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Bioinformatics Advance Access originally published online on July 20, 2009
Bioinformatics 2009 25(20):2762-2763; doi:10.1093/bioinformatics/btp448
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

The SNP ratio test: pathway analysis of genome-wide association datasets

Colm O'Dushlaine *, Elaine Kenny , Elizabeth A. Heron , Ricardo Segurado , Michael Gill , Derek W. Morris and Aiden Corvin

Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Ireland

* To whom correspondence should be addressed.


  Abstract

Summary: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways.

Availability: https://sourceforge.net/projects/snpratiotest/

Contact: codushlaine{at}gmail.com; colm.odushlaine{at}tcd.ie

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Thomas Lengauer

Received on March 24, 2009; revised on June 9, 2009; accepted on July 16, 2009

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