Germline variation at 8q24 and prostate cancer risk in men of European ancestry

ARTICLE Ge mline a ia ion a 8q24 and p os a e cance isk in men o Eu opean ances y Ma co Ma ejcic1, Edwa d J. Saunde s e al. # Ch omosome 8q24 is a suscep ibili y locus o mul iple cance s, including p os a e cance . He e we combine gene ic da a ac oss he 8q24 suscep ibili y egion om 71,535 p os a e cance cases and 52,935 con ols o Eu opean ances y o define he o e all con ibu ion o ge mline a ia ion a 8q24 o p os a e cance isk. We iden i y 12 independen isk signals o p os a e cance (p< 4.28 × 10−15), including h ee isk a ian s ha ha e ye o be epo ed. F om a polygenic isk sco e (PRS) model, de i ed o assess he cumula i e e ec o isk a ian s a 8q24, men in he op 1% o he PRS ha e a 4- old (95%CI =3.62–4.40) g ea e isk compa ed o he popula ion a e age. These 12 a ian s accoun o ~25% o wha can be cu en ly explained o he amilial isk o p os a e cance by known gene ic isk ac o s. These findings highligh he o e whelming con ibu ion o ge mline a ia ion a 8q24 on p os a e cance isk which has implica ions o popula ion isk s a ifica ion. Ma co Ma ejcic, Edwa d J. Saunde s e al. # DOI: 10.1038/s41467-018-06863-1 OPEN Co espondence and eques s o ma e ials should be add essed o C.A.H. (email: Ch is op[email p o ec ed]). # A ull lis o au ho s and hei a filia ions appea s a he end o he pape . NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 1 1234567890():,; P os a e cance (PCa) is he mos common cance among men in he US, wi h 161,360 new cases and 26,730 ela ed dea hs es ima ed in 20171. Familial and epidemiological s udies ha e p o ided e idence o subs an ial he i abili y o PCa2, and ~170 common isk loci ha e been iden ified h ough genome-wide associa ion s udies (GWAS)3. The suscep ibili y egion on ch omosome 8q24 has been shown o be a majo con ibu o o PCa isk, wi h mul iple a ian s clus e ed in fi e linkage disequilib ium (LD) blocks spanning ~600 Mb ha a e independen ly associa ed wi h isk4. Many o hese associa ion signals epo ed a 8q24 ha e been eplica ed ac oss acial/e hnic popula ions5,6, poin ing o common sha ed unc ional a ian s wi hin 8q24. Howe e , a e ances y-specific a ian s ha e also been de ec ed, which con e la ge ela i e isks o PCa (odds a ios [ORs] >2.0) han common isk a ian s in he egion and signi y allelic he e ogenei y in he con ibu ion o ge mline a - ia ion a 8q24 o PCa isk ac oss popula ions7. In he cu en s udy, we pe o m a comp ehensi e in es iga- ion o gene ic a ia ion ac oss he 1.4 Mb cance suscep ibili y egion a 8q24 (127.6–129.0 Mb) in ela ion o PCa isk. We combine geno yped and impu ed da a om wo la ge GWAS conso ia (PRACTICAL/ELLIPSE OncoA ay and iCOGS) including >124,000 indi iduals o Eu opean ances y o sea ch o no el isk a ian s, as well as o de e mine he o e all con ibu- ion o gene ic a ia ion a 8q24 o PCa he i abili y. Ou findings unde sco e he sizable impac o gene ic a ia ion in he 8q24 egion in explaining in e -indi idual di e ences in PCa isk, wi h po en ial clinical u ili y o gene ic isk p edic ion. Resul s Ma ginal and condi ional associa ion analysis. Geno ype da a om he Illumina OncoA ay and iCOGS a ay and impu a ion o 1000 Genomes P ojec (1KGP) we e gene a ed among 71,535 PCa cases and 52,935 con ols o Eu opean ances y om 86 case- con ol s udies (see Me hods). O he 5600 geno yped and impu ed a ian s a 8q24 (127.6–129.0 Mb) wi h mino allele equency (MAF) > 0.1% e ained o analysis (see Me hods), 1268 (23%) we e associa ed wi h PCa isk a p< 5×10−8while 2772 (49%) we e ma ginally associa ed a p< 0.05. These 5600 ma ke s cap u e, a 2> 0.8, 90% and 97% o all a ian s a 8q24 (127.6–129.0 Mb) wi h MAF ≥1% and ≥5%, espec i ely (based on 1KGP Phase 3 EUR panel). In a o wa d and backwa d s epwise selec ion model on a ian s ma ginally associa ed wi h PCa isk (p< 0.05, n=2772; see Me hods), we iden ified 12 a ian s wi h condi ional p- alues om he Wald es be ween 2.93 × 10−137 and 4.28 × 10−15 (Table 1). None o he o he a ian s we e s a is ically significan a p<5×10 −8a e adjus - men o he 12 independen hi s (Fig. 1). The 8q24 egion is shown in Supplemen a y Fig. 1. O hese 12 s epwise signals, h ee had alleles wi h ex eme isk allele equencies (RAFs) ha con- eyed la ge e ec s ( s77541621, RAF =2%, OR =1.85, 95%CI = 1.76–1.94; s183373024, RAF =1%, OR =2.67, 95%CI = 2.43–2.93; s190257175, RAF =99%, OR =1.60, 95%CI = 1.42–1.80). The emaining a ian s had RAFs be ween 0.11 and 0.92 and condi ional ORs ha we e mo e modes and anged om 1.10 o 1.37 (Table 1). Fo 8 o he 12 a ian s, he allele ound o be posi i ely associa ed wi h PCa isk was he p e- dominan allele (i.e., >50% in equency). Fo wo a ian s, s78511380 and s190257175, he ma ginal associa ions we e no genome-wide significan and subs an ially weake han hose in he condi ional model. Fo s78511380, he ma ginal OR was sligh ly p o ec i e (OR =0.97; p=0.027), bu e e sed di ec ion and was highly s a is ically significan when condi ioning on he o he 11 a ian s (OR =1.19; p=3.5 × 10−18; Table 1). Haplo ype analysis. The haplo ype analysis showed an addi i e e ec o he 12 independen isk a ian s consis en wi h ha p edic ed in he single a ian es ; co-occu ence o he 8q24 isk alleles on he same haplo ype does no u he inc ease he isk o PCa (Supplemen a y Table 1). The unique haplo ype ca ying he e e ence allele o s190257175 (GCTTAT, 0.5% equency) is also he sole haplo ype associa ed wi h a educed isk o PCa, sugges ing ha ha ing he C allele con e s a p o ec i e e ec . The e e ence allele o s78511380 (A, 8% equency) occu s on a haplo ype in block 2 oge he wi h he isk alleles o s190257175, s72725879 and s5013678 (haplo ype GTTTAA, 8%) which obscu es he posi i e associa ion wi h he T allele o s78511380. Thus, he ma ginal p o ec i e e ec associa ed wi h he isk allele o s78511380 eflec s an inc eased isk associa ed wi h he occu ence on a isk haplo ype wi h o he isk alleles (Supplemen a y Table 1). Table 1 Ma ginal and condi ional es ima es o gene ic ma ke s a 8q24 independen ly associa ed wi h p os a e cance isk Va ian IDaPosi ionbAllelecRAFdLD clus e eCondi ional associa ion Ma ginal associa ion OR (95%CI)gp- alue OR (95%CI)hp- alue s1914295 127910317 T/C 0.68 block 1 1.10 (1.08–1.12) 7.30 × 10−25 1.09 (1.07–1.11) 3.07 × 10−21 s1487240 128021752 A/G 0.74 block 1 1.20 (1.17–1.22) 2.77 × 10−66 1.16 (1.14–1.18) 2.97 × 10−54 s77541621 128077146 A/G 0.02 block 2 1.85 (1.76–1.94) 2.93 × 10−137 1.83 (1.74–1.92) 4.33 × 10−137 s190257175 128103466 T/C 0.99 block 2 1.60 (1.42–1.80) 4.28 × 10−15 1.36 (1.22–1.53) 6.90 × 10−8 s72725879 128103969 T/C 0.18 block 2 1.31 (1.28–1.35) 1.26 × 10−83 1.17 (1.14–1.19) 3.96 × 10−48 s5013678 128103979 T/C 0.78 block 2 1.10 (1.08–1.13) 1.58 × 10−19 1.20 (1.17–1.22) 4.44 × 10−68 s183373024 128104117 G/A 0.01 block 2 2.67 (2.43–2.93) 4.89 × 10−95 3.20 (2.92–3.50) 6.60 × 10−138 s78511380 128114146 T/A 0.92 block 2 1.19 (1.14–1.23) 3.48 × 10−18 0.97 (0.94–1.00) 0.027 s17464492 128342866 A/G 0.72 block 3 1.16 (1.14–1.18) 3.01 × 10−52 1.17 (1.15–1.19) 9.05 × 10−61 s6983267 128413305 G/T 0.51 block 4 1.18 (1.16–1.20) 5.68 × 10−84 1.23 (1.21–1.25) 3.15 × 10−135 s7812894 128520479 A/T 0.11 block 5 1.37 (1.33–1.40) 1.55 × 10−122 1.45 (1.41–1.49) 1.20 × 10−181 s12549761 128540776 C/G 0.87 block 5 1.21 (1.18–1.24) 1.61 × 10−45 1.28 (1.25–1.31) 1.38 × 10−78 aVa ian s ha emained genome-wide significan ly associa ed wi h PCa isk (p<10 −8) in he final s epwise model bCh omosome posi ion based on human genome build 37 cRisk allele/ e e ence allele dRisk allele equency eLD clus e s we e in e ed based on ecombina ion ho spo s using Haplo iew 4.229 and defined as p e iously epo ed by Al Olama e al.4 Each a ian was inco po a ed in he s epwise model based on he s eng h o ma ginal associa ion om he me a-analysis o OncoA ay and iCOGS da a gPe -allele odds a io and 95% confidence in e al adjus ed o coun y, 7(OncoA ay)/8(iCOGS) p incipal componen s and all o he a ian s in he able hPe -allele odds a io and 95% confidence in e al adjus ed o coun y and 7(OncoA ay)/8(iCOGS) p incipal componen s ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 2NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions Co ela ion wi h known isk loci. The 12 isk a ian s spanned ac oss he fi e LD blocks p e iously epo ed o ha bo isk a ian s o PCa a 8q244, wi h block 2 ha bo ing six signals, blocks 1 and 5 wo signals each, and blocks 3 and 4 only one (Supplemen a y Fig. 2). Excep o a weak co ela ion be ween s72725879 and s78511380 in block 2 ( 2=0.28), he isk a - ian s we e unco ela ed wi h each o he ( 2≤0.09; Supplemen a y Da a 1), which co obo a es hei independen associa ion wi h PCa isk. Eigh o he a ian s ( s1487240, s77541621, s72725879, s5013678, s183373024, s17464492, s6983267, s1914295 s1487240 s77541621 s190257175 s72725879 s5013678 s183373024 s78511380 s17464492 s6983267 s7812894 s12549761 0 20 40 60 80 100 120 140 160 180 200 −Log10(p) −Log10(p) Ma ginal s1914295 s1487240 s77541621 s190257175 s72725879 s5013678 s183373024 s78511380 s17464492 s6983267 s7812894 s12549761 0 20 40 60 80 100 120 140 Condi ional s1914295 s1487240 s77541621 s190257175 s72725879 s5013678 s183373024 s78511380 s17464492 s6983267 s7812894 s12549761 LD 2 Hi s His one 128,000,000 128,200,000 128,400,000 DNaseI Conse ed Ch omHMM eQTL Bio ea u es PCAT1 POU5F1B CASC8 128,000,000 128,200,000 128,400,000 Genes FAM84B POU5F1B NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 ARTICLE NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 3 s7812894) ha e been p e iously epo ed ei he di ec ly (Sup- plemen a y Table 2) o a e co ela ed ( 2≥0.42) wi h known ma ke s o PCa isk om s udies in popula ions o Eu opean, A ican o Asian ances y (Supplemen a y Da a 1)4,7–10. The ma ginal es ima es o p e iously published PCa isk a ian s a 8q24 in he cu en s udy a e shown in Supplemen a y Table 2. The a ian s1914295 in block 1 is only weakly co ela ed wi h he p e iously epo ed isk a ian s s12543663 and s10086908 ( 2=0.17 and 0.14, espec i ely), while s7851380 is modes ly co ela ed wi h he p e iously epo ed isk a ian s1016343 ( 2=0.28). The emaining wo a ian s, s190257175 and s12549761, a e no co ela ed ( 2< 0.027) wi h any known PCa isk ma ke . Polygenic isk sco e and amilial ela i e isk. To es ima e he cumula i e e ec o ge mline a ia ion a 8q24 on PCa isk, a polygenic isk sco e (PRS) was calcula ed o he 12 independen isk alleles om he final model based on allele dosages weigh ed by he pe -allele condi ionally adjus ed ORs (see Me hods). Compa ed o he men a ‘a e age isk’(i.e., he 25 h–75 h PRS ange among con ols), men in he op 10% o he PRS dis ibu ion had a 1.93- old ela i e isk (95%CI =1.86–2.01) (Table 2), wi h he isk being 3.99- old highe (95%CI = 3.62–4.40) o men in he op 1%. Risk es ima es by PRS ca ego y we e no modified by amily his o y (FamHis -yes: OR =4.24, 95%CI =2.85–6.31; FamHis -no: OR =3.38, 95%CI = 2.88–3.97). To quan i y he impac o ge mline a ia ion a 8q24, we also es ima ed he p opo ion o amilial ela i e isk (FRR) and he i abili y o PCa con ibu ed by 8q24 and compa ed his o he p opo ions explained by all known PCa isk a ian s including 8q24 (see Me hods). The 175 es ablished PCa sus- cep ibili y loci iden ified o da e3,11 a e es ima ed o explain 37.08% (95%CI =32.89–42.49) o he FRR o PCa, while he 12 independen signals a 8q24 alone cap u e 9.42% (95%CI = 8.22–10.88), which is 25.4% o he o al FRR explained by known gene ic isk ac o s o PCa (Table 3). This is simila o he p opo ion o he i abili y explained by 8q24 a ian s (22.2%) compa ed o he o al explained he i abili y by he known isk a ian s (0.118). In compa ison, he nex highes con ibu ion o an indi idual suscep ibili y egion o he FRR o PCa is he TERT egion a ch omosome 5p15, whe e 5 independen signals con- ibu ed 2.63% (95%CI =2.34–3.00). No o he indi idual GWAS Fig. 1 LocusExplo e plo s o he 12 a ian s a 8q24 significan ly associa ed wi h PCa isk. ‘Ma ginal’and ‘Condi ional’Manha an plo panels show ma ginal and condi ional associa ion esul s, espec i ely. Va ian posi ions (x-axis) and −log 10 p- alues om he Wald es (y-axis) a e shown, wi h he ed line indica ing he h eshold o genome-wide significan associa ion wi h PCa isk (p≤5×10 −8) and blue peaks local es ima es o ecombina ion a es. The posi ion o he 12 independen a ian s is labeled in each plo . Clus e s o co ela ed a ian s o each independen signal a e dis inguished using di e en colo s and also depic ed on he ‘LD 2Hi s’ ack. S onge shading indica es g ea e co ela ion wi h he lead a ian , wi h a ian s no co ela ed a 2≥0.2 wi h any lead a ian uncolo ed. Pai wise co ela ions a e based on he Eu opean ances y (EUR) panel om he 1000 Genomes P ojec (1KGP) Phase 3. The ela i e posi ion o Re Seq genes and biological anno a ions a e shown in he ‘Genes’and ‘Bio ea u es’panels, espec i ely. Genes on he posi i e s and a e deno ed in g een and hose on he nega i e s and in pu ple. Anno a ions displayed a e: his one modifica ions in ENCODE ie 1 cell lines (His one ack), he posi ions o any a ian s ha we e eQTLs wi h p os a e umo exp ession in TCGA p os a e adenoca cinoma samples and he espec i e genes o which exp ession is al e ed (eQTL ack), ch oma in s a e ca ego iza ions in he P EC cell-line by Ch omHMM (Ch omHMM ack), he posi ion o conse ed elemen peaks (Conse ed ack) and he posi ion o DNaseI hype sensi i i y si e peaks in ENCODE p os a e cell-lines (DNaseI ack). The da a displayed in his plo may be explo ed in e ac i ely h ough he LocusExplo e applica ion (h p://www.oncogene ics.ic .ac.uk/8q24/) Table 2 Rela i e isk o PCa o polygenic isk sco e (PRS) g oups Risk ca ego y pe cen ileaNo. o indi iduals Risk es ima es o PRS g oups Con ols Cases OR (95% CI)bp- alue ≤1% 530 339 0.52 (0.45–0.59) 2.11 × 10−20 1%–10% 4771 3636 0.62 (0.59–0.65) 6.26 × 10−90 10%–25% 7936 7359 0.75 (0.72–0.78) 3.62 × 10−54 25%–75% 26,464 32,743 1.00 (Re ) 75%–90% 7940 13,431 1.37 (1.32–1.41) 6.55 × 10−77 90%–99% 4766 11,451 1.93 (1.86–2.01) 4.13 × 10−249 >99% 528 2576 3.99 (3.62–4.40) 5.64 × 10−172 No e: PRS we e calcula ed o a ian s om he final s epwise model wi h allele dosage om OncoA ay and iCOGS weigh ed by he pe -allele condi ionally adjus ed odds a ios om he me a-analysis aRisk ca ego y g oups we e based on he pe cen ile dis ibu ion o isk alleles in o e all con ols bEs ima ed e ec o each PRS g oup ela i e o he in e qua ile ange (25–75%) in OncoA ay and iCOGS da ase s sepa a ely, and hen me a-analyzed ac oss he wo s udies; odds a ios we e adjus ed o coun y and 7(OncoA ay)/8(iCOGS) p incipal componen s Table 3 P opo ion o amilial ela i e isk (FRR) and he i abili y (h g 2) o PCa explained by known isk a ian s Sou ce No. o a ian s P opo ion o FRR (95%CI) % o o al FRR h g 2(SE) % o o al h g 2 8q24a12 9.42 (8.22–10.88) 25.4 0.027 (0.011) 22.2 HOXB13b1 1.91 (1.20–2.85) 5.2 0.004 (0.005) 3.0 All o he a ian sb,c 162 25.77 (22.94–29.36) 69.5 0.092 (0.010) 74.9 To al 175 37.08 (32.89–42.49) 100 0.118 (0.012) 100 aCondi ional es ima es we e de i ed by fi ing a single model wi h all a ian s om OncoA ay da a bRisk es ima es and allele equencies o egions wi h a single a ian a e om a me a-analysis o OncoA ay, iCOGS and 6 addi ional GWAS3 cRisk a ian s included om fine-mapping o PCa suscep ibili y loci in Eu opean ances y popula ions11 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 4NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions locus has been es ablished as explaining >2% o he FRR, including he low equency, non-synonymous, mode a e pene- ance HOXB13 a ian ( s138213197) a ch omosome 17q21 ha is es ima ed o explain only 1.91% (95%CI =1.20–2.85) o he FRR11. JAM analysis. We explo ed ou da a wi h a second fine-mapping app oach, JAM (Join Analysis o Ma ginal summa y s a is ics)12, which uses GWAS summa y s a is ics o iden i y c edible se s o a ian s ha define he independen associa ion signals in sus- cep ibili y egions (see Me hods). The 95% c edible se o he JAM analysis confi med all o he independen signals om s epwise analysis excep s190257175, o which e idence o an associa ion was weak ( a ian -specific Bayes ac o (BF) =1.17). The e we e 50 o al a ian s included in he 95% c edible se , and 174 a e including a ian s in high LD ( 2> 0.9) wi h hose in he c edible se (Supplemen a y Da a 2). Discussion In his la ge s udy o ge mline gene ic a ia ion ac oss he 8q24 egion, we iden ified 12 independen associa ion signals among men o Eu opean ances y, wi h h ee o he isk a ian s ( s1914295, s190257175, and s12549761) being weakly co e- la ed ( 2≤0.17) wi h known PCa isk ma ke s. The combina ion o hese 12 independen signals a 8q24 cap u e app oxima ely one qua e o he o al PCa FRR explained by known gene ic isk ac o s, which is subs an ially g ea e han any o he known PCa isk locus. The 8q24 egion is he majo suscep ibili y egion o PCa; howe e , he unde lying biological mechanism(s) h ough which ge mline a ia ion in his egion influences PCa isk emains unce ain. Fo each o he 12 isk a ian s a 8q24, he 95% c edible se defined no ewo hy (i.e., pu a i e unc ional) a ian s based on summa y s a is ics while accoun ing o LD. To in o m biological unc ionali y, we o e laid epigene ic unc ional anno- a ion using publicly a ailable da ase s (see Me hods) wi h he loca ion o he 12 independen signals (and co esponding 174 a ian s wi hin hei 95% c edible se s; Supplemen a y Da a 3). O he 12 independen lead a ian s, 6 a e si ua ed wi hin pu a i e ansc ip ional enhance s in p os a e cell-lines; ei he h ough in e sec ion wi h H3K27AC ( s72725879, s5013678, s78511380, s6983267 and s7812894) o h ough a Ch omHMM enhance anno a ion ( s17464492, s6983267, s7812894). Eigh o he 12 s epwise hi s ( s77541621, s190257175, s5013678, s183373024, s78511380, s17464492, s6983267, s7812894) also in e sec ansc ip ion ac o binding si e peaks om mul i- ple ChIP-seq da ase s ep esen ing he AR, ERG, FOXA1, GABPA, GATA2, HOXB13, and NKX3.1 ansc ip ion ac o s, wi h all 8 in e sec ing a FOXA1 ma k and hal an AR binding si e. These a ian s may he e o e exe hei e ec h ough egula ion o enhance ac i i y and long- ange exp ession o genes impo - an o cance umo igenesis and/o p og ession13. The a ian s6983267 has also been shown o ac in an allele-specific manne o egula e p os a e enhance ac i i y and exp ession o he p o o- oncogene MYC in i o and in i o14,15. Howe e , despi e he close p oximi y o he MYC locus, no di ec associa ion has been de ec ed be ween 8q24 isk alleles and MYC exp ession in no mal and umo human p os a e issues16. The a e a ian wi h he la ges e ec on isk, s183373024, shows high e idence o unc ionali y based on o e lap wi h mul iple DNaseI and ansc ip ion ac o binding si e peaks ( o AR, FOXA1, HOXB13, and NKX3.1), which suppo s p e ious findings o an allele-dependen e ec o his a ian on he dis up ion o a FOXA1 binding mo i 17. Se en independen signals ( s1914295, s1487240, s77541621, s72725879, s5013678, s183373024, s78511380) and a ian s co ela ed a 2> 0.9 wi h hese signals (Supplemen a y Da a 2) a e loca ed wi hin o nea a numbe o p os a e cance –associa ed long noncoding RNAs (lncRNAs), including PRNCR1,PCAT1, and CCAT2, p e iously epo ed o be up egula ed in human PCa cells18 and issues19,20. Based on eQTL anno a ions in p os a e adenoca cinoma cells, he inde- penden signal s1914295 and h ee co ela ed a ian s ( 2> 0.9; Supplemen a y Da a 2) a e associa ed wi h o e exp ession o FAM84B, a gene p e iously associa ed wi h p og ession and poo p ognosis o PCa in animal s udies21. Va ian s co ela ed a 2> 0.9 wi h s7812894 (n=9; Supplemen al Table 4) a e eQTLs o POU5F1B, a gene o e exp essed in cance cell lines and cance issues22,23, al hough i s ole in PCa de elopmen is unknown. Whils we ha e success ully efined he 8q24 egion and iden ified a subse o a ian s wi h pu a i e biological unc ion wi hin ou c edible se , mul i-e hnic compa isons may help efine he asso- cia ion signals e en u he and p ecisely iden i y he unc ional alleles and biological mechanisms ha modi y PCa isk. Whe eas he indi idual associa ions o he 8q24 a ian s wi h PCa isk a e ela i ely modes (ORs < 2.0, excep o s183373024), hei cumula i e e ec s a e subs an ial, wi h isk being 4- old highe o men in he op 1% o he 8q24-only PRS. The con ibu ion o he o e all FRR o PCa is subs an ially g ea e o he 8q24 egion (9.42%) han o any o he known GWAS locus, including he mode a e pene ance non-synonymous a - ian in HOXB13 (1.91%). The abili y o hese ma ke s o explain ~25.4% o wha can be cu en ly explained by all known PCa isk a ian s is a clea indica ion o he impo an con ibu ion o ge mline a ia ion a 8q24 on PCa isk. Ou s udy was p e- dominan ly powe ed o analyze a ian s wi h MAF > 1% as he impu ed a ian s wi h MAF =0.1-1% we e mos likely o ail quali y con ol (QC); howe e , he high densi y o geno yped ma ke s and haplo ypes a 8q24 in he OncoA ay and iCOGS s udies p o ided a obus backbone o impu a ion and inc eased he chances o impu e lowe MAF a ian s wi h high impu a ion quali y sco e. Unde s anding o he biology o hese a ian s and he unde lying gene ic basis o PCa could p o ide new insigh s in o he iden ifica ion o eliable isk-p edic ion bioma ke s o PCa, as well as enable he de elopmen o e ec i e s a egies o a ge ed sc eening and p e en ion. Me hods S udy subjec s, geno yping, and quali y con ol. We combined geno ype da a om he PRACTICAL/ELLIPSE OncoA ay and iCOGS conso ia3,24, which included 143,699 men o Eu opean ances y om 86 case-con ol s udies la gely based in ei he he US o Eu ope. In each s udy, cases p ima ily included men wi h inciden PCa while con ols we e men wi hou a p io diagnosis o he disease. Bo h o he OncoA ay and iCOGS cus om a ays we e designed o p o ide high co e age o common alleles (mino allele equency [MAF] > 5%) ac oss 8q24 (127.6–129.0 Mb) based on he 1000 Genomes P ojec (1KGP) Phase 3 o OncoA ay, and he Eu opean ances y (EUR) panel om HapMap Phase 2 o iCOGS. A o al o 57,580 PCa cases and 37,927 con ols o Eu opean ances y we e geno yped wi h he Illumina OncoA ay, and 24,198 PCa cases and 23,994 con ols o Eu opean ances y we e geno yped wi h he Illumina iCOGS a ay. Fo bo h s udies, sample exclusion c i e ia included duplica e samples, fi s -deg ee ela i es, samples wi h a call a e <95% o wi h ex eme he e ozygosi y (p<10 −6), and samples wi h an es ima ed p opo ion o Eu opean ances y <0.83,24. In o al, geno ype da a o 53,449 PCa cases and 36,224 con ols om OncoA ay and 18,086 PCa cases and 16,711 con ols om iCOGS we e included in he analysis. Gene ic a ian s wi h call a es <0.95, de ia ion om Ha dy-Weinbe g equilib ium (p<10 −7in con ols), and geno ype disc epancy in >2% o duplica e samples we e excluded. O he final 498,417 geno yped a ian s on he OncoA ay and 201,598 on he iCOGS a ay ha passed QC, 1581 and 1737 wi hin he 8q24 egion, espec i ely, we e e ained o impu a ion. All s udies complied wi h all ele an e hical egula ions and we e app o ed by he ins i u ional e iew boa ds a each o he pa icipa ing ins i u ions. In o med consen was ob ained om all s udy pa icipan s. Addi ional de ails o each s udy a e p o ided in he Supplemen a y No e 1. Impu a ion analysis. Impu a ion o bo h OncoA ay and iCOGS geno ype da a was pe o med using SHAPEIT25 and IMPUTE 226 o he Oc obe 2014 (Phase 3) NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 ARTICLE NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 5 elease o he 1KGP e e ence panel. A o al o 10,136 a ian s om OncoA ay and 10,360 a ian s om iCOGS wi h MAF > 0.1% we e impu ed ac oss he isk egion a 8q24 (127.6-129.0 Mb). Va ian s wi h an impu a ion quali y sco e >0.8 we e e ained o a o al o 5600 o e lapping a ian s be ween he wo da ase s. S a is ical analysis. Uncondi ional logis ic eg ession was used o es ima e pe -allele odds a ios (ORs) and 95% confidence in e als (CIs) o he associa ion be ween gene ic a ian s (single nucleo ide polymo phisms and inse ion/ dele ion polymo phisms) and PCa isk adjus ing o coun y and p incipal componen s (7 o OncoA ay and 8 o iCOGS). Allele dosage e ec s we e es ed h ough a 1-deg ee o eedom wo- ailed Wald end es . The ma ginal isk es ima es o he 5600 a ian s a 8q24 ha passed QC we e combined by a fixed e ec me a-analysis wi h in e se a iance weigh ing using METAL27.A modified o wa d and backwa d s epwise model selec ion wi h inclusion and exclusion c i e ia o p≤5×10 −8was pe o med on a ian s ma ginally associa ed wi h PCa isk om he me a esul s (p< 0.05, n=2772). A each s ep, he e ec es ima es o he candida e a ian s om bo h s udies (OncoA ay and iCOGS) we e me a-analyzed and each a ian was inco po a ed in o he model based on he s eng h o associa ion. All emaining a ian s we e included one-a -a- ime in o he logis ic eg ession model condi ioning on hose al eady inco po a ed in he model. We applied a conse a i e h eshold o independen associa ions, wi h a ian s kep in he model i hei me a p- alue om he Wald es was genome- wide significan a p≤5×10 −8a e adjus men o he o he a ian s in he model. Co ela ions be ween a ian s in he final model and p e iously published PCa isk a ian s a 8q24 we e es ima ed using he 1KGP Phase 3 EUR panel (Supplemen a y Da a 1). Haplo ype analysis. Haplo ypes we e es ima ed in he Oncoa ay da a only using a ian s om he final s epwise model selec ion (n=12) and he EM algo i hm28 wi hin LD block egions in e ed based on ecombina ion ho spo s using Haplo iew 4.2 (B oad Ins i u e, Camb idge, MA, USA)29. Only haplo ypes wi h an es ima ed equency ≥0.5% we e es ed. Polygenic isk sco e and amilial ela i e isk. An 8q24-only polygenic isk sco e (PRS) was calcula ed o a ian s om he final model (n=12) wi h allele dosage om OncoA ay and iCOGS weigh ed by he pe -allele condi ionally adjus ed ORs om he me a-analysis. Ca ego iza ion o he PRS was based on he pe cen ile dis ibu ion in con ols, and he isk o each ca ego y was es ima ed ela i e o he in e qua ile ange (25–75%) in OncoA ay and iCOGS sepa a ely, and hen me a- analyzed ac oss he wo s udies. We es ima ed he con ibu ion o 8q24 a ian s o he amilial (fi s -deg ee) ela i e isk (FRR) o PCa (FRR =2.5)30 unde a mul- iplica i e model, and compa ed his o he FRR explained by all known PCa isk a ian s including 8q24 (Supplemen a y Da a 4). We also es ima ed he i abili y o PCa using he LMM app oach as implemen ed in GCTA31. Fo egions which ha e been fine-mapped using he OncoA ay me a-analysis da a, we used he upda ed ep esen a i e lead a ian s, o he wise he o iginally epo ed a ian was included p o ided ha i had eplica ed a genome-wide significance in he me a-analysis; his iden ified a o al o 175 independen ly associa ed PCa a ian s o he FRR and he i abili y calcula ions3,11. Fo hese analyses, we used condi ional es ima es om fi ing a single model wi h all a ian s in he OncoA ay da ase o egions wi h mul iple a ian s and he o e all ma ginal me a-analysis esul s om Schumache e al.3 o egions wi h a single a ian . To co ec o po en ial bias in e ec es ima ion o newly disco e ed a ian s, we implemen ed a Bayesian e sion o he weigh ed co ec ion32, which inco po a es he unce ain y in he e ec es ima e in o he final es ima es o he bias-co ec ed ORs, 95%CIs and he co esponding calcula ions o pe cen FRR explained. JAM analysis. To confi m he s epwise esul s and iden i y candida e a ian s o po en ial unc ional ollow-up, we used a second fine-mapping app oach, JAM (Join Analysis o Ma ginal summa y s a is ics)12. JAM is a mul i a ia e Bayesian a iable selec ion amewo k ha uses GWAS summa y s a is ics o iden i y he mos likely numbe o independen associa ions wi hin a locus and define c edible se s o a ian s d i ing hose associa ions. JAM was applied o summa y s a is ics om he me a-analysis esul s using LD es ima ed om impu ed indi idual le el da a om 20,000 cases and 20,000 con ols andomly selec ed om he OncoA ay sub-s udy. LD p uning was pe o med using P io i y P une (h p://p io i yp une . sou ce o ge.ne /) on he 2772 ma ginally associa ed a ian s a 2=0.9, esul ing in 825 ag a ian s analyzed in ou independen JAM uns wi h a ying s a ing seeds. C edible se s we e de e mined as he ag a ian s ha we e selec ed in he op models ha summed o a specific cumula i e pos e io p obabili y in all ou o he independen JAM uns, plus hei designa ed high LD p oxy a ian s om he p uning s ep. Func ional anno a ion. Va ian s in he 95% c edible se (n=50) plus a ian s co ela ed a 2> 0.9 wi h hose in he c edible se (n=174) we e anno a ed o pu a i e e idence o biological unc ionali y using publicly a ailable da ase s as desc ibed by Dadae e al.11. B iefly, a ian s we e anno a ed o p oximi y o gene (GENCODE 19), miRNA ansc ip s (miRBase elease 20), e olu iona y cons ain (acco ding o GERP++, SiPhy and Phas Cons algo i hms), likelihood o pa hogenici y (CADD 1.3) and o e lap wi h p ospec i e egula o y elemen s in p os a e-specific da ase s (DNaseI hype sensi i i y si es, H3K27Ac, H3K27me3 and H3K4me3 his one modifica ions, and o AR, CTCF, ERG, FOXA1, GABPA, GATA2, HOXB13, and NKX3.1 ansc ip ion ac o binding si es) in a mix u e o LNCaP, PC-3, P EC, RWPE1, and VCaP cell lines and human p os a e umo issues downloaded om he Cis ome Da a B owse (h p://cis ome.o g/db/). The ch oma in s a e in which each a ian esides was assessed using Ch omHMM anno a ions om wo p os a e cell lines (P EC and PC3). Cis-gene egula ion was e alua ed using 359 p os a e adenoma cases om The Cance Genome A las (TCGA PRAD; h ps://gdc-po al.nci.nih.go ) ha passed QC11. The eQTL analysis was pe o med using Fas QTL wi h 1000 pe mu a ions o each gene wi hin a 1Mb window. We hen used he me hod by Nica e al.33 ha in eg a es eQTLs and GWAS esul s in o de o e eal he subse o associa ion signals ha a e due o cis eQTLs. Fo each significan eQTL, we added he candida e a ian o he linea eg ession model o assess i he inclusion be e explains he change in exp ession o he gene. We e ie ed he p- alue o he model, assigning p- alue o 1 i he eQTL and a ian a e he same. Then we anked he p- alues in descending o de o each eQTL, and finally calcula ed he colocaliza ion sco e o each pai o eQTL and a ian s. In gene al, i an eQTL and candida e a ian ep esen he same signal, his will be eflec ed by he a ian ha ing a high p- alue, a low ank and consequen ly a high colocaliza ion sco e. Da a a ailabili y The au ho s decla e ha da a suppo ing he findings o his s udy a e a ailable wi hin he pape [and in he supplemen a y in o ma ion files]. Howe e , some o he da a used o gene a e he esul s o his s udy a e a ailable om he fi s au ho and he PRAC- TICAL Conso ium upon eques . Recei ed: 7 Feb ua y 2018 Accep ed: 1 Oc obe 2018 Re e ences 1. Siegel, R. L., Mille , K. D. & Jemal, A. Cance s a is ics, 2017. CA Cance J. Clin. 67,7–30 (2017). 2. Hjelmbo g, J. B. e al. The he i abili y o p os a e cance in he No dic Twin S udy o Cance . Cance Epidemiol. P e . Bioma k. 23, 2303–2310 (2014). 3. Schumache , F. R. e al. Associa ion analyses o mo e han 140,000 men iden i y 63 new p os a e cance suscep ibili y loci. Na . Gene .50, 928–936 (2018). 4. Al Olama, A. A. e al. Mul iple loci on 8q24 associa ed wi h p os a e cance suscep ibili y. Na . Gene . 41, 1058–1060 (2009). 5. Haiman, C. A. e al. Mul iple egions wi hin 8q24 independen ly a ec isk o p os a e cance . Na . Gene . 39, 638–644 (2007). 6. Han, Y. e al. Gene alizabili y o es ablished p os a e cance isk a ian s in men o A ican ances y. In . J. Cance 136, 1210–1217 (2015). 7. 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PLoS Gene . 5, e1000597 (2009). 14. Pome an z, M. M. e al. The 8q24 cance isk a ian s6983267 shows long- ange in e ac ion wi h MYC in colo ec al cance . Na . Gene . 41, 882–884 (2009). 15. Wasse man, N. F., Aneas, I. & Nob ega, M. A. An 8q24 gene dese a ian associa ed wi h p os a e cance isk con e s di e en ial in i o ac i i y o a MYC enhance . Genome Res. 20, 1191–1197 (2010). 16. Pome an z, M. M. e al. E alua ion o he 8q24 p os a e cance isk locus and MYC exp ession. Cance Res. 69, 5568–5574 (2009). 17. Hazele , D. J., Coe zee, S. G. & Coe zee, G. A. A a e a ian , which des oys a FoxA1 si e a 8q24, is associa ed wi h p os a e cance isk. Cell Cycle Geo ge . Tex. 12, 379–380 (2013). ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 6NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 18. Chung, S. e al. Associa ion o a no el long non-coding RNA in 8q24 wi h p os a e cance suscep ibili y. Cance Sci. 102, 245–252 (2011). 19. P ensne , J. R. e al. T ansc ip ome sequencing ac oss a p os a e cance coho iden ifies PCAT-1, an unanno a ed lincRNA implica ed in disease p og ession. Na . Bio echnol. 29, 742–749 (2011). 20. Zheng, J. e al. The up- egula ion o long non-coding RNA CCAT2 indica es a poo p ognosis o p os a e cance and p omo es me as asis by a ec ing epi helial-mesenchymal ansi ion. Biochem. Biophys. Res. Commun. 480, 508–514 (2016). 21. Wong, N. e al. Up egula ion o FAM84B du ing p os a e cance p og ession. Onco a ge 8, 19218–19235 (2017). 22. Suo, G. e al. Oc 4 pseudogenes a e ansc ibed in cance s. Biochem. Biophys. Res. Commun. 337, 1047–1051 (2005). 23. Hayashi, H. e al. The OCT4 pseudogene POU5F1B is amplified and p omo es an agg essi e pheno ype in gas ic cance . Oncogene 34, 199–208 (2015). 24. Eeles, R. A. e al. Iden ifica ion o 23 new p os a e cance suscep ibili y loci using he iCOGS cus om geno yping a ay. Na . Gene . 45, 385–391 (2013). 391e1–2. 25. 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GCTA: a ool o genome-wide complex ai analysis. Am. J. Hum. Gene . 88,76–82 (2011). 32. Zhong, H. & P en ice, R. L. Bias- educed es ima o s and confidence in e als o odds a ios in genome-wide associa ion s udies. Bios a . Ox . Engl. 9, 621–634 (2008). 33. Nica, A. C. e al. Candida e causal egula o y e ec s by in eg a ion o exp ession QTLs wi h complex ai gene ic associa ions. PLoS Gene . 6, e1000895 (2010). Acknowledgemen s Geno yping o he OncoA ay was unded by he US Na ional Ins i u es o Heal h (NIH) [U19 CA 148537 o ELucida ing Loci In ol ed in P os a e Cance SuscEp ibili y (ELLIPSE) p ojec and X01HG007492 o he Cen e o Inhe i ed Disease Resea ch (CIDR) unde con ac numbe HHSN268201200008I]. Addi ional analy ic suppo was p o ided by NIH NCI U01 CA188392 (PI: Schumache ). The PRACTICAL conso ium (h p://p ac ical.ic .ac.uk/) was suppo ed by Cance Resea ch UK G an s C5047/A7357, C1287/A10118, C1287/A16563, C5047/A3354, C5047/A10692, C16913/A6135, Eu - opean Commission's Se en h F amewo k P og amme g an ag eemen n° 223175 (HEALTH-F2-2009-223175), and The Na ional Ins i u e o Heal h (NIH) Cance Pos - Cance GWAS ini ia i e g an : No. 1 U19 CA 148537-01 ( he GAME-ON ini ia i e). We wish o hank all GWAS s udy g oups con ibu ing o he da a se om which his s udy was conduc ed: OncoA ay; iCOGS; The PRACTICAL (P os a e Cance Associa ion G oup o In es iga e Cance -Associa ed Al e a ions in he Genome) Conso ium; and The GAME-ON/ELLIPSE Conso ium. De ailed acknowledgemen s and unding in o - ma ion o all GWAS s udy g oups and om all he indi idual s udies in ol ed in he PRACTICAL Conso ium a e included in Supplemen a y No e 1. We would also like o hank he ollowing o unding suppo : The Ins i u e o Cance Resea ch and The E e yman Campaign, The P os a e Cance Resea ch Founda ion, P os a e Resea ch Campaign UK (now P os a e Ac ion), The O chid Cance Appeal, The Na ional Cance Resea ch Ne wo k UK, The Na ional Cance Resea ch Ins i u e (NCRI) UK. We a e g a e ul o suppo o NIHR unding o he NIHR Biomedical Resea ch Cen e a The Ins i u e o Cance Resea ch and The Royal Ma sden NHS Founda ion T us . Au ho con ibu ions M.M. and E.J.S. con ibu ed equally o his wo k. R.A.E., Z.K.-J., D.V.C., and C.A.H. join ly supe ised his wo k. T.D. con ibu ed wi h JAM analysis. M.N.B. con ibu ed wi h FRR analysis. K.W. con ibu ed wi h o wa d and backwa d s epwise selec ion. X.S. con ibu ed wi h co e age analysis. A.A.A.O., F.R.S., S.A.I., K.G., S.B., S.I.B., D.A., S.K., K.M., V.L.S., S.M.G., C.M.T., J.B., J.C., H.G., N.P., J.S., A.W., C.W., L.Mu., P.K., G.C.-T., K.D.S., L.Ma., E.M.G., S.S.S., D.E.N., F.C.H., J.L.D., R.C.T., R.J.H., B.R., Y.-J.L., G.G.G., A.S.K., A.V., J.T.B., M.K., K.L.P., J.Y.P., J.L.S., C.C., B.G.N., H.B., C.M., J.K., M.R.T., S.L.N., K.D.R., A.R., L.F.N., D.L., R.K., N.U., F.C., P.A.T., M.G.D., M.J.R., F.M., K.-T.K., L.A.C.-A., H.P., S.N.T., D.J.S., The PRACTICAL Conso ium, F.W., S.J.C., and D.F.E. we e in ol ed in sample and da a collec ion. Addi ional in o ma ion Supplemen a y In o ma ion accompanies his pape a h ps://doi.o g/10.1038/s41467- 018-06863-1. Compe ing in e es s: The au ho s decla e no compe ing in e es s. Rep in s and pe mission in o ma ion is a ailable online a h p://npg.na u e.com/ ep in sandpe missions/ Publishe 's no e: Sp inge Na u e emains neu al wi h ega d o ju isdic ional claims in published maps and ins i u ional a filia ions. Open Access This a icle is licensed unde a C ea i e Commons A ibu ion 4.0 In e na ional License, which pe mi s use, sha ing, adap a ion, dis ibu ion and ep oduc ion in any medium o o ma , as long as you gi e app op ia e c edi o he o iginal au ho (s) and he sou ce, p o ide a link o he C ea i e Commons license, and indica e i changes we e made. The images o o he hi d pa y ma e ial in his a icle a e included in he a icle’s C ea i e Commons license, unless indica ed o he wise in a c edi line o he ma e ial. I ma e ial is no included in he a icle’s C ea i e Commons license and you in ended use is no pe mi ed by s a u o y egula ion o exceeds he pe mi ed use, you will need o ob ain pe mission di ec ly om he copy igh holde . To iew a copy o his license, isi h p://c ea i ecommons.o g/ licenses/by/4.0/. © The Au ho (s) 2018 Ma co Ma ejcic 1 , Edwa d J. Saunde s 2 , Tokhi Dadae 2 , Ma k N. B ook 2 , Kan Wang 1 , Xin Sheng 1 , Ali Amin Al Olama 3,4 , F ed ick R. Schumache 5,6 , Sue A. Ingles 1 , Ko eela Go indasami 2 , Sa a Benlloch 2,3 , Sonja I. Be nd 7 , Deme ius Albanes 7 , S ella Kou os 7 , Kenne h Mui 8,9 , Vic o ia L. S e ens 10 , Susan M. Gaps u 10 , Ca he ine M. Tangen 11 , Jyo sna Ba a 12,13 , Judi h Clemen s 12,13 , Hen ik G onbe g 14 , No a Pashayan 15,16 , Johanna Schleu ke 17,18,19 , Alicja Wolk 20 , Ca ha ine Wes 21 , Lo elei Mucci 22 , Pe e K a 23 , Gé aldine Cancel-Tassin 24,25 , Ka ina D. So ensen 26,27 , Lo ise Maehle 28 , Eli M. G indedal 28 , Sa a S. S om 29 , Da id E. Neal 30,31 , F eddie C. Hamdy 32 , Jenny L. Dono an 33 , Ru h C. T a is 34 , Robe J. Hamil on 35 , Ba y Rosens ein 36,37 , Yong-Jie Lu 38 , G aham G. Giles 39,40 , Adam S. Kibel 41 , Ana Vega 42 , Jeane e T. Bensen 43 , Manolis Koge inas 44,45,46,47 , Ka h yn L. Penney 48 , Jong Y. Pa k 49 , Jane L. S an o d 50,51 , Ceza y Cybulski 52 , Bø ge G. No des gaa d 53,54 , He mann B enne 55,56,57 , Ch is iane Maie 58 , Je i Kim 59 , NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 ARTICLE NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 7 Manuel R. Teixei a 60,61 , Susan L. Neuhausen 62 , Kim De Ruyck 63 , Azad Razack 64 , Lisa F. Newcomb 50,65 , Da o Lessel 66 , Radka Kane a 67 , Nawaid Usmani 68,69 , F ank Claessens 70 , Paul A. Townsend 71 , Manuela G. Dominguez 72,73 , Monique J. Roobol 74 , Flo ence Menegaux 75 , Kay-Tee Khaw 76 , Lisa A. Cannon-Alb igh 77,78 , Ha de Pandha 79 , S ephen N. Thibodeau 80 , Daniel J. Schaid 81 , The PRACTICAL Conso ium, F ed ik Wiklund 14 , S ephen J. Chanock 7 , Douglas F. Eas on 3,15 , Rosalind A. Eeles 2,82 , Zsofia Ko e-Ja ai 2 , Da id V. Con i 1 & Ch is ophe A. Haiman 1 1 Depa men o P e en i e Medicine, Keck School o Medicine, Uni e si y o Sou he n Cali o nia/No is Comp ehensi e Cance Cen e , Los Angeles, CA 90033, USA. 2 The Ins i u e o Cance Resea ch, London SW7 3RP, UK. 3 Cen e o Cance Gene ic Epidemiology, Depa men o Public Heal h and P ima y Ca e, S angeways Resea ch Labo a o y, Uni e si y o Camb idge, Camb idge CB1 8RN, UK. 4 Depa men o Clinical Neu osciences, Uni e si y o Camb idge, Camb idge CB2 0QQ, UK. 5 Depa men o Popula ion and Quan i a i e Heal h Sciences, Case Wes e n Rese e Uni e si y, Cle eland, OH 44106-7219, USA. 6 Seidman Cance Cen e , Uni e si y Hospi als, Cle eland, OH 44106, USA. 7 Di ision o Cance Epidemiology and Gene ics, Na ional Cance Ins i u e, NIH, Be hesda, MD 20892, USA. 8 Ins i u e o Popula ion Heal h, Uni e si y o Manches e , Manches e M13 9PL, UK. 9 Wa wick Medical School, Uni e si y o Wa wick, Co en y CV4 7AL, UK. 10 Epidemiology Resea ch P og am, Ame ican Cance Socie y, 250 Williams S ee , A lan a, GA 30303, USA. 11 SWOG S a is ical Cen e , F ed Hu chinson Cance Resea ch Cen e , Sea le, WA 98109, USA. 12 Aus alian P os a e Cance Resea ch Cen e-Qld, Ins i u e o Heal h and Biomedical Inno a ion and School o Biomedical Science, Queensland Uni e si y o Technology, B isbane, QLD 4059, Aus alia. 13 T ansla ional Resea ch Ins i u e, B isbane, QLD 4102, Aus alia. 14 Depa men o Medical Epidemiology and Bios a is ics, Ka olinska Ins i u e, SE-171 77 S ockholm, Sweden. 15 Cen e o Cance Gene ic Epidemiology, Depa men o Oncology, S angeways Resea ch Labo a o y, Uni e si y o Camb idge, Camb idge CB1 8RN, UK. 16 Depa men o Applied Heal h Resea ch, Uni e si y College London, London WC1E 7HB, UK. 17 Depa men o Medical Biochemis y and Gene ics, Ins i u e o Biomedicine, Uni e si y o Tu ku, FI-20014 Tu ku, Finland. 18 Tyks Mic obiology and Gene ics, Depa men o Medical Gene ics, Tu ku Uni e si y Hospi al, 20521 Tu ku, Finland. 19 BioMediTech, Uni e si y o Tampe e, 33520 Tampe e, Finland. 20 Di ision o Nu i ional Epidemiology, Ins i u e o En i onmen al Medicine, Ka olinska Ins i u e , SE-171 77 S ockholm, Sweden. 21 Di ision o Cance Sciences, Manches e Academic Heal h Science Cen e, Radio he apy Rela ed Resea ch, Manches e NIHR Biomedical Resea ch Cen e, The Ch is ie Hospi al NHS Founda ion T us , Uni e si y o Manches e , Manches e M13 9PL, UK. 22 Depa men o Epidemiology, Ha a d School o Public Heal h, Bos on, MA 02115, USA. 23 P og am in Gene ic Epidemiology and S a is ical Gene ics, Depa men o Epidemiology, Ha a d T.H. Chan School o Public Heal h, Bos on, MA 02115, USA. 24 GRC N°5 ONCOTYPE-URO, UPMC Uni Pa is 06, Tenon Hospi al, F-75020 Pa is, F ance. 25 CeRePP, Tenon Hospi al, F-75020 Pa is, F ance. 26 Depa men o Molecula Medicine, Aa hus Uni e si y Hospi al, 8200 Aa hus N, Denma k. 27 Depa men o Clinical Medicine, Aa hus Uni e si y, 8200 Aa hus N, Denma k. 28 Depa men o Medical Gene ics, Oslo Uni e si y Hospi al, 0424 Oslo, No way. 29 Depa men o Epidemiology, The Uni e si y o Texas MD Ande son Cance Cen e , Hous on, TX 77030, USA. 30 Depa men o Oncology, Addenb ooke’s Hospi al, Uni e si y o Camb idge, Camb idge CB2 0QQ, UK. 31 Cance Resea ch UK Camb idge Resea ch Ins i u e, Li Ka Shing Cen e, Camb idge CB2 0RE, UK. 32 Nu field Depa men o Su gical Sciences, Uni e si y o Ox o d, Ox o d OX1 2JD, UK. 33 School o Social and Communi y Medicine, Uni e si y o B is ol, Canynge Hall, 39 Wha ley Road, B is ol BS8 2PS, UK. 34 Cance Epidemiology, Nu field Depa men o Popula ion Heal h, Uni e si y o Ox o d, Ox o d OX3 7LF, UK. 35 Depa men o Su gical Oncology, P incess Ma ga e Cance Cen e, To on o, ON M5G 2M9, Canada. 36 Depa men o Radia ion Oncology, Icahn School o Medicine a Moun Sinai, New Yo k, NY 10029, USA. 37 Depa men o Gene ics and Genomic Sciences, Icahn School o Medicine a Moun Sinai, New Yo k, NY 10029-5674, USA. 38 Cen e o Molecula Oncology, John Vane Science Cen e, Ba s Cance Ins i u e, Queen Ma y Uni e si y o London, London EC1M 6BQ, UK. 39 Cance Epidemiology & In elligence Di ision, Cance Council Vic o ia, Melbou ne, VIC 3004, Aus alia. 40 Cen e o Epidemiology and Bios a is ics, Melbou ne School o Popula ion and Global Heal h, The Uni e si y o Melbou ne, Melbou ne, VIC 3010, Aus alia. 41 Di ision o U ologic Su ge y, B igham and Womens Hospi al, Bos on, MA 02115, USA. 42 Fundación Pública Galega de Medicina Xenómica-SERGAS, G upo de Medicina Xenómica, CIBERER, IDIS, 15706 San iago de Compos ela, Spain. 43 Depa men o Epidemiology, Gillings School o Global Public Heal h, Uni e si y o No h Ca olina, Columbia, SC 29208, USA. 44 Cen e o Resea ch in En i onmen al Epidemiology (CREAL), Ba celona Ins i u e o Global Heal h (ISGlobal), 08003 Ba celona, Spain. 45 CIBER Epidemiología y Salud Pública (CIBERESP), 28029 Mad id, Spain. 46 IMIM (Hospi al del Ma Resea ch Ins i u e), 08003 Ba celona, Spain. 47 Uni e si a Pompeu Fab a (UPF), 08002 Ba celona, Spain. 48 Channing Di ision o Ne wo k Medicine, Depa men o Medicine, B igham and Women’s Hospi al/ Ha a d Medical School, Bos on, MA 02184, USA. 49 Depa men o Cance Epidemiology, Mo fi Cance Cen e , Tampa, FL 33612, USA. 50 Di ision o Public Heal h Sciences, F ed Hu chinson Cance Resea ch Cen e , Sea le, WA 98109-1024, USA. 51 Depa men o Epidemiology, School o Public Heal h, Uni e si y o Washing on, Sea le, WA 98195, USA. 52 In e na ional He edi a y Cance Cen e , Depa men o Gene ics and Pa hology, Pome anian Medical Uni e si y, 70-115 Szczecin, Poland. 53 Facul y o Heal h and Medical Sciences, Uni e si y o Copenhagen, 2200 Copenhagen, Denma k. 54 Depa men o Clinical Biochemis y, He le and Gen o e Hospi al, Copenhagen Uni e si y Hospi al, He le , 2200 Copenhagen, Denma k. 55 Di ision o Clinical Epidemiology and Aging Resea ch, Ge man Cance Resea ch Cen e (DKFZ), D-69120 Heidelbe g, Ge many. 56 Ge man Cance Conso ium (DKTK), Ge man Cance Resea ch Cen e (DKFZ), D-69120 Heidelbe g, Ge many. 57 Di ision o P e en i e Oncology, Ge man Cance Resea ch Cen e (DKFZ) and Na ional Cen e o Tumo Diseases (NCT), 69120 Heidelbe g, Ge many. 58 Ins i u e o Human Gene ics, Uni e si y Hospi al Ulm, 89075 Ulm, Ge many. 59 Depa men o Geni ou ina y Medical Oncology, The Uni e si y o Texas MD Ande son Cance Cen e , Hous on, TX 77030, USA. 60 Depa men o Gene ics, Po uguese Oncology Ins i u e o Po o, 4200-072 Po o, Po ugal. 61 Biomedical Sciences Ins i u e (ICBAS), Uni e si y o Po o, 4050-313 Po o, Po ugal. 62 Depa men o Popula ion Sciences, Beckman Resea ch Ins i u e o he Ci y o Hope, Dua e, CA 91010, USA. 63 Ghen Uni e si y, Facul y o Medicine and Heal h Sciences, Basic Medical Sciences, B-9000 Gen , Belgium. 64 Depa men o Su ge y, Facul y o Medicine, Uni e si y o Malaya, 50603 Kuala Lumpu , Malaysia. 65 Depa men o U ology, Uni e si y o Washing on, Sea le, WA 98195, USA. 66 Ins i u e o Human Gene ics, Uni e si y Medical Cen e Hambu g- Eppendo , D-20246 Hambu g, Ge many. 67 Molecula Medicine Cen e , Depa men o Medical Chemis y and Biochemis y, Medical Uni e si y o Sofia, 1431 Sofia, Bulga ia. 68 Depa men o Oncology, C oss Cance Ins i u e, Uni e si y o Albe a, Edmon on, AB T6G 1Z2, Canada. 69 Di ision o Radia ion Oncology, C oss Cance Ins i u e, Uni e si y o Albe a, Edmon on, AB T6G 1Z2, Canada. 70 Molecula Endoc inology Labo a o y, Depa men o Cellula and Molecula Medicine, KU Leu en, BE-3000 Leu en, Belgium. 71 Manches e Cance Resea ch Cen e, Facul y o Biology Medicine and Heal h, Manches e Academic Heal h Science Cen e, NIHR Manches e Biomedical Resea ch Cen e, Heal h Inno a ion Manches e , Uni e si y o Manches e , Manches e M13 9WL, UK. 72 Genomic Medicine G oup, Galician Founda ion o Genomic Medicine, Ins i u o de In es igacion Sani a ia de San iago de Compos ela (IDIS), Complejo Hospi ala io Uni e si a io de San iago, Se icio Galego de Saúde, SERGAS, ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 8NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 15706 San iago de Compos ela, Spain. 73 Moo es Cance Cen e , Uni e si y o Cali o nia San Diego, La Jolla, CA 92037, USA. 74 Depa men o U ology, E asmus Uni e si y Medical Cen e , 3015 CE Ro e dam, The Ne he lands. 75 Cance and En i onmen G oup, Cen e o Resea ch in Epidemiology and Popula ion Heal h (CESP), INSERM, Uni e si y Pa is-Sud, Uni e si y Pa is-Saclay, 94807 Villejui Cédex, F ance. 76 Clinical Ge on ology Uni , Uni e si y o Camb idge, Camb idge CB2 2QQ, UK. 77 Di ision o Gene ic Epidemiology, Depa men o Medicine, Uni e si y o U ah School o Medicine, Sal Lake Ci y, UT 84112, USA. 78 Geo ge E. Wahlen Depa men o Ve e ans A ai s Medical Cen e , Sal Lake Ci y, UT 84148, USA. 79 The Uni e si y o Su ey, Guild o d, Su ey GU2 7XH, UK. 80 Depa men o Labo a o y Medicine and Pa hology, Mayo Clinic, Roches e , MN 55905, USA. 81 Di ision o Biomedical S a is ics and In o ma ics, Mayo Clinic, Roches e , MN 55905, USA. 82 Royal Ma sden NHS Founda ion T us , London SW3 6JJ, UK. These au ho s con ibu ed equally: Ma co Ma ejcic, Edwa d J. Saunde s. These au ho s join ly supe ised his wo k: Rosalind A. Eeles, Zsofia Ko e‑Ja ai, Da id V. Con i, Ch is ophe A. Haiman. A ull lis o conso ium membe s appea s a he end o he pape . The PRACTICAL (P os a e Cance Associa ion G oup o In es iga e Cance -Associa ed Al e a ions in he Genome) Conso ium B ian E. Hende son 1 , Ma iana C. S e n 1 , Alison Thwai es 2 , Michelle Guy 2 , Ian Whi mo e 2 , Angela Mo gan 2 , Cy il Fishe 2 , S e e Hazel 2 , Naomi Li ni 2 , Ma ga e Cook 3 , Lau a Fachal 3,42 , S ephanie Weins ein 7 , Lau a E. Beane F eeman 7 , Robe N. Hoo e 7 , Mi chell J. Machiela 7 , A i aya Lopha ananon 8,9 , B ian D. Ca e 10 , Phyllis Goodman 11 , Lei e Moya 12,13 , S ilakshmi S ini asan 12,13 , Ma y-Anne Kedda 12,13 , T ina Yeadon 12,13 , Allison Ecke 12,13 , Ma in Eklund 14 , Ca in Ca alli-Bjoe kman 14 , Alison M. Dunning 15 , Csilla Sipeky 17 , Niclas Hakansson 20 , Rebecca Ellio 21 , Ha deep Ranu 22 , Edwa d Gio annucci 22 , Cons ance Tu man 23 , Da id J. Hun e 23 , Oli ie Cusseno 24,25 , To ben Falck O n o 26,27 , A hene Lane 33 , Sa ah J. Lewis 33 , Michael Da is 33 , Tim J. Key 34 , Paul B own 35 , Gi ish S. Kulka ni 35 , Alexand e R. Zlo a 35 , Neil E. Fleshne 35 , An onio Finelli 35 , Xueying Mao 38 , Jacek Ma zec 38 , Robe J. MacInnis 39,40 , Roge Milne 39,40 , John L. Hoppe 40 , Miguel Aguado 42 , Ma iona Bus aman e 44 , Gemma Cas año-Vinyals 44,45,46,47 , Es he G acia-La edan 44,45,46,47 , Lluís Cecchini 46 , Mei S amp e 48 , Jing Ma 48 , Thomas A. Selle s 49 , Milan S. Geybels 49 , Hyun Pa k 49 , Babu Zacha iah 49 , Suzanne Kolb 50 , Dominika Wokolo czyk 52 , Jan Lubinski 52 , Wojciech Kluzniak 52 , Sune F. Nielsen 53,54 , Ma en Weishe 54 , Ka a ina Cuk 55 , Wal he Vogel 58 , Manuel Luedeke 58 , Ch is ophe J. Logo he is 59 , Paula Paulo 60 , Ma a Ca doso 60 ,Sofia Maia 60 , Ma ia P. Sil a 60 , Linda S eele 62 , Yuan Chun Ding 62 , Ge De Mee lee 63 ,Sofie De Langhe 63 , Hube Thie ens 63 , Jasmine Lim 64 , Meng H. Tan 64 , Aik T. Ong 64 , Daniel W. Lin 50,65 , Da ina Kachako a 67 , A anaska Mi ko a 67 , Vanio Mi e 67 , Ma hew Pa liamen 68,69 , Guido Jens e 74 , Ch is ophe Bangma 74 , F.H. Sch ode 74 , Thé èse T uong 75 , Y es Akoli Koudou 75 , Agnieszka Michael 79 , And zej Kie zek 79 , Ami Ka lsson 79 , Michael B oms 79 , Huihai Wu 79 , Clai e Aukim-Has ie 79 , Lo i Tillmans 80 , Shaun Riska 80 , Shannon K. McDonnell 81 , Da id Dea naley 2,82 , Amanda Spu dle 83 , Robe Ga dine 84,85 , Vanessa Hayes 86 , Lisa Bu le 87 , Renea Taylo 88 , Melissa Papa gi is 88 , Pamela Saunde s 89 , Paula Kujala 90 , Ki si Talala 91 , Kimmo Taa i 92 , Sø en Ben zen 93 , Belynda Hicks 94 , Au elie Vog 94 , Amy Hu chinson 95 , Angela Cox 96 , Anne Geo ge 97 , An s Toi 98 , And ew E ans 99 , Theodo us H. an de Kwas 99 , Takashi Imai 100 , Shi o Sai o 101 , Shan-Chao Zhao 102 , Guoping Ren 103 , Yangling Zhang 103 , Yongwei Yu 104 , Yudong Wu 105 ,JiWu 106 , Bo Zhou 107 , John Pede sen 108 , Ramón Loba o-Bus o 109 , José Manuel Ruiz-Dominguez 110 , Lou des Mengual 111,112 , An onio Alca az 113 , Julio Pow-Sang 114 , Ka hleen He komme 115 , Aleksand ina Vlaho a 116 , Tihomi Diko 116 , S e lana Ch is o a 116 , Angel Ca acedo 42,117,118 , B igi e T e a e 119 , Xa ie Rebilla d 120 , Clai e Mulo 121 , Jan Adol sson 122,123 , Pa S a in 124,125 , Jan-E ik Johansson 126 , Richa d M. Ma in 33,127,128 , Ian M. Thompson J . 129 , Suzanne Chambe s 130,131 , Joanne Ai ken 130,131 , Lisa Ho a h 132,133 , Anne-Ma ee Haynes 86,133 , Wayne Tilley 134 , Gail Risb idge 135,136 , Ma kus Aly 14,137 , Tobias No ds öm 14,138 , Paul Pha oah 3,139 , Teu o L.J. Tammela 140 , Teemu Mu ola 140,141 , Anssi Au inen 142 , Neil Bu ne 143 , Gill Ba ne 143 , Ge ald And iole 144 , Aleksand a Klim 144 , Be ina F. D ake 144 , Michael Bo e 27,145 , Sa ah Ke ns 146 , Ha y Os e 147 , Hong-Wei Zhang 148 , Guangwen Cao 148 , Ji Lin 148 , Jin Ling 148 , Meiling Li 148 , Ninghan Feng 149 , Jie Li 150 , Weiyang He 150 , Xin Guo 150,151 , Zan Sun 151 , NATURE COMMUNICATIONS | DOI: 10.1038/s41467-018-06863-1 ARTICLE NATURE COMMUNICATIONS | (2018) 9:4616 | DOI: 10.1038/s41467-018-06863-1 | www.na u e.com/na u ecommunica ions 9