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A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11

A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11
A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11
Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ? 1 × 10(-5) in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry. We identified two novel loci for breast cancer at 20q11 and 6q14. SNP rs2284378 at 20q11 was associated with ER-negative breast cancer (combined two-stage OR = 1.16; P = 1.1 × 10(-8)) but showed a weaker association with overall breast cancer (OR = 1.08, P = 1.3 × 10(-6)) based on 17 869 cases and 43 745 controls and no association with ER-positive disease (OR = 1.01, P = 0.67) based on 9965 cases and 22 902 controls. Similarly, rs17530068 at 6q14 was associated with breast cancer (OR = 1.12; P = 1.1 × 10(-9)), and with both ER-positive (OR = 1.09; P = 1.5 × 10(-5)) and ER-negative (OR = 1.16, P = 2.5 × 10(-7)) disease. We also confirmed three known loci associated with ER-negative (19p13) and both ER-negative and ER-positive breast cancer (6q25 and 12p11). Our results highlight the value of large-scale collaborative studies to identify novel breast cancer risk loci.
5373-5384
Siddiq, A.
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Couch, F.J.
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Chen, G.K.
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Lindstrom, S.
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Eccles, D.
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Millikan, R.C.
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Michailidou, K.
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Stram, D.O.
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Beckmann, L.
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Aittomaki, K.
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Baglietto, L.
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Blomqvist, C.
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Buring, J.E.
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Chang-Claude, J.
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Chen, C.
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Clavel-Chapelon, F.
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Ekici, A.B.
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Fletcher, O.
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Flesch-Janys, D.
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Gaudet, M.M.
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Gerty, S.M.
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Rodriguez-Gil, J.L.
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Graham, N.
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Hall, P.
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Hankinson, S.E.
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Hu, J.J.
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Huntsman, S.
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Lesnick, T.
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Lichtner, P.
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Siddiq, A., Couch, F.J., Chen, G.K., Lindstrom, S., Eccles, D., Millikan, R.C., Michailidou, K., Stram, D.O., Beckmann, L., Rhie, S.K., Ambrosone, C.B., Aittomaki, K., Amiano, P., Apicella, C., Baglietto, L., Bandera, E.V., Beckmann, M.W., Berg, C.D., Bernstein, L., Blomqvist, C., Brauch, H., Brinton, L., Bui, Q.M., Buring, J.E., Buys, S.S., Campa, D., Carpenter, J.E., Chasman, D.I., Chang-Claude, J., Chen, C., Clavel-Chapelon, F., Cox, A., Cross, S.S., Czene, K., Deming, S.L., Diasio, R.B., Diver, W.R., Dunning, A.M., Durcan, L., Ekici, A.B., Fasching, P.A., Feigelson, H.S., Fejerman, L., Figueroa, J.D., Fletcher, O., Flesch-Janys, D., Gaudet, M.M., Gerty, S.M., Rodriguez-Gil, J.L., Giles, G.G., van Gils, C.H., Godwin, A.K., Graham, N., Greco, D., Hall, P., Hankinson, S.E., Hartmann, A., Hein, R., Heinz, J., Hoover, R.N., Hopper, J.L., Hu, J.J., Huntsman, S., Ingles, S.A., Irwanto, A., Isaacs, C., Jacobs, K.B., John, E.M., Justenhoven, C., Kaaks, R., Kolonel, L.N., Coetzee, G.A., Lathrop, M., Le Marchand, L., Lee, A.M., Lee, I.-M., Lesnick, T., Lichtner, P., Liu, J., Lund, E., Makalic, E., Martin, N.G., McLean, C.A., Meijers-Heijboer, H., Meindl, A., Miron, P., Monroe, K.R., Montgomery, G.W., Muller-Myhsok, B., Nickels, S., Nyante, S.J., Olswold, C., Overvad, K., Palli, D., Park, D.J., Palmer, J.R., Pathak, H., Peto, J., Pharoah, P., Rahman, N., Rivadeneira, F., Schmidt, D.F., Schmutzler, R.K., Slager, S., Southey, M.C., Stevens, K.N., Sinn, H.-P., Press, M.F., Ross, E., Riboli, E., Ridker, P.M., Schumacher, F.R., Severi, G., dos Santos Silva, I., Stone, J., Sund, M., Tapper, W.J., Thun, M.J., Travis, R.C., Turnbull, C., Uitterlinden, A.G., Waisfisz, Q., Wang, X., Wang, Z., Weaver, J., Schulz-Wendtland, R., Wilkens, L.R., Van Den Berg, D., Zheng, W., Ziegler, R.G., Ziv, E., Nevanlinna, H., Easton, D.F., Hunter, D.J., Henderson, B.E., Chanock, S.J., Garcia-Closas, M., Kraft, P., Haiman, C.A. and Vachon, C.M. (2012) A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11. Human Molecular Genetics, 21 (24), 5373-5384. (doi:10.1093/hmg/dds381). (PMID:22976474)

Record type: Article

Abstract

Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ? 1 × 10(-5) in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry. We identified two novel loci for breast cancer at 20q11 and 6q14. SNP rs2284378 at 20q11 was associated with ER-negative breast cancer (combined two-stage OR = 1.16; P = 1.1 × 10(-8)) but showed a weaker association with overall breast cancer (OR = 1.08, P = 1.3 × 10(-6)) based on 17 869 cases and 43 745 controls and no association with ER-positive disease (OR = 1.01, P = 0.67) based on 9965 cases and 22 902 controls. Similarly, rs17530068 at 6q14 was associated with breast cancer (OR = 1.12; P = 1.1 × 10(-9)), and with both ER-positive (OR = 1.09; P = 1.5 × 10(-5)) and ER-negative (OR = 1.16, P = 2.5 × 10(-7)) disease. We also confirmed three known loci associated with ER-negative (19p13) and both ER-negative and ER-positive breast cancer (6q25 and 12p11). Our results highlight the value of large-scale collaborative studies to identify novel breast cancer risk loci.

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Published date: 15 December 2012
Organisations: Cancer Sciences, Human Development & Health

Identifiers

Local EPrints ID: 352314
URI: http://eprints.soton.ac.uk/id/eprint/352314
DOI: doi:10.1093/hmg/dds381
PURE UUID: fb94571a-8a7c-40ea-8988-b6830b45169d
ORCID for D. Eccles: ORCID iD orcid.org/0000-0002-9935-3169
ORCID for W.J. Tapper: ORCID iD orcid.org/0000-0002-5896-1889

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Date deposited: 09 May 2013 11:47
Last modified: 15 Mar 2024 03:02

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Contributors

Author: A. Siddiq
Author: F.J. Couch
Author: G.K. Chen
Author: S. Lindstrom
Author: D. Eccles ORCID iD
Author: R.C. Millikan
Author: K. Michailidou
Author: D.O. Stram
Author: L. Beckmann
Author: S.K. Rhie
Author: C.B. Ambrosone
Author: K. Aittomaki
Author: P. Amiano
Author: C. Apicella
Author: L. Baglietto
Author: E.V. Bandera
Author: M.W. Beckmann
Author: C.D. Berg
Author: L. Bernstein
Author: C. Blomqvist
Author: H. Brauch
Author: L. Brinton
Author: Q.M. Bui
Author: J.E. Buring
Author: S.S. Buys
Author: D. Campa
Author: J.E. Carpenter
Author: D.I. Chasman
Author: J. Chang-Claude
Author: C. Chen
Author: F. Clavel-Chapelon
Author: A. Cox
Author: S.S. Cross
Author: K. Czene
Author: S.L. Deming
Author: R.B. Diasio
Author: W.R. Diver
Author: A.M. Dunning
Author: L. Durcan
Author: A.B. Ekici
Author: P.A. Fasching
Author: H.S. Feigelson
Author: L. Fejerman
Author: J.D. Figueroa
Author: O. Fletcher
Author: D. Flesch-Janys
Author: M.M. Gaudet
Author: S.M. Gerty
Author: J.L. Rodriguez-Gil
Author: G.G. Giles
Author: C.H. van Gils
Author: A.K. Godwin
Author: N. Graham
Author: D. Greco
Author: P. Hall
Author: S.E. Hankinson
Author: A. Hartmann
Author: R. Hein
Author: J. Heinz
Author: R.N. Hoover
Author: J.L. Hopper
Author: J.J. Hu
Author: S. Huntsman
Author: S.A. Ingles
Author: A. Irwanto
Author: C. Isaacs
Author: K.B. Jacobs
Author: E.M. John
Author: C. Justenhoven
Author: R. Kaaks
Author: L.N. Kolonel
Author: G.A. Coetzee
Author: M. Lathrop
Author: L. Le Marchand
Author: A.M. Lee
Author: I.-M. Lee
Author: T. Lesnick
Author: P. Lichtner
Author: J. Liu
Author: E. Lund
Author: E. Makalic
Author: N.G. Martin
Author: C.A. McLean
Author: H. Meijers-Heijboer
Author: A. Meindl
Author: P. Miron
Author: K.R. Monroe
Author: G.W. Montgomery
Author: B. Muller-Myhsok
Author: S. Nickels
Author: S.J. Nyante
Author: C. Olswold
Author: K. Overvad
Author: D. Palli
Author: D.J. Park
Author: J.R. Palmer
Author: H. Pathak
Author: J. Peto
Author: P. Pharoah
Author: N. Rahman
Author: F. Rivadeneira
Author: D.F. Schmidt
Author: R.K. Schmutzler
Author: S. Slager
Author: M.C. Southey
Author: K.N. Stevens
Author: H.-P. Sinn
Author: M.F. Press
Author: E. Ross
Author: E. Riboli
Author: P.M. Ridker
Author: F.R. Schumacher
Author: G. Severi
Author: I. dos Santos Silva
Author: J. Stone
Author: M. Sund
Author: W.J. Tapper ORCID iD
Author: M.J. Thun
Author: R.C. Travis
Author: C. Turnbull
Author: A.G. Uitterlinden
Author: Q. Waisfisz
Author: X. Wang
Author: Z. Wang
Author: J. Weaver
Author: R. Schulz-Wendtland
Author: L.R. Wilkens
Author: D. Van Den Berg
Author: W. Zheng
Author: R.G. Ziegler
Author: E. Ziv
Author: H. Nevanlinna
Author: D.F. Easton
Author: D.J. Hunter
Author: B.E. Henderson
Author: S.J. Chanock
Author: M. Garcia-Closas
Author: P. Kraft
Author: C.A. Haiman
Author: C.M. Vachon

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