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Bioinformatics Advance Access originally published online on December 19, 2008
Bioinformatics 2009 25(4):504-511; doi:10.1093/bioinformatics/btn652
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies

Can Yang 1,*, Zengyou He 1, Xiang Wan 1, Qiang Yang 2, Hong Xue 3 and Weichuan Yu 1

1Laboratory for Bioinformatics and Computational Biology, Department of Electronic and Computer Engineering, 2Department of Computer Science and Engineering and 3Department of Biochemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

*To whom correspondence should be addressed.


  Abstract

Motivation: Hundreds of thousands of single nucleotide polymorphisms (SNPs) are available for genome-wide association (GWA) studies nowadays. The epistatic interactions of SNPs are believed to be very important in determining individual susceptibility to complex diseases. However, existing methods for SNP interaction discovery either suffer from high computation complexity or perform poorly when marginal effects of disease loci are weak or absent. Hence, it is desirable to develop an effective method to search epistatic interactions in genome-wide scale.

Results: We propose a new method SNPHarvester to detect SNP–SNP interactions in GWA studies. SNPHarvester creates multiple paths in which the visited SNP groups tend to be statistically associated with diseases, and then harvests those significant SNP groups which pass the statistical tests. It greatly reduces the number of SNPs. Consequently, existing tools can be directly used to detect epistatic interactions. By using a wide range of simulated data and a real genome-wide data, we demonstrate that SNPHarvester outperforms its recent competitor significantly and is promising for practical disease prognosis.

Availability: http://bioinformatics.ust.hk/SNPHarvester.html

Contact: eeyang{at}ust.hk

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Alex Bateman

Received on September 19, 2008; revised on November 15, 2008; accepted on December 17, 2008

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