Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1: Supplemental Data

Glubb, DM; Maranian, MJ; Michailidou, K; Pooley, KA; Meyer, KB; Kar, S; Carlebur, S; O’Reilly, M; Betts, JA; Hillman, KM; Kaufmann, S; Beesley, J; Canisius, S; Hopper, JL; Southey, MC; Tsimiklis, H; Apicella, C; Schmidt, MK; Broeks, A; Hogervorst, FB; van der Schoot, CE; Muir, K; Lophatananon, A; Stewart-Brown, S; Siriwanarangsan, P; Fasching, PA; Ruebner, M; Ekici, AB; Beckmann, MW; Peto, J; Silva, I; Fletcher, O; Johnson, N; Pharoah, PD; Bolla, MK; Wang, Q; Dennis, J; Sawyer, EJ; Tomlinson, I; Kerin, MJ; Miller, N; Burwinkel, B; Marme, F; Yang, R; Surowy, H; Guénel, P; Truong, T; Menegaux, F; Sanchez, M; Bojesen, SE; Nordestgaard, BG; Nielsen, SF; Flyger, H; González-Neira, A; Benitez, J; Zamora, MP; Arias Perez, JI; Anton-Culver, H; Neuhausen, SL; Brenner, H; Dieffenbach, AK; Arndt, V; Stegmaier, C; Meindl, A; Schmutzler, RK; Brauch, H; Ko, Y; Brüning, T; Nevanlinna, H; Muranen, TA; Aittomäki, K; Blomqvist, C; Matsuo, K; Ito, H; Iwata, H; Tanaka, H; Dörk, T; Bogdanova, NV; Helbig, S; Lindblom, A; Margolin, S; Mannermaa, A; Kataja, V; Kosma, V; Hartikainen, JM; Wu, AH; Tseng, C; Van Den Berg, D; Stram, DO; Lambrechts, D; Zhao, H; Weltens, C; van Limbergen, E; Chang-Claude, J; Flesch-Janys, D; Rudolph, A; Seibold, P; Radice, P; Peterlongo, P; Barile, M; Capra, F; Couch, FJ; Olson, JE; Hallberg, E; Vachon, C; Giles, GG; Milne, RL; McLean, C; Haiman, CA; Henderson, BE; Schumacher, F; Le Marchand, L; Simard, J; Goldberg, MS; Labrèche, F; Dumont, M; Teo, SH; Yip, CH; See, M; Cornes, B; Cheng, C; Ikram, MK; Kristensen, V; Zheng, W; Halverson, SL; Shrubsole, M; Long, J; Winqvist, R; Pylkäs, K; Jukkola-Vuorinen, A; Kauppila, S; Andrulis, IL; Knight, JA; Glendon, G; Tchatchou, S; Devilee, P; Tollenaar, RA; Seynaeve, C; Van Asperen, CJ; García-Closas, M; Figueroa, J; Chanock, SJ; Lissowska, J; Czene, K; Klevebring, D; Darabi, H; Eriksson, M; Hooning, MJ; Hollestelle, A; Martens, JW; Collée, JM; Hall, P; Li, J; Humphreys, K; Shu, X; Lu, W; Gao, Y; Cai, H; Cox, A; Cross, SS; Reed, MW; Blot, W; Signorello, LB; Cai, Q; Shah, M; Ghoussaini, M; Kang, D; Choi, J; Park, SK; Noh, D; Hartman, M; Miao, H; Lim, WY; Tang, A; Hamann, U; Torres, D; Jakubowska, A; Lubinski, J; Jaworska, K; Durda, K; Sangrajrang, S; Gaborieau, V; Brennan, P; McKay, J; Olswold, C; Slager, S; Toland, AE; Yannoukakos, D; Shen, C; Wu, P; Yu, J; Hou, M; Swerdlow, A; Ashworth, A; Orr, N; Jones, M; Pita, G; Alonso, MR; Álvarez, N; Herrero, D; Tessier, DC; Vincent, D; Bacot, F; Luccarini, C; Baynes, C; Ahmed, S; Healey, CS; Brown, MA; Ponder, BA; Chenevix-Trench, G; Thompson, DJ; Edwards, SL; Easton, DF; Dunning, AM and French, JD (2014). Fine-Scale Mapping of the 5q11.2 Breast Cancer Locus Reveals at Least Three Independent Risk Variants Regulating MAP3K1: Supplemental Data. [Dataset]. Elsevier, London, United Kingdom. 10.1016/j.ajhg.2014.11.009.
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Genome-wide association studies (GWASs) have revealed SNP rs889312 on 5q11.2 to be associated with breast cancer risk in women of European ancestry. In an attempt to identify the biologically relevant variants, this study analyzed 909 genetic variants across 5q11.2 in 103,991 breast cancer individuals and control individuals from 52 studies in the Breast Cancer Association Consortium.

Keywords

Breast Cancer; Risk variants; MAP3K1; Genome-wide Association Study; SNP rs889312

Item Type Dataset
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Dataset
UNSPECIFIED
Description of data capture Using the March 2010 release of the 1000 Genomes Project, we searched a 305 kb interval on 5q11.2 (GRCh37 positions 55,983,657–56,288,810) and identified all SNPs with a minor allele frequency (MAF) > 0.02 in Europeans. SNPs with an Illumina designability score > 0.8 (and r2 > 0.1 with rs889312), together with a tagging set (r2 > 0.9) for all other known SNPs in the interval, were selected for inclusion on the iCOGS custom array. A total of 352 SNPs, of which 300 passed postgenotyping quality-control criteria, were selected. For improvement of SNP coverage across the locus, 16 further SNPs selected from the October 2010 release of the 1000 Genomes Project were genotyped in a subset of two BCAC studies (SEARCH and the combined Copenhagen studies CPGS [Copenhagen General Population Study] and CCHS [Copenhagen City Heart Study]) by using a Fluidigm array according to the manufacturer’s instructions. These two data sets, as well as IMPUTE2 and the January 2012 release of the 1000 Genomes Project as references, were used for imputing all genotypes of other common variants in this interval. All participants provided written informed consent, and all BCAC studies had local human ethical approvals. Study characteristics and iCOGS methodology have been previously reported.
Capture method Experiment: Laboratory
Collection Period
From
To
March 2010
October 2010
Date 18 December 2014
Language(s) of written materials English
Creator(s) Glubb, DM; Maranian, MJ; Michailidou, K; Pooley, KA; Meyer, KB; Kar, S; Carlebur, S; O’Reilly, M; Betts, JA; Hillman, KM; Kaufmann, S; Beesley, J; Canisius, S; Hopper, JL; Southey, MC; Tsimiklis, H; Apicella, C; Schmidt, MK; Broeks, A; Hogervorst, FB; van der Schoot, CE; Muir, K; Lophatananon, A; Stewart-Brown, S; Siriwanarangsan, P; Fasching, PA; Ruebner, M; Ekici, AB; Beckmann, MW; Peto, J; Silva, I; Fletcher, O; Johnson, N; Pharoah, PD; Bolla, MK; Wang, Q; Dennis, J; Sawyer, EJ; Tomlinson, I; Kerin, MJ; Miller, N; Burwinkel, B; Marme, F; Yang, R; Surowy, H; Guénel, P; Truong, T; Menegaux, F; Sanchez, M; Bojesen, SE; Nordestgaard, BG; Nielsen, SF; Flyger, H; González-Neira, A; Benitez, J; Zamora, MP; Arias Perez, JI; Anton-Culver, H; Neuhausen, SL; Brenner, H; Dieffenbach, AK; Arndt, V; Stegmaier, C; Meindl, A; Schmutzler, RK; Brauch, H; Ko, Y; Brüning, T; Nevanlinna, H; Muranen, TA; Aittomäki, K; Blomqvist, C; Matsuo, K; Ito, H; Iwata, H; Tanaka, H; Dörk, T; Bogdanova, NV; Helbig, S; Lindblom, A; Margolin, S; Mannermaa, A; Kataja, V; Kosma, V; Hartikainen, JM; Wu, AH; Tseng, C; Van Den Berg, D; Stram, DO; Lambrechts, D; Zhao, H; Weltens, C; van Limbergen, E; Chang-Claude, J; Flesch-Janys, D; Rudolph, A; Seibold, P; Radice, P; Peterlongo, P; Barile, M; Capra, F; Couch, FJ; Olson, JE; Hallberg, E; Vachon, C; Giles, GG; Milne, RL; McLean, C; Haiman, CA; Henderson, BE; Schumacher, F; Le Marchand, L; Simard, J; Goldberg, MS; Labrèche, F; Dumont, M; Teo, SH; Yip, CH; See, M; Cornes, B; Cheng, C; Ikram, MK; Kristensen, V; Zheng, W; Halverson, SL; Shrubsole, M; Long, J; Winqvist, R; Pylkäs, K; Jukkola-Vuorinen, A; Kauppila, S; Andrulis, IL; Knight, JA; Glendon, G; Tchatchou, S; Devilee, P; Tollenaar, RA; Seynaeve, C; Van Asperen, CJ; García-Closas, M; Figueroa, J; Chanock, SJ; Lissowska, J; Czene, K; Klevebring, D; Darabi, H; Eriksson, M; Hooning, MJ; Hollestelle, A; Martens, JW; Collée, JM; Hall, P; Li, J; Humphreys, K; Shu, X; Lu, W; Gao, Y; Cai, H; Cox, A; Cross, SS; Reed, MW; Blot, W; Signorello, LB; Cai, Q; Shah, M; Ghoussaini, M; Kang, D; Choi, J; Park, SK; Noh, D; Hartman, M; Miao, H; Lim, WY; Tang, A; Hamann, U; Torres, D; Jakubowska, A; Lubinski, J; Jaworska, K; Durda, K; Sangrajrang, S; Gaborieau, V; Brennan, P; McKay, J; Olswold, C; Slager, S; Toland, AE; Yannoukakos, D; Shen, C; Wu, P; Yu, J; Hou, M; Swerdlow, A; Ashworth, A; Orr, N; Jones, M; Pita, G; Alonso, MR; Álvarez, N; Herrero, D; Tessier, DC; Vincent, D; Bacot, F; Luccarini, C; Baynes, C; Ahmed, S; Healey, CS; Brown, MA; Ponder, BA; Chenevix-Trench, G; Thompson, DJ; Edwards, SL; Easton, DF; Dunning, AM and French, JD
LSHTM Faculty/Department Faculty of Epidemiology and Population Health > Dept of Non-Communicable Disease Epidemiology
Participating Institutions London School of Hygiene & Tropical Medicine
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Cancer Research UK
UNSPECIFIED
UNSPECIFIED
Date Deposited 19 Jan 2016 10:40
Last Modified 28 Sep 2018 21:18
Publisher Elsevier

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