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Research Article

A large-scale, exome-wide association study of Han Chinese women identifies three novel loci predisposing to breast cancer

Bo Zhang, Men-Yun Chen, Yu-Jun Sheng, Xian-Bo Zhuo, Ping Gao, Fu-Sheng Zhou, Bo Liang, Jun Zu, Qin Zhang, Sufyan Suleman, Yi-Hui Xu, Min-Gui Xu, Jin-Kai Xu, Chen-Cheng Liu, Nikolaos Giannareas, Ji-Han Xia, Yuan Zhao, Zhong-Lian Huang, Zhen Yang, Huaidong Cheng, Na Li, Yan-Yan Hong, Wei Li, Min-Jun Zhang, Ke-Da Yu, Guoliang Li, Meng-Hong Sun, Zhen-Dong Chen, Gong-Hong Wei and Zhi-Ming Shao
Bo Zhang
Department of Oncology at No.2 Hospital, Anhui Medical University, Institute of Oncology
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  • For correspondence: alvinbo@163.com
Men-Yun Chen
Anhui Medical University
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Yu-Jun Sheng
Department of Dermatology, Anhui Medical University
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Xian-Bo Zhuo
Anhui Medical University
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Ping Gao
Faculty of Biochemistry and Molecular Medicine, University of Oulu
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Fu-Sheng Zhou
Key Laboratory of Gene Resource Utilization for Genetic Diseases of Ministry of Education, Anhui Medical University
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Bo Liang
Anhui Medical University
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Jun Zu
Anhui Medical University
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Qin Zhang
Faculty of Biochemistry and Molecular Medicine, University of Oulu
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Sufyan Suleman
Faculty of biochemistry and molecular medicine, University of Oulu
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  • ORCID record for Sufyan Suleman
Yi-Hui Xu
Anhui Medical University
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Min-Gui Xu
Anhui Medical University
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Jin-Kai Xu
Anhui Medical University
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Chen-Cheng Liu
Anhui Medical University
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Nikolaos Giannareas
University of Oulu
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Ji-Han Xia
University of Oulu
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Yuan Zhao
Anhui Medical University, State Key Laboratory Incubation Base of Dermatology
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Zhong-Lian Huang
Institute of Oncology
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Zhen Yang
oncology, Anhui Medical University
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Huaidong Cheng
Department of Oncology at No.2 Hospital, Anhui Medical University, Institute of Oncology
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Na Li
Anhui Medical University
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Yan-Yan Hong
oncology department, Anhui Medical University
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Wei Li
The department of oncology, Anhui Medical University
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Min-Jun Zhang
Department of Oncology at No.2 Hospital, Anhui Medical University, Institute of Oncology
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Ke-Da Yu
Department of Breast Surgery, Fudan University
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Guoliang Li
Bio-Medical Center, College of Informatics, Huazhong Agricultural University
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Meng-Hong Sun
Fudan University Shanghai Cancer Center
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Zhen-Dong Chen
The First Affiliated Hospital of Anhui Medical Unviersity, Dept. of Oncology
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Gong-Hong Wei
Biocenter Oulu, University
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Zhi-Ming Shao
Department of Breast Surgery, Breast Cancer Institution, Cancer Hospital,Fudan University
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DOI: 10.1158/0008-5472.CAN-17-1721
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Abstract

Genome-wide association studies have identified more than 90 susceptibility loci for breast cancer. However, the missing heritability is evident, and the contributions of coding variants to breast cancer susceptibility have not yet been systematically evaluated. Here we present a large-scale whole-exome association study for breast cancer consisting of 24,162 individuals (10,055 cases and 14,107 controls). In addition to replicating known susceptibility loci (e.g. ESR1, FGFR2 and TOX3), we identify two novel missense variants in C21orf58 (rs13047478, Pmeta = 4.52 × 10-8) and ZNF526 (rs3810151, Pmeta = 7.60 × 10-9) and one new non-coding variant at 7q21.11 (P < 5 × 10-8). C21orf58 and ZNF526 possessed functional roles in the control of breast cancer cell growth, and the two coding variants were found to be the eQTL for several nearby genes. rs13047478 was significantly (P < 5.00 x 10-8) associated with the expression of genes MCM3AP and YBEY in breast mammary tissues. rs3810151 was found to be significantly associated with the expression of genes PAFAH1B3 (P = 8.39 x 10-8) and CNFN (P = 3.77 x 10-4) in human blood samples. C21orf58 and ZNF526, together with these eQTL genes, were differentially expressed in breast tumors versus normal breast. Our study reveals additional loci and novel genes for genetic predisposition to breast cancer and highlights a polygenic basis of disease development.

  • Received June 14, 2017.
  • Revision received October 25, 2017.
  • Accepted March 20, 2018.
  • Copyright ©2018, American Association for Cancer Research.
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Published OnlineFirst March 23, 2018
doi: 10.1158/0008-5472.CAN-17-1721

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A large-scale, exome-wide association study of Han Chinese women identifies three novel loci predisposing to breast cancer
Bo Zhang, Men-Yun Chen, Yu-Jun Sheng, Xian-Bo Zhuo, Ping Gao, Fu-Sheng Zhou, Bo Liang, Jun Zu, Qin Zhang, Sufyan Suleman, Yi-Hui Xu, Min-Gui Xu, Jin-Kai Xu, Chen-Cheng Liu, Nikolaos Giannareas, Ji-Han Xia, Yuan Zhao, Zhong-Lian Huang, Zhen Yang, Huaidong Cheng, Na Li, Yan-Yan Hong, Wei Li, Min-Jun Zhang, Ke-Da Yu, Guoliang Li, Meng-Hong Sun, Zhen-Dong Chen, Gong-Hong Wei and Zhi-Ming Shao
Cancer Res March 23 2018 DOI: 10.1158/0008-5472.CAN-17-1721

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A large-scale, exome-wide association study of Han Chinese women identifies three novel loci predisposing to breast cancer
Bo Zhang, Men-Yun Chen, Yu-Jun Sheng, Xian-Bo Zhuo, Ping Gao, Fu-Sheng Zhou, Bo Liang, Jun Zu, Qin Zhang, Sufyan Suleman, Yi-Hui Xu, Min-Gui Xu, Jin-Kai Xu, Chen-Cheng Liu, Nikolaos Giannareas, Ji-Han Xia, Yuan Zhao, Zhong-Lian Huang, Zhen Yang, Huaidong Cheng, Na Li, Yan-Yan Hong, Wei Li, Min-Jun Zhang, Ke-Da Yu, Guoliang Li, Meng-Hong Sun, Zhen-Dong Chen, Gong-Hong Wei and Zhi-Ming Shao
Cancer Res March 23 2018 DOI: 10.1158/0008-5472.CAN-17-1721
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