Identification of a functional genetic variant at 16q12.1 for breast cancer risk: results from the Asia Breast Cancer Consortium.

• Main Authors: Jirong Long, Qiuyin Cai, Xiao-Ou Shu, Shimian Qu, Chun Li, Ying Zheng, Kai Gu, Wenjing Wang, Yong-Bing Xiang, Jiarong Cheng, Kexin Chen, Lina Zhang, Hong Zheng, Chen-Yang Shen, Chiun-Sheng Huang, Ming-Feng Hou, Hongbing Shen, Zhibin Hu, Furu Wang, Sandra L Deming, Mark C Kelley, Martha J Shrubsole, Ui Soon Khoo, Kelvin Y K Chan, Sum Yin Chan, Christopher A Haiman, Brian E Henderson, Loic Le Marchand, Motoki Iwasaki, Yoshio Kasuga, Shoichiro Tsugane, Keitaro Matsuo, Kazuo Tajima, Hiroji Iwata, Bo Huang, Jiajun Shi, Guoliang Li, Wanqing Wen, Yu-Tang Gao, Wei Lu, Wei Zheng
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2010-06-01
• Series: PLoS Genetics
• Online Access: http://europepmc.org/articles/PMC2891809?pdf=render

Genetic factors play an important role in the etiology of breast cancer. We carried out a multi-stage genome-wide association (GWA) study in over 28,000 cases and controls recruited from 12 studies conducted in Asian and European American women to identify genetic susceptibility loci for breast cancer. After analyzing 684,457 SNPs in 2,073 cases and 2,084 controls in Chinese women, we evaluated 53 SNPs for fast-track replication in an independent set of 4,425 cases and 1,915 controls of Chinese origin. Four replicated SNPs were further investigated in an independent set of 6,173 cases and 6,340 controls from seven other studies conducted in Asian women. SNP rs4784227 was consistently associated with breast cancer risk across all studies with adjusted odds ratios (95% confidence intervals) of 1.25 (1.20-1.31) per allele (P = 3.2 x 10(-25)) in the pooled analysis of samples from all Asian samples. This SNP was also associated with breast cancer risk among European Americans (per allele OR = 1.19, 95% CI = 1.09-1.31, P = 1.3 x 10(-4), 2,797 cases and 2,662 controls). SNP rs4784227 is located at 16q12.1, a region identified previously for breast cancer risk among Europeans. The association of this SNP with breast cancer risk remained highly statistically significant in Asians after adjusting for previously-reported SNPs in this region. In vitro experiments using both luciferase reporter and electrophoretic mobility shift assays demonstrated functional significance of this SNP. These results provide strong evidence implicating rs4784227 as a functional causal variant for breast cancer in the locus 16q12.1 and demonstrate the utility of conducting genetic association studies in populations with different genetic architectures.