The chromosome 2p21 region harbors a complex genetic architecture for association with risk for renal cell carcinoma

Hum Mol Genet. 2012 Mar 1;21(5):1190-200. doi: 10.1093/hmg/ddr551. Epub 2011 Nov 23.

Abstract

In follow-up of a recent genome-wide association study (GWAS) that identified a locus in chromosome 2p21 associated with risk for renal cell carcinoma (RCC), we conducted a fine mapping analysis of a 120 kb region that includes EPAS1. We genotyped 59 tagged common single-nucleotide polymorphisms (SNPs) in 2278 RCC and 3719 controls of European background and observed a novel signal for rs9679290 [P = 5.75 × 10(-8), per-allele odds ratio (OR) = 1.27, 95% confidence interval (CI): 1.17-1.39]. Imputation of common SNPs surrounding rs9679290 using HapMap 3 and 1000 Genomes data yielded two additional signals, rs4953346 (P = 4.09 × 10(-14)) and rs12617313 (P = 7.48 × 10(-12)), both highly correlated with rs9679290 (r(2) > 0.95), but interestingly not correlated with the two SNPs reported in the GWAS: rs11894252 and rs7579899 (r(2) < 0.1 with rs9679290). Genotype analysis of rs12617313 confirmed an association with RCC risk (P = 1.72 × 10(-9), per-allele OR = 1.28, 95% CI: 1.18-1.39) In conclusion, we report that chromosome 2p21 harbors a complex genetic architecture for common RCC risk variants.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Basic Helix-Loop-Helix Transcription Factors / genetics*
  • Carcinoma, Renal Cell / genetics*
  • Case-Control Studies
  • Chromosome Mapping
  • Chromosomes, Human, Pair 2 / genetics*
  • Female
  • Genetic Predisposition to Disease*
  • Genotype
  • HapMap Project
  • Haplotypes
  • Humans
  • Kidney Neoplasms / genetics*
  • Male
  • Polymorphism, Single Nucleotide*
  • Smoking

Substances

  • Basic Helix-Loop-Helix Transcription Factors
  • endothelial PAS domain-containing protein 1