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Detecting Genetic Interactions in Pathway‐Based Genome‐Wide Association Studies
Author(s) -
Huang Anhui,
Martin Eden R.,
Vance Jeffery M.,
Cai Xiaodong
Publication year - 2014
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.21803
Subject(s) - genome wide association study , epistasis , computational biology , genetic association , single nucleotide polymorphism , biology , biological pathway , genetic architecture , lasso (programming language) , genetics , quantitative trait locus , genotype , computer science , gene , gene expression , world wide web
Pathway‐based genome‐wide association studies (GWAS) can exploit collective effects of causal variants in a pathway to increase power of detection. However, current methods for pathway‐based GWAS do not consider epistatic effects of genetic variants, although interactions between genetic variants may play an important role in influencing complex traits. In this paper, we employed a Bayesian Lasso logistic regression model for pathway‐based GWAS to include all possible main effects and a large number of pairwise interactions of single nucleotide polymorphisms (SNPs) in a pathway, and then inferred the model with an efficient group empirical Bayesian Lasso (EBLasso) method. Using the inferred model, the statistical significance of a pathway was tested with the Wald statistics. Reliable effects in a significant pathway were selected using the stability selection technique. Extensive computer simulations demonstrated that our group EBlasso method significantly outperformed two competitive methods in most simulation setups and offered similar performance in other simulation setups. When applying to a GWAS dataset for Parkinson disease, EBLasso identified three significant pathways including the primary bile acid biosynthesis pathway, the neuroactive ligand–receptor interaction, and the MAPK signaling pathway. All effects identified in the primary bile acid biosynthesis pathway and many of effects in the other two pathways were epistatic effects. The group EBLasso method provides a valuable tool for pathway‐based GWAS to identify main and epistatic effects of genetic variants.