Supplementary Figure 1. Quantile-quantile (Q-Q) plot of the log 10 p-value association results from logistic regression models for prostate cancer

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1 Supplementary Figure 1. Quantile-quantile (Q-Q) plot of the log 10 p-value association results from logistic regression models for prostate cancer risk in stage 1 (red) and after removing any SNPs within 500 kb of a previously established locus (green). 1

Supplementary Figure 2. Manhattan plot showing the statistical significance of the association for all genotyped SNPs in the stage 1 analysis.

2 Supplementary Figure 2. Manhattan plot showing the statistical significance of the association for all genotyped SNPs in the stage 1 analysis. SNPs are plotted on the x- axis according to their position on each chromosome against the significance of the association on the y-axis (shown as log 10 P-value). P-values are based on logistic regression models for prostate cancer risk. Red line denotes P=5x10-8 statistical significance. 2

3 (a) Combined Stage 1 (b) Combined Stage 1 Supplementary Figure 3. Regional association plots of the two suggestive loci associated with prostate cancer risk: (a) chromosome 16q22.2 (rs ) and (b) chromosome 6p22.3 (rs ). Shown are the log 10 association p-values for stage 1 (dots and lower pink diamond) and log 10 p-value for the combined stage 1-3 analysis (upper diamond) based on logistic regression models. 3

4 Supplementary Figure 4. Quantile-quantile (Q-Q) plot of the association results (-log 10 p-values) for Gleason score as a quantitative trait among prostate cancer cases in stage 1 (red). P-values were calculated from linear regression models. 4

5 Supplementary Figure 5. Plot of estimated admixture for individuals in stage 1. Individuals with < 80% European ancestry were excluded. 5

6 Supplementary Figure 6. Plot of top eigenvectors from stage 1 data based on principal components analysis. 6

7 Stage 1 4,600 cases/2,941 controls 1,531,807 SNPs Stage 2 iselect Replication 5 Studies 6,575 cases/6,392 controls 57,497 SNPs Rapid Replication 7 Studies 5,139 cases/5,591 controls 16 SNPs Meta Analysis Stage 3 In Silico Replication (prostate cancer) 4 Studies 1,204 cases/1,231 controls 8,337,739 SNPs Stage 3 De Novo Replication (Gleason score) 1 study 2,618 cases/1,728 controls 5 SNPs Meta Analysis Meta Analysis Supplementary Figure 7. Flowchart describing the multistage study design 7

8 Supplementary Table 1. Baseline characteristics of the subjects included in stage 1 and stage 2 Stage 1 Stage 2 Studies Pegasus ATBC CPSII CeRePP HPFS PLCO (4600 cases, 2941 controls) (979 cases, 942 controls) (2714 cases, 2440 controls) (1338 cases, 1340 controls) (885 cases, 893 controls) (659 cases, 777 controls) Mean age (±SD) Cases 68.8 ± ± ± ± ± ± 5.4 Controls 67.9 ± ± ± ± ± ± 5.7 Gleason score (58.5%) 196 (20.0%) 1389 (51.2%) 420 (31.4%) 418 (47.2%) 274 (41.6%) (31.1%) 80 (8.2%) 661 (24.4%) 668 (49.9%) 238 (26.9%) 267 (40.5%) (9.2%) 52 (5.3%) 271 (10.0%) 246 (18.4%) 64 (7.2%) 111 (16.8%) Unknown 55 (1.2%) 651 (66.5%) 356 (13.1%) (17.4%) 7 (1.1%) Disease aggressiveness Stage I/II and Gleason < (81.1%) 163 (16.6%) 1858 (68.5%) 844 (63.1%) 590 (66.7%) 503 (76.3%) Stage III/IV or Gleason (17.7%) 112 (11.4%) 458 (16.9%) 490 (36.6%) 119 (13.4%) 149 (22.6%) Unknown 56 (1.2%) 704 (71.9%) 398 (14.7%) 4 (0.3%) 176 (19.9%) 7 (1.1%) 8

9 Supplementary Table 2. Stage 1 association results for risk of prostate cancer with previously reported loci SNP Chr Position Discovered in Europeans Effect allele Other allele Info EAF No. cases/ No. controls OR Lower CI Upper CI P Reference PUBMED ID rs p A G ,599/2, Al Olama A rs q G A ,600/2, Al Olama A rs q A G ,600/2, Eeles RA rs q T C ,599/2, Al Olama A rs q A C ,600/2, Eeles RA rs p C T ,600/2, Kote Jarai Z rs p A G ,600/2, Gudmundsson J rs p C T ,600/2, Eeles RA rs p T C ,600/2, Al Olama A rs p T C ,600/2, Eeles RA rs q G A ,600/2, Eeles RA rs q G A ,600/2, Kote Jarai Z rs q G A ,600/2, Schumacher FR rs q T C ,600/2, Eeles RA rs p C T ,600/2, Eeles RA rs p A G ,600/2, Eeles RA rs q C A ,600/2, Eeles RA rs q A C ,600/2, Gudmundsson J rs q A G ,600/2, Kote Jarai Z rs q A C ,599/2, E 05 Kote Jarai Z rs q T C ,600/2, Al Olama A rs q A G ,600/2, Eeles RA rs q T C ,599/2, Eeles RA rs q C A ,600/2, Eeles RA rs q A C ,600/2, E 05 Eeles RA rs p A C ,600/2, Kote Jarai Z rs p A G ,600/2, Kote Jarai Z rs q T C ,600/2, Eeles RA

10 SNP Chr Position Effect allele Other allele Info EAF No. cases/ No. controls OR Lower CI Upper CI P Reference PUBMED ID rs p C G ,599/2, Al Olama A rs p G A ,600/2, Eeles RA rs p G T ,600/2, Kote Jarai Z rs p A G ,599/2, Al Olama A rs p T C ,599/2, Al Olama A rs q G A ,599/2, Al Olama A rs q G A ,600/2, Eeles RA rs q G A ,600/2, Eeles RA Eeles RA, , rs q G A ,600/2, Schumacher FR rs q T C ,600/2, E 08 Eeles RA rs p A G ,600/2, Al Olama A rs p G A ,600/2, Eeles RA rs q T C ,600/2, Eeles RA rs p C T ,600/2, Eeles RA rs p T C ,600/2, Eeles RA rs q G A ,599/2, Gudmundsson J rs q T C ,600/2, E 09 Schumacher FR rs q A C ,600/2, E 09 Gudmundsson J rs q C T ,600/2, E 05 Gudmundsson J rs q T G ,600/2, E 10 Yeager M, Thomas G, Eeles RA , , rs q C A ,600/2, E 09 Gudmundsson J, Yeager M , rs q G A ,600/2, E 10 Thomas G rs q A C ,600/2, E 10 Eeles RA, Schumacher FR , rs p G C ,599/2, Al Olama A rs q C T ,599/2, Al Olama A rs q T C ,600/2, Eeles RA rs q C T ,600/2, E 05 Thomas G, Eeles RA , 10

11 SNP Chr Position Effect allele Other allele Info EAF No. cases/ No. controls OR Lower CI Upper CI P Reference PUBMED ID rs q G A ,600/2, Eeles RA rs p G A ,600/2, Eeles RA rs q A G ,600/2, Gudmundsson J rs q G T ,600/2, E 05 Eeles RA rs q G A ,600/2, E 05 Thomas G rs q G A ,600/2, Eeles RA, Schumacher FR , rs q C T ,600/2, Eeles RA rs q A G ,600/2, Al Olama A rs q C A ,599/2, Al Olama A rs q C T ,600/2, Kote Jarai Z rs q A G ,600/2, E 05 Schumacher FR rs q G A ,600/2, Eeles RA rs q C T ,600/2, Eeles RA rs q G C ,599/2, Al Olama A rs q A G ,600/2, Al Olama A rs q C T ,600/2, Eeles RA rs q A G ,599/2, Al Olama A rs p C T ,600/2, Eeles RA Gudmundsson J, , rs q A G ,600/2, E 09 Thomas G rs q C T ,600/2, E 08 Eeles RA rs q A G ,600/2, Eeles RA rs q T G ,600/2, E 06 Gudmundsson J, Eeles RA, Schumacher FR , , rs q T C ,600/2, Eeles RA rs q T C ,600/2, Gudmundsson J rs q G A ,600/2, Amin Al Olama A rs q G A ,600/2, Eeles RA

12 SNP Chr Position Effect allele Other allele Info EAF No. cases/ No. controls OR Lower CI Upper CI P Reference PUBMED ID rs q C T ,600/2, Al Olama A rs q T C ,600/2, Eeles RA rs q T G ,600/2, Eeles RA rs q G A ,600/2, Al Olama A rs q A G ,600/2, Al Olama A rs q T G ,600/2, E 07 Eeles RA rs Xp T C ,625/2, E 06 Al Olama A rs Xp T C ,625/2, E 05 Eeles RA rs Xp G A ,625/2, Gudmundsson J rs Xp T C ,625/2, E 05 Eeles RA rs Xq T C ,625/2, Kote Jarai Z rs Xq T A ,625/2, Al Olama A rs Xq G A ,625/2, Al Olama A Discovered in non Europeans rs p G A ,599/2, Takata R rs p G A ,600/2, Takata R rs p T C ,600/2, E 05 Takata R rs p T C ,600/2, Takata R rs q C T ,600/2, Takata R rs p C T ,600/2, Takata R rs q C T ,600/2, Xu J rs q C T ,600/2, Takata R rs q G T ,600/2, E 10 Takata R rs q T C ,600/2, Xu J rs q C T ,600/2, E 05 Takata R rs q T G ,600/2, Takata R rs q C T ,600/2, E 08 Takata R rs q T C ,600/2, Xu J

13 Supplementary Table 3. Meta-analysis results of promising SNPs from stage 1 selected for rapid replication SNP Chr Position a Effect Other Stage EAF b No. cases / OR 95% CI P c P heterogeneity allele allele no. controls rs q ,056,440 T G Stage / ( ) 5.58E 07 Stage / ( ) 0.06 Replication FHCRC / ( ) 6.16E 03 Combined 8042/ ( ) 4.19E rs q ,374,513 T C Stage / ( ) 4.90E 06 Stage / ( ) 0.29 Replication FHCRC / ( ) 0.93 Replication AHS / ( ) 0.21 Combined 8953/ ( ) 7.16E rs q ,038,006 A G Stage / ( ) 1.07E 05 Stage / ( ) 0.08 Replication FHCRC / ( ) 0.67 Replication MEC / ( ) 0.12 Replication AHS / ( ) 0.22 Combined 9701/ ( ) 3.12E rs p25.3 9,418,510 A G Stage / ( ) 5.43E 06 Stage / ( ) 0.89 Replication FHCRC / ( ) 0.22 Replication AHS / ( ) 0.02 Combined 8929/ ( ) 9.86E rs q ,341,562 C A Stage / ( ) 7.86E 06 Stage / ( ) 0.72 Replication FHCRC / ( ) 0.32 Replication MEC / ( ) 0.98 Replication AHS / ( ) 0.70 Combined 9664/ ( ) rs Xp22.2 9,871,958 A G Stage / ( ) 6.82E 07 Stage / ( ) 0.10 Replication FHCRC / ( ) 0.50 Replication MEC / ( ) 0.76 Replication AHS / ( )

14 SNP Chr Position a Effect Other Stage EAF b No. cases / OR 95% CI P c P heterogeneity allele allele no. controls Combined 9460/ ( ) rs q ,338,261 C T Stage / ( ) 4.93E 06 Stage / ( ) 0.46 Replication FHCRC / ( ) 0.35 Replication MEC / ( ) 0.66 Replication AHS / ( ) 0.56 Combined 9664/ ( ) rs p ,040,199 T C Stage / ( ) 1.43E 05 Stage / ( ) 0.36 Replication FHCRC / ( ) 0.12 Replication MEC / ( ) 0.97 Replication AHS / ( ) 0.27 Combined 9537/ ( ) rs q ,217,064 G T Stage / ( ) 8.42E 06 Stage / ( ) 0.68 Replication FHCRC / ( ) 0.77 Replication MEC / ( ) 0.50 Replication AHS / ( ) 0.71 Combined 9579/ ( ) rs q ,372,633 A G Stage / ( ) 1.53E 05 Stage / ( ) 0.35 Replication FHCRC / ( ) 0.50 Replication AHS / ( ) 0.67 Combined 8960/ ( ) rs p23 9,022,312 T C Stage / ( ) 1.16E 05 Stage / ( ) 0.98 Replication FHCRC / ( ) 0.57 Replication MEC / ( ) 0.55 Replication AHS / ( ) 0.63 Combined 9669/ ( ) rs q ,704,705 T G Stage / ( ) 9.20E 06 Stage / ( )

15 SNP Chr Position a Effect Other Stage EAF b No. cases / OR 95% CI P c P heterogeneity allele allele no. controls Replication FHCRC / ( ) 0.30 Replication MEC / ( ) 0.84 Replication AHS / ( ) 0.24 Combined 9706/ ( ) rs p ,318,721 T G Stage / ( ) 1.43E 05 Stage / ( ) 0.83 Replication FHCRC / ( ) 0.56 Replication MEC / ( ) 0.08 Replication AHS / ( ) 0.12 Combined 9728/ ( ) rs q ,865,325 A G Stage / ( ) 9.00E 06 Stage / ( ) 0.14 Replication FHCRC / ( ) 0.42 Replication MEC / ( ) 0.01 Replication AHS / ( ) 0.24 Combined 9717/ ( ) E 05 rs Xq28 153,297,392 A G Stage / ( ) 2.11E 08 Stage / ( ) 0.25 Replication FHCRC / ( ) 0.15 Replication MEC / ( ) 0.16 Replication AHS / ( ) 0.60 Combined 9479/ ( ) E 07 rs Xq28 150,911,107 A G Stage / ( ) 1.28E 05 Stage / ( ) 0.37 Replication FHCRC / ( ) 0.81 Replication MEC / ( ) 0.37 Replication AHS / ( ) 0.06 Combined 9524/ ( ) a Position based on GRCh37/hg19 b EAF: Effect allele frequency c P value for the heterogeneity between studies 15

16 Supplementary Table 4. Association results for 13 previously reported loci that reach genome-wide significance (P < 5 x 10-8 ) in the combined meta-analysis SNP Chr Position Nearest gene(s) Effect allele a Other allele rs q ,840,252 SLC22A3 T G Stage / ( ) 7.16E Stage No. cases/ no. controls EAF b OR 95% CI P rs q ,517,573 LOC727677, CASC8 G A Stage / ( ) 5.03E 10 Stage / ( ) 3.77E 22 Stage / ( ) 6.64E 06 Combined 12377/ ( ) 1.48E 34 rs q12 36,101,586 HNF1B C A Stage / ( ) 2.64E 10 Stage / ( ) 7.35E 15 Stage / ( ) 2.37E 07 Combined 12356/ ( ) 8.03E 29 rs q ,106,874 BC039327, CASC17 G A Stage / ( ) 3.00E 06 Stage / ( ) 7.26E 13 Stage / ( ) 3.04E 05 Combined 12372/ ( ) 4.28E 21 rs q ,500,212 BIK T G Stage / ( ) 2.97E 07 Stage / ( ) 1.53E 08 Stage / ( ) Combined 12375/ ( ) 1.40E 16 rs q ,549,496 PARG,TIMM23,MSMB C T Stage / ( ) 5.60E 05 Stage / ( ) 9.92E 12 Stage / ( ) 0.07 Combined 12372/ ( ) 1.05E 15 rs q ,999,216 PRKCI G T Stage / ( ) 5.75E 07 Stage / ( ) 1.09E 07 Stage / ( ) 0.05 Combined 12377/ ( ) 8.22E 14 rs q ,985,583 LOC338694, MYEOV T C Stage / ( ) 1.74E 05 Stage / ( ) 3.79E 07 Stage / ( ) Combined 12365/ ( ) 2.37E 13

17 SNP Chr Position Nearest gene(s) Effect allele a Other allele Stage No. cases/ no. controls EAF b OR 95% CI P Stage / ( ) 1.77E 06 Stage / ( ) 0.13 Combined 12370/ ( ) 4.40E 12 rs p15 63,178,111 EHBP1 T C Stage / ( ) 6.81E 05 Stage / ( ) 1.41E 08 Stage / ( ) 0.40 Combined 12204/ ( ) 9.04E 12 rs p ,134,800 LINC00506, BC G A Stage / ( ) Stage / ( ) 1.19E 08 Stage / ( ) Combined 12338/ ( ) 1.40E 11 rs p ,282,414 TERT,hTERT A G Stage / ( ) Stage / ( ) 9.99E 08 Stage / ( ) 0.10 Combined 12297/ ( ) 3.08E 11 rs q ,666,202 TBX5 T G Stage / ( ) Stage / ( ) 6.18E 06 Stage / ( ) 0.03 Combined 12368/ ( ) 2.60E 10 rs q24 106,061,534 TET2 A C Stage / ( ) 1.06E 05 a Effect allele is the allele associated with the change in risk b Frequency of the effect allele Stage / ( ) Stage / ( ) 0.15 Combined 12337/ ( ) 4.03E 09 17

18 Supplementary Table 5. New suggestive loci associated with prostate risk (P<5x10-7 ) SNP Chr Position Nearest gene Risk allele a Other No. cases/ allele Stage RAF b no. controls OR 95% CI P rs q ,030,970 PKD1L3 G T Stage / ( ) Stage / ( ) 4.16E 04 Stage / ( ) 0.01 Combined 12377/ ( ) 9.67E 08 rs p ,330,293 CDKAL1 T G Stage / ( ) a Risk allele is the allele associated with an increased risk of prostate cancer b Frequency of the risk allele Stage / ( ) Stage / ( ) 2.40E 04 Combined 12366/ ( ) 2.13E 07 18

19 Supplementary Table 6. Association results from stage 1 for SNPs previously reported to be associated with aggressive prostate cancer SNP Chr Position Case Only Analysis of Gleason Score (continuous trait) Effect allele a / No. of Other allele EAF b Info c cases Beta SE P Case Control Analysis of Aggressive Prostate Cancer (Gleason 8 vs. controls) No. of cases/ No. of controls OR 95% CI P Reference rs q G/A / ( ) 0.87 Nam et al. (2011) rs q C/T / ( ) 0.12 FitzGerald et al. (2011) rs q A/G / ( ) 0.25 Nam et al. (2011) rs p T/C / ( ) 0.01 Xu et al. (2010) rs q G/A / ( ) 0.92 Al Olama et al. (2013) rs q G/A / ( ) 0.15 FitzGerald et al. (2011) a Effect allele is the allele associated with the change in beta or odds ratio. The results are orientated so that the effect allele corresponds to the risk allele from the published study. b EAF=Effect allele frequency among controls c Info=Information score from IMPUTE2 19

20 Supplementary Table 7. Case-control association results for prostate cancer risk stratified by disease aggressiveness for the three SNPs associated with Gleason score SNP Cytoband Position Novel loci Risk allele a / Other allele Stage Gleason 6 Gleason 8 No. of cases/ controls OR (95% CI) P No. of cases/ controls OR (95% CI) P P heterogeneity rs q ,610,989 C/A Stage / ( ) / ( ) 1.04x x10 4 Stage / ( ) / ( ) 5.18x x10 4 Stage / ( ) / ( ) Combined 6803/ ( ) / ( ) 8.85x x10 4 rs q ,252,736 C/T Stage / ( ) / ( ) Previously reported loci Stage / ( ) / ( ) Stage / ( ) / ( ) Combined 6798/ ( ) / ( ) rs q ,360,840 T/C Stage / ( ) 3.05x / ( ) x10 5 Stage / ( ) 4.16x / ( ) x10 5 Stage / ( ) / ( ) Combined 6802/ ( ) 3.51x / ( ) x10 10 a Risk allele is the allele associated with an increased risk of aggressive prostate cancer (Gleason 8) 20

21 Supplementary Table 8. Association results for prostate cancer risk stratified by disease aggressiveness from the African American Prostate Cancer (AAPC) Consortium for the three SNPs associated with Gleason score SNP Chr Position Info Risk allele/ other allele RAF Gleason 6 Gleason 8 No. cases/ No. controls OR (95% CI) P No. cases/ No. controls OR (95% CI) P rs q C/A / ( ) / ( ) 0.72 rs q C/T / ( ) / ( ) 0.92 rs q T/C / ( ) / ( )

22 Supplementary Table 9. HaploReg results for SNPs reaching genome-wide significance (P < 5 x10-8 ) for Gleason score among cases DNase enrichment analysis Cell type DNase ID Description Treatment Center Obs Exp Fold p GM12891 HSMM_emb GM12878 B lymphocyte, lymphoblastoid embryonic myoblast B lymphocyte, lymphoblastoid None Duke None Duke None AWG Query SNP: rs and variants with r 2 >= 0.8 SNP chr: pos (hg19) LD (r 2 ) LD (D') Ref Alt EUR Freq SiPhy cons Promoter histone marks Enhancer histone marks DNAse Proteins bound eqtl tissue Motifs changed rs chr 5: A G altered motifs RASA1 intronic rs chr 5: T A 0.23 NHLF, HMEC 7 cell types EWSR1 FLI1,PPAR rs chr 5: A C 0.26 Foxm1,SIX5,YY1 RASA1 intronic rs chr 5: T C 0.24 NHLF, HSMM, NHEK 28 cell types RASA1 intronic Query SNP: rs and variants with r 2 >= 0.8 rs chr 3: C T 0.01 NF Y NAALADL2 intronic Query SNP: rs and variants with r 2 >= 0.8 rs chr 19: C T 0.08 GM12878 GM12878,G M12891,HS Sin3Ak 20,Znf143 KLK3 intronic MM_emb rs chr 19: T C 0.08 H1 GM12892 NF AT,STAT KLK3 missense rs chr 19: T G 0.08 H1 HMEC 7 altered motifs KLK3 intronic rs chr 19: T G 0.08 H1 4 altered motifs KLK3 intronic rs chr 19: C T 0.08 BE2_C HIF1,HIF1::Arnt 1.4kb 3' of KLK3 GENCO DE genes RASA1 dbsnp funct annot intronic 22

Supplementary Figure 1: Attenuation of association signals after conditioning for the lead SNP. a) attenuation of association signal at the 9p22.

Supplementary Figure 1: Attenuation of association signals after conditioning for the lead SNP. a) attenuation of association signal at the 9p22.32 PCOS locus after conditioning for the lead SNP rs10993397;