Journal Article

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

Can Yang, Zengyou He, Xiang Wan, Qiang Yang, Hong Xue and Weichuan Yu

in Bioinformatics

Volume 25, issue 4, pages 504-511
Published in print February 2009 | ISSN: 1367-4803
Published online December 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn652
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies

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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@ust.hk

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  4941 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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