Associating disease-related genetic variants in intergenic regions to the genes they impact.

ABSTRACT: We present a method to assist in interpretation of the functional impact of intergenic disease-associated SNPs that is not limited to search strategies proximal to the SNP. The method builds on two sources of external knowledge: the growing understanding of three-dimensional spatial relationships in the genome, and the substantial repository of information about relationships among genetic variants, genes, and diseases captured in the published biomedical literature. We integrate chromatin conformation capture data (HiC) with literature support to rank putative target genes of intergenic disease-associated SNPs. We demonstrate that this hybrid method outperforms a genomic distance baseline on a small test set of expression quantitative trait loci, as well as either method individually. In

SUBMITTER: Macintyre G 

PROVIDER: S-EPMC4217187 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature