Genome-wide association study in Chinese men identifies two new prostate cancer risk loci at 9q31.2 and 19q13.4

Abstract

Prostate cancer risk–associated variants have been reported in populations of European descent, African-Americans and Japanese using genome-wide association studies (GWAS). To systematically investigate prostate cancer risk–associated variants in Chinese men, we performed the first GWAS in Han Chinese. In addition to confirming several associations reported in other ancestry groups, this study identified two new risk-associated loci for prostate cancer on chromosomes 9q31.2 (rs817826, P = 5.45 × 10−14) and 19q13.4 (rs103294, P = 5.34 × 10−16) in 4,484 prostate cancer cases and 8,934 controls. The rs103294 marker at 19q13.4 is in strong linkage equilibrium with a 6.7-kb germline deletion that removes the first six of seven exons in LILRA3, a gene regulating inflammatory response, and was significantly associated with the mRNA expression of LILRA3 in T cells (P < 1 × 10−4). These findings may advance the understanding of genetic susceptibility to prostate cancer.

Genome-Wide Association Study of Bladder Cancer in a Chinese Cohort Reveals a New Susceptibility Locus at 5q12.3

“…In the GWAS stage, 599 bladder cancer cases were recruited from Nanjing (China) starting in May 2003, and 1,008 controls were collected from four districts and counties in Shanghai beginning in April 2010. The GWAS control subjects were shared with ChinaPCa (21). Replication 1 included 1,156 cases and 1,273 controls collected from Nanjing.…”

Prostate cancer research in China

“…5 This is the first confirmation of the unique characteristics of Chinese PCa in a large population. A total of 4484 PCa patients and 8934 healthy controls were involved in the study, and two new loci, 9q31.2 and 19q13.4, were found to be significantly associated with PCa risk.…”

Validation of the novel susceptibility loci for prostate cancer in a Chinese population

“…A total of 2,425 subjects including 1,417 patients with PCa and 1,008 controls were recruited in the present study. All patients were part of the China PCa consortium from the southeast of China (11)(12)(13) recruited during January 2010 and December 2011, from which data were obtained. All cases were pathologically diagnosed with primary PCa and all the controls were recruited from the community or selected from subjects who had undergone routine physical examination in local hospitals.…”

“…A posterior probability of >0.9 was applied to call imputed genotypes. Imputed SNPs were excluded if they exhibited: i) A call rate <95%; ii) a minor allele frequency <0.05; or iii) P<1x10 -3 in a Hardy-Weinberg equilibrium test in controls, as previously described (13).…”