)

# novel SNPs (Ts/Tv) 3,167 (3.44) 3,545 (3.08)

# Singleton (Ts/Tv) 1,430(4.68) 1,692 (3.26)

580136(23.45%)

2.09

BC911

89(9.77%)1.56

5,4592,736(50.12%)

3.67

Broad

SNP#dBSnp(%)Ts/Tv

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Broad & BC calls: TSIPopulation: TSI (66 samples) BC Broad

# SNPs called (Ts/Tv) 3,729 (2.78) 4,285 (2.39)

#dbSNP (Ts/Tv) 2,257 (3.42) 2,200 (3.40)

# novel SNPs (Ts/Tv) 1,472 (2.10) 2,085 (1.72)

# Singleton (Ts/Tv) 1,264(3.36) 1,911 (1.72)

448105(23.44%)

0.71

BC1,004

48(4.78%)0.85

3,2812152(65.59%)

3.54

Broad

SNP#dBSnp(%)Ts/Tv

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Broad & BC calls: YRIPopulation: TSI (66 samples) BC Broad

# SNPs called (Ts/Tv) 5,891(2.92) 5,869 (3.15)

#dbSNP (Ts/Tv) 2897 (3.38) 2,856 (3.34)

# novel SNPs (Ts/Tv) 2,994 (2.56) 3,013 (2.99)

# Singleton (Ts/Tv) 1,489 (3.04) 1,457 (2.73)

716112(15.64%)

0.95

BC694

71(1023%)1.48

5,1752,785(53.82%)

3.56

Broad

SNP#dBSnp(%)Ts/Tv

BC vs. BI allele frequency comparisons per population at SNPs in the BC∩BI call

set

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BC/BI genotype calls (CHB & CHD)

All SNPs SNPs with >= 80% called genotypes


#sites=3415r=0.9925

#sites=3431r=0.9941

CHD

CHB

#sites=3028r=0.9993

#sites=3310r=0.9991

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BC/BI genotype calls (TSI & JPT)

#sites=2900r=0.9922

#sites=2370r=0.9991

#sites=3108r=0.9973

#sites=3281r=0.9912

TSI

JPT



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BC/BI genotype calls (LWK & YRI)

#sites=5337r=0.9984

#sites=5459r=0.9924

#sites=4276r=0.9978

#sites=5175r=0.9917

YRI

LWK



Low frequency / singleton validation design

Recap: Novel singletons from 66 CEU samples chosen for validation

• Interesting singleton: a putative SNP…1. that is novel (not in dbSNP 129)2. that has been identified by the BC or BI caller3. that only occurs in 1 out of 66 of the test

individuals4. where the individual in whom the SNP is identified

is the same among callers5. that is also identified by one other caller6. whose locus has nominal coverage in other non-

variant samples

Data and Definitions

• Sequenom validation run on 46 of 66 individuals (Broad did not have DNA for all 66 samples)

• Sequenom calls filtered by Broad standard metrics (no significant deviation from Hardy-Weinberg; no-call rate of <5%)

• Concordance checked across call sets which were used for selection, and the new Broad and BC calls

Validated true singletons may not be singletons

• Because 20 members of the population were unable to be genotyped, it is possible that true novel singletons are actually present in one or more of the additional 20 individuals

• Basic pop-gen gives some ballpark estimates:– Probability that a validated singleton is in one of the

other 20 individuals:• 1.2% ( = 1 – ( 1 – θ )20 )

– All validated singletons are truly singletons• 33.5% ( = ( 1 – P[event above] )89 )

*θ = 1/1600

Per population PPV and sensitivity

Variant PPV/Sensitivity – unadjusted for depth

0 50 100 150 200 250 300 3500.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV


Individual in Pilot 3 (318 overlapping individuals)

Variant PPV/Sensitivity for CEU

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 700.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



CEU Individual in Pilot 3 (68 well-covered individuals)

Per-Locus FP Rate: 5.3%Per-Locus FN Rate: < 5%

*No FN observed

Variant PPV/Sensitivity for CEU – Counting Low Depth

0 10 20 30 40 50 60 70 800.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV


CEU Individual in Pilot 3 (69 individuals)

Variant PPV/Sensitivity for CHB

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 150.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



CHB Individual in Pilot 3 (13 well-covered individuals)

Per-Locus FP Rate: 9.4%Per-Locus FN Rate: < 5%*No Locus FN observed

Variant PPV/Sensitivity for CHB – Counting Low Depth

0 2 4 6 8 10 12 14 160.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV


CHB Individual in Pilot 3 (14 individuals)

Variant PPV/Sensitivity for CHD

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 290.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



CHD Individual in Pilot 3 (28 well-covered individuals)

Per-Locus FP Rate: 3.4%Per-Locus FN Rate: < 5%

* 3 FN in 555 TP observed

Variant PPV/Sensitivity for CHD – Counting Low Depth

0 5 10 15 20 25 300.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV


CHD Individual in Pilot 3 (28 individuals)

Variant PPV/Sensitivity for JPT

0 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99102

0.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



JPT Individual in Pilot 3 (104 well-covered individuals)

Per-Locus FP Rate: 2.2%Per-Locus FN Rate: < 5%* No Locus FN observed

Variant PPV/Sensitivity for JPT – Counting Low Depth

0 20 40 60 80 100 1200.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV


JPT Individual in Pilot 3 (104 individuals)

Variant PPV/Sensitivity for LWK

0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 700.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



LWK Individual in Pilot 3 (70 well-covered individuals)

Per-Locus FP Rate:1.3%Per-Locus FN Rate: < 5%


Variant PPV/Sensitivity for LWK – Counting Low Depth

0 10 20 30 40 50 60 70 800.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV


LWK Individual in Pilot 3 (70 individuals)

Variant PPV/Sensitivity for TSI

1 2 30.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



TSI Individual in Pilot 3 (3 well-covered individuals)

Per-Locus FP Rate: 16%Per-Locus FN Rate: < 5%


Contaminated individuals (not shown on plot) are counted in the FP and FN rates.

High Locus FP rate may indicate contamination by an individual outside of

the population.

Variant PPV/Sensitivity for TSI – Counting Low Depth

0.5 1 1.5 2 2.5 3 3.5 4 4.50.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV% Variant Sensitivity

TSI Individual in Pilot 3 (4 individuals)

Variant PPV/Sensitivity for YRI

0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 260.0%5.0%

10.0%15.0%20.0%25.0%30.0%35.0%40.0%45.0%50.0%55.0%60.0%65.0%70.0%75.0%80.0%85.0%90.0%95.0%

100.0%105.0%

% Variant PPV



YRI Individual in Pilot 3 (25 well-covered individuals)

Per-Locus FP Rate:20%Per-Locus FN Rate: < 5%


Contaminated individuals (not shown on plot) are counted in the FP and FN rates.

High Locus FP rate may indicate contamination by an individual outside of

the population.

Variant PPV/Sensitivity for YRI – Counting Low Depth

0 5 10 15 20 25 30 350.0%

5.0%

10.0%

15.0%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

60.0%

65.0%

70.0%

75.0%

80.0%

85.0%

90.0%

95.0%

100.0%

105.0%

% Variant PPV


YRI Individual in Pilot 3 (29 individuals)

1000g pilot 3 progress (in silico analysis and comparison to experimental validation) amit indap,...

Documents

total samples

samples snp

gatk slx gatk

analysis samples

snp calls

sequencing technology

union number of sites

coverage medians