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Open Access

Genome-Wide Interaction-Based Association of Human Diseases — A Survey

Xuan Guo, Ning Yu, Feng Gu, Xiaojun Ding, Jianxin Wang( ), Yi Pan( )
Department of Computer Science, Georgia State University, Atlanta, GA 30303, USA.
Department of Computer Science, College of Staten Island, Staten Island, NY 10314, USA.
Central South University, Changsha 410083, China.
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Abstract

Genome-Wide Association Studies (GWASs) aim to identify genetic variants that are associated with disease by assaying and analyzing hundreds of thousands of Single Nucleotide Polymorphisms (SNPs). Although traditional single-locus statistical approaches have been standardized and led to many interesting findings, a substantial number of recent GWASs indicate that for most disorders, the individual SNPs explain only a small fraction of the genetic causes. Consequently, exploring multi-SNPs interactions in the hope of discovering more significant associations has attracted more attentions. Due to the huge search space for complicated multi-locus interactions, many fast and effective methods have recently been proposed for detecting disease-associated epistatic interactions using GWAS data. In this paper, we provide a critical review and comparison of eight popular methods, i.e., BOOST, TEAM, epiForest, EDCF, SNPHarvester, epiMODE, MECPM, and MIC, which are used for detecting gene-gene interactions among genetic loci. In views of the assumption model on the data and searching strategies, we divide the methods into seven categories. Moreover, the evaluation methodologies, including detecting powers, disease models for simulation, resources of real GWAS data, and the control of false discover rate, are elaborated as references for new approach developers. At the end of the paper, we summarize the methods and discuss the future directions in genome-wide association studies for detecting epistatic interactions.

Keywords

Single Nucleotide Polymorphism (SNP)genome-wide associationepistasisepistatic interactioncomplex disease

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Tsinghua Science and Technology
Volume 19 Issue 6,
December 2014
Pages 596-616
DOI: 10.1109/TST.2014.6961029
Cite this article:
Guo X, Yu N, Gu F, et al. Genome-Wide Interaction-Based Association of Human Diseases — A Survey. Tsinghua Science and Technology, 2014, 19(6): 596-616. https://doi.org/10.1109/TST.2014.6961029

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Received: 16 June 2014
Accepted: 23 June 2014
Published: 20 November 2014
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