SNP2GO: Functional Analysis of Genome-Wide Association Studies
David Szkiba, Martin Kapun, Arndt von Haeseler, Miguel Gallach

Abstract

Genome-wide association studies (GWAS) are designed to identify the portion of single-nucleotide polymorphisms (SNPs) in genome sequences associated with a complex trait. Strategies based on the gene list enrichment concept are currently applied for the functional analysis of GWAS, according to which a significant overrepresentation of candidate genes associated with a biological pathway is used as a proxy to infer overrepresentation of candidate SNPs in the pathway. Here we show that such inference is not always valid and introduce the program SNP2GO, which implements a new method to properly test for the overrepresentation of candidate SNPs in biological pathways.

  • Received December 2, 2013.
  • Accepted February 19, 2014.
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