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Genome-wide association analysis in East Asians identifies breast cancer susceptibility loci at 1q32.1, 5q14.3 and 15q26.1

Nature Genetics volume 46, pages 886–890 (2014)Cite this article

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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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Figure 1: Forest plots for risk variants in the three newly identified breast cancer risk loci by study site and stage.
Figure 2: Regional plots of association results for the three newly identified risk loci for 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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Author notes

  1. qiuyin.cai@vanderbilt.edu

Authors and Affiliations

  1. Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Qiuyin Cai, Ben Zhang, Jiajun Shi, Jirong Long, Wanqing Wen, Ryan J Delahanty, Yanfeng Zhang, Xiao-Ou Shu & Wei Zheng

  2. Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea

    Hyuna Sung, Ji-Yeob Choi, Sue K Park & Daehee Kang

  3. Division of Epidemiology and Genetics, Genetic Epidemiology Branch, National Cancer Institute, Rockville, Maryland, USA

    Hyuna Sung

  4. Laboratory for Statistical Analysis, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan

    Siew-Kee Low & Atsushi Takahashi

  5. Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, South Korea

    Sun-Seog Kweon & Min-Ho Shin

  6. Jeonnam Regional Cancer Center, Chonnam National University Hwasun Hospital, Hwasun, South Korea

    Sun-Seog Kweon

  7. Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China

    Wei Lu & Ying Zheng

  8. Cancer Research Institute, Seoul National University College of Medicine, Seoul, South Korea

    Ji-Yeob Choi, Dong-Young Noh, Sue K Park & Daehee Kang

  9. Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea

    Dong-Young Noh

  10. Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

    Chen-Yang Shen, Pei-Ei Wu & Chia-Ni Hsiung

  11. Taiwan Biobank, Academia Sinica, Taipei, Taiwan

    Chen-Yang Shen, Pei-Ei Wu & Chia-Ni Hsiung

  12. Department of Public Health, College of Public Health, China Medical University, Taichung, Taiwan

    Chen-Yang Shen

  13. Department of Preventive Medicine, Kyushu University Faculty of Medical Sciences, Fukuoka, Japan

    Keitaro Matsuo

  14. Cancer Research Initiatives Foundation, Sime Darby Medical Centre, Subang Jaya, Malaysia

    Soo-Hwang Teo, Peter Kang & Shivaani Mariapun

  15. University Malaya Cancer Research Institute, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia

    Soo-Hwang Teo & Shivaani Mariapun

  16. Division of Cancer Epidemiology and Management, National Cancer Center, Gyeonggi-do, South Korea

    Mi Kyung Kim

  17. Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China

    Ui Soon Khoo, Kelvin Y K Chan & Ellen P S Man

  18. Epidemiology Division, Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan

    Motoki Iwasaki

  19. Saw Swee Hock School of Public Health, National University of Singapore, Singapore

    Mikael Hartman & Hui Miao

  20. Department of Surgery, National University of Singapore, Singapore

    Mikael Hartman & Hui Miao

  21. Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden

    Mikael Hartman

  22. Laboratory for Genotyping Development, Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan

    Kyota Ashikawa & Michiaki Kubo

  23. Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan

    Koichi Matsuda

  24. Department of Surgery, Chonnam National University Medical School, Gwangju, South Korea

    Min Ho Park

  25. Department of Epidemiology, Shanghai Cancer Institute, Shanghai, China

    Yong-Bing Xiang & Yu-Tang Gao

  26. Division of Cancer Epidemiology and Genetics, US Department of Health and Human Services, National Cancer Institute, US National Institutes of Health, Bethesda, Maryland, USA

    Bu-Tian Ji

  27. Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, South Korea

    Sue K Park & Daehee Kang

  28. Division of Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan

    Hidemi Ito

  29. Department of Surgery, Nagano Matsushiro General Hospital, Nagano, Japan

    Yoshio Kasuga

  30. Department of Surgery, College of Medicine, University of Ulsan, Asan Medical Center, Seoul, South Korea

    Sei Hyun Ahn

  31. Center for Breast Cancer, National Cancer Center, Gyeonggi-do, South Korea

    Han Sung Kang

  32. Department of Obstetrics and Gynaecology, Queen Mary Hospital, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong, China

    Kelvin Y K Chan

  33. Department of Breast Oncology, Aichi Cancer Center Central Hospital, Nagoya, Japan

    Hiroji Iwata

  34. Research Center for Cancer Prevention and Screening, National Cancer Center, Tokyo, Japan

    Shoichiro Tsugane

  35. Singapore Eye Research Institute, Singapore

    Jiemin Liao

  36. Department of Ophthalmology, National University of Singapore and National University Health System, Singapore

    Jiemin Liao

  37. Department of Medicine, University of Chicago, Chicago, Illinois, USA

    Yusuke Nakamura

  38. Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Bingshan Li

  39. Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA

    Chun Li

Authors
  1. Qiuyin Cai
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  2. Ben Zhang
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Consortia

DRIVE GAME-ON Consortium

Contributions

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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The authors declare no competing financial interests.

Additional information

A full list of members and affiliations appears in the Supplementary Note.

Integrated supplementary information

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.

Supplementary information

Supplementary Text and Figures

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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