Cancer Characterizing Genetic Susceptibility to Breast ...cebp.· Characterizing Genetic...
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Characterizing Genetic Susceptibility to BreastCancer in Women of African AncestryYe Feng1, Suhn Kyong Rhie1, Dezheng Huo2, Edward A. Ruiz-Narvaez3,Stephen A. Haddad3, Christine B. Ambrosone4, Esther M. John5,6, Leslie Bernstein7,Wei Zheng8, Jennifer J. Hu9, Regina G. Ziegler10, Sarah Nyante11, Elisa V. Bandera12,Sue A. Ingles1, Michael F. Press13, Sandra L. Deming8, Jorge L. Rodriguez-Gil9,Yonglan Zheng14, Song Yao15, Yoo-Jeong Han14, Temidayo O. Ogundiran16,Timothy R. Rebbeck17, Clement Adebamowo18,OladosuOjengbede19, AdeyinkaG. Falusi20,Anselm Hennis21,22, Barbara Nemesure22, Stefan Ambs23,William Blot8, Qiuyin Cai8,Lisa Signorello24, Katherine L. Nathanson25, Kathryn L. Lunetta26,Lara E. Sucheston-Campbell15, Jeannette T. Bensen11, Stephen J. Chanock10,Loic Le Marchand27, Andrew F. Olshan11, Laurence N. Kolonel27, David V. Conti1,Gerhard A. Coetzee1, Daniel O. Stram1, Olufunmilayo I. Olopade14, Julie R. Palmer3, andChristopher A. Haiman1
Background:Genome-wide association studies have identifiedapproximately 100 common genetic variants associated withbreast cancer risk, the majority of which were discovered inwomen of European ancestry. Because of different patterns oflinkage disequilibrium, many of these genetic markers may notrepresent signals in populations of African ancestry.
Methods: We tested 74 breast cancer risk variants and con-ducted fine-mapping of these susceptibility regions in 6,522breast cancer cases and 7,643 controls of African ancestry fromthree genetic consortia (AABC, AMBER, and ROOT).
Results: Fifty-four of the 74 variants (73%) were found tohave ORs that were directionally consistent with those previ-ously reported, of which 12 were nominally statistically signif-icant (P < 0.05). Through fine-mapping, in six regions (3p24,
12p11, 14q13, 16q12/FTO, 16q23, 19p13), we observed sevenmarkers that better represent the underlying risk variant foroverall breast cancer or breast cancer subtypes, whereas inanother two regions (11q13, 16q12/TOX3), we identified sug-gestive evidence of signals that are independent of the reportedindex variant. Overlapping chromatin features and regulatoryelements suggest that many of the risk alleles lie in regions withbiological functionality.
Conclusions: Through fine-mapping of known susceptibilityregions, we have revealed alleles that better characterize breastcancer risk in women of African ancestry.
Impact: The risk alleles identified represent genetic markers formodeling and stratifying breast cancer risk in women of Africanancestry. Cancer Epidemiol Biomarkers Prev; 26(7); 101626.2017 AACR.
1Department of Preventive Medicine, Keck School of Medicine and Norris Compre-hensive Cancer Center, University of Southern California, Los Angeles, California.2Department of Public Health Sciences, University of Chicago, Chicago, Illinois.3Slone Epidemiology Center at BostonUniversity, Boston, Massachusetts. 4Depart-ment ofCancer Prevention andControl, Roswell Park Cancer Institute, Buffalo, NewYork. 5CancerPrevention Institute of California, Fremont, California. 6Department ofHealth Research and Policy (Epidemiology) and Stanford Cancer Institute, StanfordUniversity School of Medicine, Stanford, California. 7Division of Cancer Etiology,Department of Population Sciences, Beckman Research Institute, City of Hope,Duarte, California. 8Division of Epidemiology, Department of Medicine, VanderbiltEpidemiology Center, and Vanderbilt-Ingram Cancer Center, Vanderbilt UniversitySchool of Medicine, Nashville, Tennessee. 9Sylvester Comprehensive Cancer Centerand Department of Epidemiology and Public Health, University of Miami MillerSchool of Medicine, Miami, Florida. 10Epidemiology and Biostatistics Program,Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda,Maryland. 11Departmentof Epidemiology,Gillings SchoolofGlobal PublicHealth andLineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill,North Carolina. 12Rutgers Cancer Institute of New Jersey, New Brunswick, NewJersey. 13Department of Pathology, Keck School of Medicine and Norris Compre-hensive Cancer Center, University of Southern California, Los Angeles, California.14Department of Medicine, University of Chicago, Chicago, Illinois. 15Roswell ParkCancer Institute, Buffalo, New York. 16Department of Surgery, College of Medicine,University of Ibadan, Ibadan, Nigeria. 17Dana Farber Cancer Institute & Harvard T. H.Chan School of Public Health, Boston, Maryland. 18Department of Epidemiology &Preventive Medicine, University of Maryland, Baltimore, Maryland. 19Center forPopulation and Reproductive Health, College of Medicine, University of Ibadan,
Ibadan, Nigeria. 20Institute for Medical Research and Training, College of Medicine,University of Ibadan, Ibadan, Nigeria. 21Chronic Disease Research Centre, TropicalMedicine Research Institute, University of the West Indies, Bridgetown, Barbados.22Department of PreventiveMedicine, State University of NewYork at Stony Brook,Stony Brook, New York. 23Laboratory of Human Carcinogenesis, National CancerInstitute, Bethesda, Maryland. 24Cancer Prevention Fellowship Program, NationalCancer Institute, Bethesda, Maryland. 25Department of Medicine, University ofPennsylvania, Philadelphia, Pennsylvania. 26Department of Biostatistics, BostonUniversity School of Public Health, Boston, Massachusetts. 27Epidemiology Pro-gram, University of Hawaii Cancer Center, Honolulu, Hawaii.
Note: Supplementary data for this article are available at Cancer Epidemiology,Biomarkers & Prevention Online (http://cebp.aacrjournals.org/).
Y. Feng and S.K. Rhie contributed equally to this article.
Y. Feng and S.K. Rhie are the co-first authors of this article.
Current address for L.E. Sucheston-Campbell: The Ohio State University, Colum-bus, OH; and current address for G.A. Coetzee: Van Andel Research Institute,Grand Rapids, MI.
Corresponding Authors: Christopher A. Haiman, 1450 Biggy Street, LosAngeles, CA, 90033. Phone: 323-442-7755; Fax: 323-442-7749; E-mail:firstname.lastname@example.org; and Ye Feng, 1441 Eastlake Ave. Los Angeles, CA, 90033.Phone: 609-252-6198; E-mail: email@example.com
2017 American Association for Cancer Research.
Cancer Epidemiol Biomarkers Prev; 26(7) July 20171016
on July 8, 2018. 2017 American Association for Cancer Research. cebp.aacrjournals.org Downloaded from
Published OnlineFirst April 4, 2017; DOI: 10.1158/1055-9965.EPI-16-0567
IntroductionGenome-wide association (GWAS) and large-scale fine-
mapping studies have led to the identification of >100 breastcancer susceptibility loci that are estimated to explain approx-imately 20% of the 2-fold familial risk of breast cancer inwomen of European descendant (113). For populations ofAfrican ancestry, where the span of linkage disequilibrium (LD)has been shortened by recombination events (more genera-tions), a weaker correlation between an "index" marker (fromGWAS in Asian and European ancestry populations) and bio-logically relevant risk variants is expected. As a consequence,the index marker might not accurately capture the risk associ-ated with the biologically functional variant in African ancestrypopulations. Comprehensive testing in a large African ancestrysample is needed to identify a set of markers that better capturerisk associated with the functional allele at known risk regions,which is an important prerequisite for constructing genetic riskmodels for this population. Previous fine-mapping investiga-tions in women of African ancestry have been limited in size,with the largest study including 3,016 breast cancer cases and2,745 controls and having 80% power to detect reported effectsizes for only 10 of 72 variants examined (115).
To obtain greater statistical power for fine-mapping of knownbreast cancer susceptibility regions, we combined genotype andimputed data for 6,522 breast cancer cases and 7,643 controlsfrom three large consortia of African ancestry breast cancertheAfrican American Breast Cancer GWAS Consortium (AABC;ref. 16), the African American Breast Cancer Epidemiology andRisk Consortium (AMBER; refs. 17, 18), and the Genome-WideAssociation Study of Breast Cancer in the African Diaspora Con-sortium (ROOT; ref. 19). In addition to testing the reported indexvariants from previous GWAS, we conducted association analysesand functional annotation across each region in search ofmarkersthat might best define breast cancer risk in women of Africanancestry.
Materials and MethodsStudies
The genetic data included in this analysis were from threeconsortia of breast cancer in women of African ancestry (AABC,AMBER, and ROOT). For this analysis, the African AmericanBreast Cancer Consortium (AABC) included seven epidemiologicstudies: TheMultiethnic Cohort study (MEC), 734/1,003; The LosAngeles component of The Women's Contraceptive and Repro-ductive Experiences (CARE) Study, 380/224; The San FranciscoBay Area Breast Cancer Study (SFBCS), 172/23; The NorthernCalifornia site of the Breast Cancer Family Registry (NC-BCFR),440/53; The Prostate, Lung, Colorectal, and Ovarian CancerScreening Trial (PLCO) Cohort, 64/133; The Nashville BreastHealth Study (NBHS), 310/186; and The Wake Forest UniversityBreast Cancer Study (WFBC), 125/153). The current analysisincludes GWAS data for 2,225 invasive cases and 1,983 controlsfrom AABC (14). Although the Women's Circle of Health Study(WCHS) and The Carolina Breast Cancer Study (CBCS) partici-pated in AABC, samples from those studies are included as part ofthe AMBER consortium described below.
The AMBER consortium (18) in