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SNP2GO: functional analysis of genome-wide association studies.

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.

SUBMITTER: Szkiba D

PROVIDER: S-EPMC4012486 | biostudies-literature | 2014 May

REPOSITORIES: biostudies-literature

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SNP2GO: functional analysis of genome-wide association studies.

Szkiba David D Kapun Martin M von Haeseler Arndt A Gallach Miguel M

Genetics 20140221 1

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 infer ...[more]

PMID: 24561481

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