Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation.

ABSTRACT: The identification of true causal loci to unravel the statistical evidence of genotype-phenotype correlations and the biological relevance of selected single-nucleotide polymorphisms (SNPs) is a challenging issue in genome-wide association studies (GWAS). Here, we introduced a novel method for the prioritization of SNPs based on p-values from GWAS. The method uses functional evidence from populations, including phenotype-associated gene expressions. Based on the concept of genetic interactions, such as perturbation of gene expression by genetic variation, phenotype and gene expression related SNPs were prioritized by adjusting the p-values of SNPs. We applied our method to GWAS data related to drug-induced cytotoxicity. Then, we prioritized loci that potentially play a role in druginduced

SUBMITTER: Paik H 

PROVIDER: S-EPMC3887803 | biostudies-literature | 2012 Apr

REPOSITORIES: biostudies-literature