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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: 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?

SUBMITTER: Zeng C 

PROVIDER: S-EPMC4962376 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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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.

Zeng Chenjie C   Guo Xingyi X   Long Jirong J   Kuchenbaecker Karoline B KB   Droit Arnaud A   Michailidou Kyriaki K   Ghoussaini Maya M   Kar Siddhartha S   Freeman Adam A   Hopper John L JL   Milne Roger L RL   Bolla Manjeet K MK   Wang Qin Q   Dennis Joe J   Agata Simona S   Ahmed Shahana S   Aittomäki Kristiina K   Andrulis Irene L IL   Anton-Culver Hoda H   Antonenkova Natalia N NN   Arason Adalgeir A   Arndt Volker V   Arun Banu K BK   Arver Brita B   Bacot Francois F   Barrowdale Daniel D   Baynes Caroline C   Beeghly-Fadiel Alicia A   Benitez Javier J   Bermisheva Marina M   Blomqvist Carl C   Blot William J WJ   Bogdanova Natalia V NV   Bojesen Stig E SE   Bonanni Bernardo B   Borresen-Dale Anne-Lise AL   Brand Judith S JS   Brauch Hiltrud H   Brennan Paul P   Brenner Hermann H   Broeks Annegien A   Brüning Thomas T   Burwinkel Barbara B   Buys Saundra S SS   Cai Qiuyin Q   Caldes Trinidad T   Campbell Ian I   Carpenter Jane J   Chang-Claude Jenny J   Choi Ji-Yeob JY   Claes Kathleen B M KB   Clarke Christine C   Cox Angela A   Cross Simon S SS   Czene Kamila K   Daly Mary B MB   de la Hoya Miguel M   De Leeneer Kim K   Devilee Peter P   Diez Orland O   Domchek Susan M SM   Doody Michele M   Dorfling Cecilia M CM   Dörk Thilo T   Dos-Santos-Silva Isabel I   Dumont Martine M   Dwek Miriam M   Dworniczak Bernd B   Egan Kathleen K   Eilber Ursula U   Einbeigi Zakaria Z   Ejlertsen Bent B   Ellis Steve S   Frost Debra D   Lalloo Fiona F   Fasching Peter A PA   Figueroa Jonine J   Flyger Henrik H   Friedlander Michael M   Friedman Eitan E   Gambino Gaetana G   Gao Yu-Tang YT   Garber Judy J   García-Closas Montserrat M   Gehrig Andrea A   Damiola Francesca F   Lesueur Fabienne F   Mazoyer Sylvie S   Stoppa-Lyonnet Dominique D   Giles Graham G GG   Godwin Andrew K AK   Goldgar David E DE   González-Neira Anna A   Greene Mark H MH   Guénel Pascal P   Haeberle Lothar L   Haiman Christopher A CA   Hallberg Emily E   Hamann Ute U   Hansen Thomas V O TV   Hart Steven S   Hartikainen Jaana M JM   Hartman Mikael M   Hassan Norhashimah N   Healey Sue S   Hogervorst Frans B L FB   Verhoef Senno S   Hendricks Carolyn B CB   Hillemanns Peter P   Hollestelle Antoinette A   Hulick Peter J PJ   Hunter David J DJ   Imyanitov Evgeny N EN   Isaacs Claudine C   Ito Hidemi H   Jakubowska Anna A   Janavicius Ramunas R   Jaworska-Bieniek Katarzyna K   Jensen Uffe Birk UB   John Esther M EM   Joly Beauparlant Charles C   Jones Michael M   Kabisch Maria M   Kang Daehee D   Karlan Beth Y BY   Kauppila Saila S   Kerin Michael J MJ   Khan Sofia S   Khusnutdinova Elza E   Knight Julia A JA   Konstantopoulou Irene I   Kraft Peter P   Kwong Ava A   Laitman Yael Y   Lambrechts Diether D   Lazaro Conxi C   Le Marchand Loic L   Lee Chuen Neng CN   Lee Min Hyuk MH   Lester Jenny J   Li Jingmei J   Liljegren Annelie A   Lindblom Annika A   Lophatananon Artitaya A   Lubinski Jan J   Mai Phuong L PL   Mannermaa Arto A   Manoukian Siranoush S   Margolin Sara S   Marme Frederik F   Matsuo Keitaro K   McGuffog Lesley L   Meindl Alfons A   Menegaux Florence F   Montagna Marco M   Muir Kenneth K   Mulligan Anna Marie AM   Nathanson Katherine L KL   Neuhausen Susan L SL   Nevanlinna Heli H   Newcomb Polly A PA   Nord Silje S   Nussbaum Robert L RL   Offit Kenneth K   Olah Edith E   Olopade Olufunmilayo I OI   Olswold Curtis C   Osorio Ana A   Papi Laura L   Park-Simon Tjoung-Won TW   Paulsson-Karlsson Ylva Y   Peeters Stephanie S   Peissel Bernard B   Peterlongo Paolo P   Peto Julian J   Pfeiler Georg G   Phelan Catherine M CM   Presneau Nadege N   Radice Paolo P   Rahman Nazneen N   Ramus Susan J SJ   Rashid Muhammad Usman MU   Rennert Gad G   Rhiem Kerstin K   Rudolph Anja A   Salani Ritu R   Sangrajrang Suleeporn S   Sawyer Elinor J EJ   Schmidt Marjanka K MK   Schmutzler Rita K RK   Schoemaker Minouk J MJ   Schürmann Peter P   Seynaeve Caroline C   Shen Chen-Yang CY   Shrubsole Martha J MJ   Shu Xiao-Ou XO   Sigurdson Alice A   Singer Christian F CF   Slager Susan S   Soucy Penny P   Southey Melissa M   Steinemann Doris D   Swerdlow Anthony A   Szabo Csilla I CI   Tchatchou Sandrine S   Teixeira Manuel R MR   Teo Soo H SH   Terry Mary Beth MB   Tessier Daniel C DC   Teulé Alex A   Thomassen Mads M   Tihomirova Laima L   Tischkowitz Marc M   Toland Amanda E AE   Tung Nadine N   Turnbull Clare C   van den Ouweland Ans M W AM   van Rensburg Elizabeth J EJ   Ven den Berg David D   Vijai Joseph J   Wang-Gohrke Shan S   Weitzel Jeffrey N JN   Whittemore Alice S AS   Winqvist Robert R   Wong Tien Y TY   Wu Anna H AH   Yannoukakos Drakoulis D   Yu Jyh-Cherng JC   Pharoah Paul D P PD   Hall Per P   Chenevix-Trench Georgia G   Dunning Alison M AM   Simard Jacques J   Couch Fergus J FJ   Antoniou Antonis C AC   Easton Douglas F DF   Zheng Wei W  

Breast cancer research : BCR 20160621 1


<h4>Background</h4>Multiple recent genome-wide association studies (GWAS) have identified a single nucleotide polymorphism (SNP), rs10771399, at 12p11 that is associated with breast cancer risk.<h4>Method</h4>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 th  ...[more]

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