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Bioinformatics Advance Access originally published online on July 23, 2009
Bioinformatics 2009 25(18):2444-2446; doi:10.1093/bioinformatics/btp431
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Path: a tool to facilitate pathway-based genetic association analysis

David Zamar , Ben Tripp , George Ellis and Denise Daley *

James Hogg iCAPTURE Center, University of British Columbia (UBC), Vancouver, BC, Canada V6Z1Y6

*To whom correspondence should be addressed.


  Abstract

Summary: Traditional methods of genetic study design and analysis work well under the scenario that a handful of single nucleotide polymorphisms (SNPs) independently contribute to the risk of disease. For complex diseases, susceptibility may be determined not by a single SNP, but rather a complex interplay between SNPs. For large studies involving hundreds of thousands of SNPs, a brute force search of all possible combinations of SNPs associated with disease is not only inefficient, but also results in a multiple testing paradigm, whereby larger and larger sample sizes are needed to maintain statistical power. Pathway-based methods are an example of one of the many approaches in identifying a subset of SNPs to test for interaction. To help determine which SNP–SNP interactions to test, we developed Path, a software application designed to help researchers interface their data with biological information from several bioinformatics resources. To this end, our application brings together currently available information from nine online bioinformatics resources including the National Center for Biotechnology Information (NCBI), Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), UCSC Genome Browser, Seattle SNPs, PharmGKB, Genetic Association Database, the Single Nucleotide Polymorphism database (dbSNP) and the Innate Immune Database (IIDB).

Availability: The software, example datasets and tutorials are freely available from http://genapha.icapture.ubc.ca/PathTutorial.

Contact: ddaley{at}mrl.ubc.ca

Associate Editor: Jeffrey Barrett

Received on March 9, 2009; revised on July 11, 2009; accepted on July 13, 2009

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