Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Zeng, Chenjie; Guo, Xy Y.; Kuchenbaecker, Kb B. (Karoline); Long, Jirong R.; Doerk, Thilo; Droit, Arnaud; Hoya, M. (Miguel) de La; Hopper, Jl L. (John); Michailidou, Kyriaki; Díez, Orland; Ghoussaini, Maya; Milne, Rl L. (Roger); Kar, Siddhartha; Freeman, Adam; Santos Silva, I. (Isabel) dos; Bolla, Mk K. (Manjeet K.); Antonenkova, Natalia Nn; Dos Santos Silva, Isabel; Agata, Simona; Andrulis, Il L. (Irene); Arason, Adalgeir; Arndt, Volker; Wang, Qin; Ahmed, Shahana; Dennis, Joe; Arver, Brita; Aittomaki, Kristiina; Bacot, Francois; Dork, T.; Barrowdale, Daniel; Baynes, Caroline; Anton-Culver, Hoda; Beeghly-Fadiel, Alicia; Arun, Bk K. (Banu); Benitez, Javier; Bermisheva, Marina; Blomqvist, Carl; Brennan, Paul; Brauch, Hiltrud; Brenner, Hermann; Bonanni, Bernardo; Broeks, Annegien; Blot, Wj J. (William); Bruning, Thomas; Bogdanova, Nv V. (Natalia); Bojesen, Se E. (Stig); Cross, Simon Ss; Daly, Mb B. (Mary B.); Burwinkel, Barbara; Kb, Kuchenbaecker; de la Hoya, Miguel; Buys, Saundra Ss; Borresen-Dale, Al-L. (Anne-Lise); Czene, Kamila; Brand, Js S. (Judith S.); Caldes, Trinidad; Cai, Qy Y.; De Leeneer, Kim; Domchek, Sm M. (Susan); Campbell, Ian; dos-Santos-Silva, Isabel; Carpenter, Jane; Devilee, Peter; Dörk, Thilo; Guenel, Pascal; Dorfling, Cm M. (Cecilia); Diez, Orland; Chang-Claude, Jenny; Claes, Kathleen B. M. (Kathleen B. M.); Doody, Michele; Clarke, Christine; Choi, Jy-Y. (Ji-Yeob); Cox, Angela; Dumont, Martine; Dwek, Miriam; Dworniczak, Bernd; Egan, Kathleen M. (Kathleen); Eilber, Ursula; Fasching, Pa A. (Peter); Einbeigi, Zakaria; Ejlertsen, Bent; Ellis, Steve D. (Steve); Frost, Debra; Lalloo, Fiona; Figueroa, Jonine D. (Jonine); Flyger, Henrik; Gao, Yt-T. (Yu-Tang); Friedlander, Michael; Friedman, Eitan; Gambino, Gaetana; Garber, Judy; Garcia-Closas, Montserrat; Gehrig, Andrea; Damiola, Francesca; Goldgar, De E.; Godwin, Ak K. (Andrew K.); Lesueur, Fabienne; Mazoyer, Sylvie; Stoppa-Lyonnet, Dominique; Giles, Graham Gg; Greene, Mh H. (Mark H.); Gonzalez-Neira, Anna; Lázaro, Conxi; Guénel, Pascal; Haiman, Ca A. (Christopher A.); Haeberle, Lothar; Hallberg, Emily; Hansen, Tvo V. O. (Thomas); Hamann, Ute; Hart, Steven; Hartikainen, Jm M. (J.); Hartman, Mikael; Hassan, Norhashimah; Hogervorst, Fbl B. L. (Frans); Healey, Sue; Verhoef, Senno; Hendricks, Cb B. (Carolyn B.); Hillemanns, Peter; Hulick, Pj J. (Peter); Hollestelle, Antoinette; Hunter, Dj J.; Marchand, Loic Le; Imyanitov, En N. (Evgeny); Isaacs, Claudine; Ito, Hidemi; Jakubowska, Anna; Janavicius, Ramunas; Jaworska-Bieniek, Katarzyna; Jensen, Ub B.; John, Em M. (Esther); Joly Beauparlant, Charles; Jones, Michael; Kabisch, Maria; Kang, Daehee; Karlan, By Y. (Beth Y.); Kauppila, Saila; Kerin, Mj J.; Khan, Sofia; Khusnutdinova, Elza K. (Elza); Knight, Ja A. (Julia); Konstantopoulou, Irene; Kraft, Peter; Kwong, Ava; Laitman, Yael; Lambrechts, Diether; Lazaro, Conxi; Jl, Hopper; Le Marchand, Loic; Lee, Cn N. (Chuen); Lee, Mh H. (Min Hyuk); Lester, Jenny; Li, Jm M.; Liljegren, Annelie; Lindblom, Annika; Lophatananon, Artitaya; Lubinski, Jan; Mai, Pl L. (Phuong); Mannermaa, Arto; Manoukian, Siranoush; Margolin, Sara; Marme, Frederik; Rl, Milne; Matsuo, Keitaro; McGuffog, Lesley; Meindl, Alfons; Menegaux, Florence; Montagna, Marco; Muir, Kenneth R. (K.); Mulligan, Am-M. (Anna-Marie); Nathanson, Kl L. (Katherine); Neuhausen, Sl L. (Susan); Nevanlinna, Heli; Newcomb, Pa A.; Nord, Silje; Nussbaum, Rl L. (Robert L.); Offit, Kenneth; Olah, Edith; Mk, Bolla; Olopade, Oi I. (Olufunmilayo I.); Olswold, Curtis; Osorio, Ana; Papi, Laura; Park-Simon, Tw-W.; Paulsson-Karlsson, Ylva; Peeters, Stephanie T. H. (Stephanie); Peissel, Bernard; Peterlongo, Paolo; Peto, Julian; Pfeiler, Georg; Beauparlant, Cj J.; Phelan, Cm M.; Presneau, Nadege; Radice, Paolo; Schuermann, Peter; Rahman, Nazneen; Ramus, Sj J. (Susan); Rashid, Mu U. (Muhammad); Rennert, Gad; Rhiem, Kerstin; Rudolph, Anja; Salani, Ritu; Sangrajrang, Suleeporn; Sawyer, Ej J. (Elinor); Schmidt, Mk K. (Marjanka); van den Ouweland, Amw M. W.; Teixeira, P. J.; Schmutzler, Rk K. (Rita); Schoemaker, Mj J.; ven den Berg, David; van Rensburg, Ej J.; Schurmann, Peter; Seynaeve, Caroline M. (Caroline); Shen, Cy-Y. (Chen-Yang); Shrubsole, Mj J.; Ouweland, A. M. W. (Ans) van den; Shu, Xo-O. (Xiao-Ou); Sigurdson, Alice J. (Alice); Singer, Cf F. (Christian); Slager, Susan; Soucy, Penny; Southey, Melissa C. (Melissa); Rensburg, E. J. (Elizabeth) van; Steinemann, Doris; Szabo, Ci I.; Swerdlow, Anthony J. (Anthony ); Tchatchou, Sandrine; Teixeira, Mr R.; Teo, Sh-H.; Terry, Mb B. (Mary Beth); Tessier, Dc C. (Daniel C.); Teule, Alex; Thomassen, Mads; Il, Andrulis; Tihomirova, Laima; Tischkowitz, Marc; Toland, Ae E. (Amanda); Bruening, Thomas; Tung, Nadine; Turnbull, Clare; Vijai, Joseph; Embrace,; Wang-Gohrke, Shan; Weitzel, Jn N. (Jeffrey); Whittemore, As S. (Alice); Carpenter, T. A. (Adrian); Zheng, Wei; Winqvist, Robert; Wong, Ty Y. (Tien Y.); Berg, David Ven den; Wu, Ah H. (Anna); Yannoukakos, Drakoulis; Yu, Jc-C. (Jyh-Cherng); Pharoah, Paul D. Pdp; Hall, Per; Chenevix-Trench, Georgia; Bonnani, B. (Bernardo); Dunning, Am M. (Alison); Simard, Jacques; Couch, Fj J. (Fergus); Collaborators, Gemo Study; Easton, Df F. (Douglas F.); Antoniou, Ac C. (Antonis C.); Hebon,; KconFab,; Investigators, Aocs; Nn, Antonenkova

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BioMed Central, Breast Cancer Research, 1(18), 2016

DOI: 10.1186/s13058-016-0718-0

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Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Journal article published in 2016 by Chenjie Zeng, Xy Y. Guo, Kb B. (Karoline) Kuchenbaecker, Jirong R. Long, Thilo Doerk, Arnaud Droit, M. (Miguel) de La Hoya, Jl L. (John) Hopper, Kyriaki Michailidou, Orland Díez, Maya Ghoussaini, Rl L. (Roger) Milne, Siddhartha Kar, Adam Freeman, I. (Isabel) dos Santos Silva and other authors.

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Abstract

BACKGROUND: Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk. METHOD: We performed a fine-scale mapping study of a 700 kb region including 441 genotyped and more than 1300 imputed genetic variants in 48,155 cases and 43,612 controls of European descent, 6269 cases and 6624 controls of East Asian descent and 1116 cases and 932 controls of African descent in the Breast Cancer Association Consortium (BCAC; http://bcac.ccge.medschl.cam.ac.uk/ ), and in 15,252 BRCA1 mutation carriers in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA). Stepwise regression analyses were performed to identify independent association signals. Data from the Encyclopedia of DNA Elements project (ENCODE) and the Cancer Genome Atlas (TCGA) were used for functional annotation. RESULTS: Analysis of data from European descendants found evidence for four independent association signals at 12p11, represented by rs7297051 (odds ratio (OR) = 1.09, 95 % confidence interval (CI) = 1.06-1.12; P = 3 × 10(-9)), rs805510 (OR = 1.08, 95 % CI = 1.04-1.12, P = 2 × 10(-5)), and rs1871152 (OR = 1.04, 95 % CI = 1.02-1.06; P = 2 × 10(-4)) identified in the general populations, and rs113824616 (P = 7 × 10(-5)) identified in the meta-analysis of BCAC ER-negative cases and BRCA1 mutation carriers. SNPs rs7297051, rs805510 and rs113824616 were also associated with breast cancer risk at P

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Identification of independent association signals and putative functional variants for breast cancer risk through fine-scale mapping of the 12p11 locus

Abstract