Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alterna...

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Bibliographic Details
Published in:Nucleic acids research 2009-07, Vol.37 (suppl-2), p.W340-W344
Main Authors: Medina, Ignacio, Montaner, David, Bonifaci, Nuria, Pujana, Miguel Angel, Carbonell, José, Tarraga, Joaquin, Al-Shahrour, Fatima, Dopazo, Joaquin
Format: Article
Language:English
Subjects:
Biological Phenomena - genetics
Breast Neoplasms - genetics
Female
Genes
Genetic Variation
Genome-Wide Association Study
Humans
Polymorphism, Single Nucleotide
Software
User-Computer Interface
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Summary:Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap/
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkp481