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This article is part of the supplement: SNP-SIG 2012: Identification and annotation of SNPs in the context of structure, function, and disease

Open Access Research

GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS

Benjamin Goudey12*, David Rawlinson13, Qiao Wang12, Fan Shi12, Herman Ferra1, Richard M Campbell13, Linda Stern2, Michael T Inouye45, Cheng Soon Ong12 and Adam Kowalczyk12*

Author Affiliations

1 National ICT Australia Victorian Research Lab, The University of Melbourne, Parkville, Victoria, Australia

2 Computing and Information Systems, The University of Melbourne, Parkville, Victoria, Australia

3 Electrical and Electronic Engineering, The University of Melbourne, Parkville, Victoria, Australia

4 Pathology, The University of Melbourne, Parkville, Victoria, Australia

5 Microbiology & Immunology, The University of Melbourne, Parkville, Victoria, Australia

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BMC Genomics 2013, 14(Suppl 3):S10  doi:10.1186/1471-2164-14-S3-S10

Published: 28 May 2013

Abstract

Background

It has been hypothesized that multivariate analysis and systematic detection of epistatic interactions between explanatory genotyping variables may help resolve the problem of "missing heritability" currently observed in genome-wide association studies (GWAS). However, even the simplest bivariate analysis is still held back by significant statistical and computational challenges that are often addressed by reducing the set of analysed markers. Theoretically, it has been shown that combinations of loci may exist that show weak or no effects individually, but show significant (even complete) explanatory power over phenotype when combined. Reducing the set of analysed SNPs before bivariate analysis could easily omit such critical loci.

Results

We have developed an exhaustive bivariate GWAS analysis methodology that yields a manageable subset of candidate marker pairs for subsequent analysis using other, often more computationally expensive techniques. Our model-free filtering approach is based on classification using ROC curve analysis, an alternative to much slower regression-based modelling techniques. Exhaustive analysis of studies containing approximately 450,000 SNPs and 5,000 samples requires only 2 hours using a desktop CPU or 13 minutes using a GPU (Graphics Processing Unit). We validate our methodology with analysis of simulated datasets as well as the seven Wellcome Trust Case-Control Consortium datasets that represent a wide range of real life GWAS challenges. We have identified SNP pairs that have considerably stronger association with disease than their individual component SNPs that often show negligible effect univariately. When compared against previously reported results in the literature, our methods re-detect most significant SNP-pairs and additionally detect many pairs absent from the literature that show strong association with disease. The high overlap suggests that our fast analysis could substitute for some slower alternatives.

Conclusions

We demonstrate that the proposed methodology is robust, fast and capable of exhaustive search for epistatic interactions using a standard desktop computer. First, our implementation is significantly faster than timings for comparable algorithms reported in the literature, especially as our method allows simultaneous use of multiple statistical filters with low computing time overhead. Second, for some diseases, we have identified hundreds of SNP pairs that pass formal multiple test (Bonferroni) correction and could form a rich source of hypotheses for follow-up analysis.

Availability

A web-based version of the software used for this analysis is available at http://bioinformatics.research.nicta.com.au/gwis webcite.