A genome-wide association study of breast cancer in women of African ancestry

Fang Chen; Gary K. Chen; Daniel O. Stram; Robert C. Millikan; Christine B. Ambrosone; Esther M. John; Leslie Bernstein; Wei Zheng; Julie R. Palmer; Jennifer J. Hu; Tim R. Rebbeck; Regina G. Ziegler; Sarah Nyante; Elisa V. Bandera; Sue A. Ingles; Michael F. Press; Edward A. Ruiz-Narvaez; Sandra L. Deming; Jorge L. Rodriguez-Gil; Angela Demichele; Stephen J. Chanock; William Blot; Lisa Signorello; Qiuyin Cai; Guoliang Li; Jirong Long; Dezheng Huo; Yonglan Zheng; Nancy J. Cox; Olufunmilayo I. Olopade; Temidayo O. Ogundiran; Clement Adebamowo; Katherine L. Nathanson; Susan M. Domchek; Michael S. Simon; Anselm Hennis; Barbara Nemesure; Suh Yuh Wu; M. Cristina Leske; Stefan Ambs; Carolyn M. Hutter; Alicia Young; Charles Kooperberg; Ulrike Peters; Suhn K. Rhie; Peggy Wan; Xin Sheng; Loreall C. Pooler; David J. Van Den Berg; Loic Le Marchand; Laurence N. Kolonel; Brian E. Henderson; Christopher A. Haiman

doi:10.1007/s00439-012-1214-y

A genome-wide association study of breast cancer in women of African ancestry

Fang Chen
, Gary K. Chen
, Daniel O. Stram
, Robert C. Millikan
, Christine B. Ambrosone
, Esther M. John
, Leslie Bernstein
, Wei Zheng
, Julie R. Palmer
, Jennifer J. Hu
, Tim R. Rebbeck
, Regina G. Ziegler
, Sarah Nyante
, Elisa V. Bandera
, Sue A. Ingles
, Michael F. Press
, Edward A. Ruiz-Narvaez
, Sandra L. Deming
, Jorge L. Rodriguez-Gil
, Angela Demichele

Stephen J. Chanock, William Blot, Lisa Signorello, Qiuyin Cai, Guoliang Li, Jirong Long, Dezheng Huo, Yonglan Zheng, Nancy J. Cox, Olufunmilayo I. Olopade, Temidayo O. Ogundiran, Clement Adebamowo, Katherine L. Nathanson, Susan M. Domchek, Michael S. Simon, Anselm Hennis, Barbara Nemesure, Suh Yuh Wu, M. Cristina Leske, Stefan Ambs, Carolyn M. Hutter, Alicia Young, Charles Kooperberg, Ulrike Peters, Suhn K. Rhie, Peggy Wan, Xin Sheng, Loreall C. Pooler, David J. Van Den Berg, Loic Le Marchand, Laurence N. Kolonel, Brian E. Henderson, Christopher A. Haiman

Family , Population and Preventative Medicine

University of Southern California
University of North Carolina at Chapel Hill
Roswell Park Cancer Institute
Cancer Prevention Institute of California
Stanford University
City of Hope National Med Center
Vanderbilt University
Boston University
University of Miami
University of Pennsylvania
National Cancer Institute
Rutgers - The State University of New Jersey, New Brunswick
The University of Chicago
University of Ibadan
University of Maryland, Baltimore
Wayne State University
The University of the West Indies
Stony Brook University
National Institutes of Health
Fred Hutchinson Cancer Research Center
University of Hawai'i at Mānoa

Research output: Contribution to journal › Article › peer-review

71 Scopus citations

Abstract

Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10^-6 and 10^-5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10 ^-6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10 ^-5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.

Original language	English
Pages (from-to)	39-48
Number of pages	10
Journal	Human Genetics
Volume	132
Issue number	1
DOIs	https://doi.org/10.1007/s00439-012-1214-y
State	Published - Jan 2013

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Chen, F., Chen, G. K., Stram, D. O., Millikan, R. C., Ambrosone, C. B., John, E. M., Bernstein, L., Zheng, W., Palmer, J. R., Hu, J. J., Rebbeck, T. R., Ziegler, R. G., Nyante, S., Bandera, E. V., Ingles, S. A., Press, M. F., Ruiz-Narvaez, E. A., Deming, S. L., Rodriguez-Gil, J. L., ... Haiman, C. A. (2013). A genome-wide association study of breast cancer in women of African ancestry. Human Genetics, 132(1), 39-48. https://doi.org/10.1007/s00439-012-1214-y

@article{683ca9a869f542fb980a63cfdf4eb835,

title = "A genome-wide association study of breast cancer in women of African ancestry",

abstract = "Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10-6 and 10-5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 {\texttimes} 10 -6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 {\texttimes} 10 -5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.",

author = "Fang Chen and Chen, \{Gary K.\} and Stram, \{Daniel O.\} and Millikan, \{Robert C.\} and Ambrosone, \{Christine B.\} and John, \{Esther M.\} and Leslie Bernstein and Wei Zheng and Palmer, \{Julie R.\} and Hu, \{Jennifer J.\} and Rebbeck, \{Tim R.\} and Ziegler, \{Regina G.\} and Sarah Nyante and Bandera, \{Elisa V.\} and Ingles, \{Sue A.\} and Press, \{Michael F.\} and Ruiz-Narvaez, \{Edward A.\} and Deming, \{Sandra L.\} and Rodriguez-Gil, \{Jorge L.\} and Angela Demichele and Chanock, \{Stephen J.\} and William Blot and Lisa Signorello and Qiuyin Cai and Guoliang Li and Jirong Long and Dezheng Huo and Yonglan Zheng and Cox, \{Nancy J.\} and Olopade, \{Olufunmilayo I.\} and Ogundiran, \{Temidayo O.\} and Clement Adebamowo and Nathanson, \{Katherine L.\} and Domchek, \{Susan M.\} and Simon, \{Michael S.\} and Anselm Hennis and Barbara Nemesure and Wu, \{Suh Yuh\} and Leske, \{M. Cristina\} and Stefan Ambs and Hutter, \{Carolyn M.\} and Alicia Young and Charles Kooperberg and Ulrike Peters and Rhie, \{Suhn K.\} and Peggy Wan and Xin Sheng and Pooler, \{Loreall C.\} and \{Van Den Berg\}, \{David J.\} and \{Le Marchand\}, Loic and Kolonel, \{Laurence N.\} and Henderson, \{Brian E.\} and Haiman, \{Christopher A.\}",

year = "2013",

month = jan,

doi = "10.1007/s00439-012-1214-y",

language = "English",

volume = "132",

pages = "39--48",

journal = "Human Genetics",

issn = "0340-6717",

number = "1",

}

Chen, F, Chen, GK, Stram, DO, Millikan, RC, Ambrosone, CB, John, EM, Bernstein, L, Zheng, W, Palmer, JR, Hu, JJ, Rebbeck, TR, Ziegler, RG, Nyante, S, Bandera, EV, Ingles, SA, Press, MF, Ruiz-Narvaez, EA, Deming, SL, Rodriguez-Gil, JL, Demichele, A, Chanock, SJ, Blot, W, Signorello, L, Cai, Q, Li, G, Long, J, Huo, D, Zheng, Y, Cox, NJ, Olopade, OI, Ogundiran, TO, Adebamowo, C, Nathanson, KL, Domchek, SM, Simon, MS, Hennis, A, Nemesure, B, Wu, SY, Leske, MC, Ambs, S, Hutter, CM, Young, A, Kooperberg, C, Peters, U, Rhie, SK, Wan, P, Sheng, X, Pooler, LC, Van Den Berg, DJ, Le Marchand, L, Kolonel, LN, Henderson, BE & Haiman, CA 2013, 'A genome-wide association study of breast cancer in women of African ancestry', Human Genetics, vol. 132, no. 1, pp. 39-48. https://doi.org/10.1007/s00439-012-1214-y

TY - JOUR

T1 - A genome-wide association study of breast cancer in women of African ancestry

AU - Chen, Fang

AU - Chen, Gary K.

AU - Stram, Daniel O.

AU - Millikan, Robert C.

AU - Ambrosone, Christine B.

AU - John, Esther M.

AU - Bernstein, Leslie

AU - Zheng, Wei

AU - Palmer, Julie R.

AU - Hu, Jennifer J.

AU - Rebbeck, Tim R.

AU - Ziegler, Regina G.

AU - Nyante, Sarah

AU - Bandera, Elisa V.

AU - Ingles, Sue A.

AU - Press, Michael F.

AU - Ruiz-Narvaez, Edward A.

AU - Deming, Sandra L.

AU - Rodriguez-Gil, Jorge L.

AU - Demichele, Angela

AU - Chanock, Stephen J.

AU - Blot, William

AU - Signorello, Lisa

AU - Cai, Qiuyin

AU - Li, Guoliang

AU - Long, Jirong

AU - Huo, Dezheng

AU - Zheng, Yonglan

AU - Cox, Nancy J.

AU - Olopade, Olufunmilayo I.

AU - Ogundiran, Temidayo O.

AU - Adebamowo, Clement

AU - Nathanson, Katherine L.

AU - Domchek, Susan M.

AU - Simon, Michael S.

AU - Hennis, Anselm

AU - Nemesure, Barbara

AU - Wu, Suh Yuh

AU - Leske, M. Cristina

AU - Ambs, Stefan

AU - Hutter, Carolyn M.

AU - Young, Alicia

AU - Kooperberg, Charles

AU - Peters, Ulrike

AU - Rhie, Suhn K.

AU - Wan, Peggy

AU - Sheng, Xin

AU - Pooler, Loreall C.

AU - Van Den Berg, David J.

AU - Le Marchand, Loic

AU - Kolonel, Laurence N.

AU - Henderson, Brian E.

AU - Haiman, Christopher A.

PY - 2013/1

Y1 - 2013/1

N2 - Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10-6 and 10-5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10 -6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10 -5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.

AB - Genome-wide association studies (GWAS) in diverse populations are needed to reveal variants that are more common and/or limited to defined populations. We conducted a GWAS of breast cancer in women of African ancestry, with genotyping of >1,000,000 SNPs in 3,153 African American cases and 2,831 controls, and replication testing of the top 66 associations in an additional 3,607 breast cancer cases and 11,330 controls of African ancestry. Two of the 66 SNPs replicated (p < 0.05) in stage 2, which reached statistical significance levels of 10-6 and 10-5 in the stage 1 and 2 combined analysis (rs4322600 at chromosome 14q31: OR = 1.18, p = 4.3 × 10 -6; rs10510333 at chromosome 3p26: OR = 1.15, p = 1.5 × 10 -5). These suggestive risk loci have not been identified in previous GWAS in other populations and will need to be examined in additional samples. Identification of novel risk variants for breast cancer in women of African ancestry will demand testing of a substantially larger set of markers from stage 1 in a larger replication sample.

UR - https://www.scopus.com/pages/publications/84872329858

U2 - 10.1007/s00439-012-1214-y

DO - 10.1007/s00439-012-1214-y

M3 - Article

C2 - 22923054

AN - SCOPUS:84872329858

SN - 0340-6717

VL - 132

SP - 39

EP - 48

JO - Human Genetics

JF - Human Genetics

IS - 1

ER -

A genome-wide association study of breast cancer in women of African ancestry

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