Abstract
In a three-stage genome-wide association study among East Asian women including 22,780 cases and 24,181 controls, we identified 3 genetic loci newly associated with breast cancer risk, including rs4951011 at 1q32.1 (in intron 2 of the ZC3H11A gene; P = 8.82 × 10−9), rs10474352 at 5q14.3 (near the ARRDC3 gene; P = 1.67 × 10−9) and rs2290203 at 15q26.1 (in intron 14 of the PRC1 gene; P = 4.25 × 10−8). We replicated these associations in 16,003 cases and 41,335 controls of European ancestry (P = 0.030, 0.004 and 0.010, respectively). Data from the ENCODE Project suggest that variants rs4951011 and rs10474352 might be located in an enhancer region and transcription factor binding sites, respectively. This study provides additional insights into the genetics and biology of breast cancer.
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Acknowledgements
The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of the funding agencies. The authors wish to thank the study participants and research staff for their contributions and commitment to this project. We thank R. Courtney, J. Wu, J. He, H. Cai, X. Guo, B. Rammer and K. Kreth for their help with sample preparation and genotyping, statistical and bioinformatics analyses for the project, and editing and preparation of the manuscript at Vanderbilt.
This research was supported in part by US National Institutes of Health grants R01CA124558, R01CA148667 and R37CA070867 (to W.Z.); R01CA118229, R01CA092585 and R01CA064277 (to X.-O.S.); R01CA122756 (to Q.C.); and R01CA137013 (to J. Long), US Department of Defense Idea Awards BC011118 (to X.-O.S.) and BC050791 (to Q.C.), and Ingram Professorship and Research Reward funds (to W.Z.). Sample preparation and genotyping assays at Vanderbilt were conducted at the Survey and Biospecimen Shared Resources and the Vanderbilt Microarray Shared Resource, which are supported in part by the Vanderbilt-Ingram Cancer Center (P30CA068485). SeBCS was supported by the BRL (Basic Research Laboratory) program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (2011-0001564). KOHBRA/KOGES was supported by a grant from the National R&D Program for Cancer Control, Ministry for Health, Welfare and Family Affairs, Republic of Korea (1020350).
Studies participating in the ABCC include (principal investigator, grant support) the Shanghai Breast Cancer Study (W.Z. and X.-O.S., R01CA064277), the Shanghai Women's Health Study (W.Z., R37CA070867), the Shanghai Breast Cancer Survival Study (X.-O.S., R01CA118229), the Shanghai Endometrial Cancer Study (X.-O.S., R01CA092585, controls only), the Seoul Breast Cancer Study (D.K., BRL program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology (2012-0000347)), the BioBank Japan Project (S.-K.L., the Ministry of Education, Culture, Sports, Science and Technology of Japan), the Hwasun Cancer Epidemiology Study-Breast (S.-S.K., the National R&D Program for Cancer Control, Ministry of Health and Welfare, Republic of Korea, 1020010), the Taiwan Study (C.-Y.S., Institute of Biomedical Sciences, Academia Sinica, Taiwan and National Science Council, DOH97-01), the Hong Kong Study (U.S.K., Research Grant Council, Hong Kong, China, HKU 7520/05M and 76730M), the Korean-NCC Study (M.K.K., grant-in-aid from the Korea National Cancer Center, NCC-0910310), the Nagano Breast Cancer Study (S.T., Grants-in-Aid for the Third-Term Comprehensive Ten-Year Strategy for Cancer Control from the Ministry of Health, Labor and Welfare of Japan, for Scientific Research on Priority Areas, 17015049 and for Scientific Research on Innovative Areas, 221S0001, from the Ministry of Education, Culture, Sports, Science and Technology of Japan), the Hospital-Based Epidemiologic Research Program at the Aichi Cancer Center (K. Tajima, Grant-in-Aid for Scientific Research (C) (24590776) and Grant-in-Aid for Scientific Research on Priority Areas of Cancer (17015018) and Scientific Research on Innovative Areas (221S0001) from the Ministry of Education, Culture, Sports, Science and Technology of Japan), the Malaysian Breast Cancer Genetic Study (S.-H.T., the Malaysian Ministry of Science, Technology and Innovation, Malaysian Ministry of Higher Education (UM.C/HlR/MOHE/06) and the Cancer Research Initiatives Foundation; controls were recruited by the Malaysian More than a Mammo Programme, which was supported by a grant from Yayasan Sime Darby LPGA) and the Singapore Breast Cancer Study (M.H., National Medical Research Council Start-Up Grant and Centre Grant (NMRC/CG/NCIS/2010); additional controls were recruited by the Singapore Consortium of Cohort Studies–Multi-Ethnic Cohort (SCCS-MEC), which was funded by the Biomedical Research Council, grant 05/1/21/19/425). The DRIVE GAME-ON Consortium is funded by US NIH grant U19CA148065 (D. Hunter). We thank I. Soong, A. Chan and T.Y. Leung for their assistance in facilitating recruitment of the breast cancer cases included in the Hong Kong Study.
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W.Z. conceived and directed the Asia Breast Cancer Consortium (ABCC) and the Shanghai Breast Cancer Genetics Study. Q.C. and W.Z. wrote the manuscript with significant contributions from B.Z., J.S., J. Long, R.J.D., B.L. and X.-O.S. Q.C., B.Z., J. Long and W.W. coordinated the project. Q.C. directed the laboratory operations. J.S. performed the genotyping experiments. B.Z., J. Long and W.W. managed the study data. B.Z., J. Long and W.W. performed the statistical analyses with significant contributions from B.L. and C.L. Q.C., J. Long, R.J.D., Y. Zhang and B.L. performed the bioinformatics analyses. H.S., S.-K.L., S.-S.K., W.L., J.-Y.C., D.-Y.N., C.-Y.S., K. Matsuo, S.-H.T., M.K.K., U.S.K., M.I., M.H., A.T., K.A., K. Matsuda, M.-H.S., M.H.P., Y. Zheng, Y.-B.X., B.-T.J., S.K.P., P.-E.W., C.-N.H., H. Ito, Y.K., P.K., S.M., S.H.A., H.S.K., K.Y.K.C., E.P.S.M., H. Iwata, S.T., H.M., J. Liao, Y.N., M.K., Y.-T.G., X.-O.S., D.K. and W.Z. contributed to the collection of the data and biological samples for the original studies. All authors have reviewed and approved the final manuscript.
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Supplementary Figure 1 Quantile-quantile plot of P values in –log10 scale among stage 1 samples.
(a) Chinese GWAS (SBCGS-1). (b) Korean GWAS (SeBCS1).
Supplementary Figure 2 Association of rs2290203 (15q26.1) with RCCD1 gene expression.
Data from 458 tumor tissues and 66 adjacent normal tissue samples included in TCGA. (a) Tumor tissues. (b) Adjacent normal tissues.
Supplementary Figure 3 Regional plots of cis-eQTL association results for rs2290203 (15q26.1) with the RCCD1 gene in breast cancer tissue included in TCGA.
(a) Tumor tissue. (b) Adjacent normal tissue. The LDs among SNPs located within 500 kb of rs2290203 were calculated based on European-ancestry population data from the 1000 Genomes Project.
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Supplementary Figures 1–3, Supplementary Tables 1–8 and Supplementary Note. (PDF 1647 kb)
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Cai, Q., Zhang, B., Sung, H. et al. Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1. Nat Genet 46, 886–890 (2014). https://doi.org/10.1038/ng.3041
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DOI: https://doi.org/10.1038/ng.3041
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