IGENT: efficient entropy based algorithm for genome-wide gene-gene interaction analysis

Min-Seok Kwon, Mira Park, Taesung Park
2014 BMC Medical Genomics  
With the development of high-throughput genotyping and sequencing technology, there are growing evidences of association with genetic variants and complex traits. In spite of thousands of genetic variants discovered, such genetic markers have been shown to explain only a very small proportion of the underlying genetic variance of complex traits. Gene-gene interaction (GGI) analysis is expected to unveil a large portion of unexplained heritability of complex traits. Methods: In this work, we
more » ... ose IGENT, Information theory-based GEnome-wide gene-gene iNTeraction method. IGENT is an efficient algorithm for identifying genome-wide gene-gene interactions (GGI) and geneenvironment interaction (GEI). For detecting significant GGIs in genome-wide scale, it is important to reduce computational burden significantly. Our method uses information gain (IG) and evaluates its significance without resampling. Results: Through our simulation studies, the power of the IGENT is shown to be better than or equivalent to that of that of BOOST. The proposed method successfully detected GGI for bipolar disorder in the Wellcome Trust Case Control Consortium (WTCCC) and age-related macular degeneration (AMD).
doi:10.1186/1755-8794-7-s1-s6 pmid:25077411 pmcid:PMC4101351 fatcat:swo2rmblp5fxhk7g2dieewebi4