title: Using biological knowledge to discover higher order interactions in genetic association studies.
abstract: The recent successes of genome-wide association studies (GWAS) have revealed that many of the replicated findings have explained only a small fraction of the heritability of common diseases. One hypothesis that investigators have suggested is that higher order interactions between SNPs or SNPs and environmental risk factors may account for some of this missing heritability. Searching for these interactions poses great statistical and computational challenges. In this article, we propose a novel method that addresses these challenges by incorporating external biological knowledge into a fully Bayesian analysis. The method is designed to be scalable for high-dimensional search spaces (where it supports interactions of any order) because priors that use such knowledge focus the search in regions that are more biologically plausible and avoid having to enumerate all possible interactions. We provide several examples based on simulated data demonstrating how external information can enhance power, specificity, and effect estimates in comparison to conventional approaches based on maximum likelihood estimates. We also apply the method to data from a GWAS for breast cancer, revealing a set of interactions enriched for the Gene Ontology terms growth, metabolic process, and biological regulation.
authors.affiliation: Division of Biostatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California 90089-9601, USA. gary.k.chen@usc.edu
authors.forename: Gary K
authors.initials: GK
authors.lastname: Chen
authors.forename: Duncan C
authors.initials: DC
authors.lastname: Thomas
mesh_terms: D000465:Algorithms; D001499:Bayes Theorem; D001943:Breast Neoplasms / Q000235:genetics; D003198:Computer Simulation; D005260:Female; D005492:Folic Acid / Q000235:genetics / Q000378:metabolism; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study / Q000379:methods; D006801:Humans; D016014:Linear Models; D053858:Metabolic Networks and Pathways; D020641:Polymorphism, Single Nucleotide; D012307:Risk Factors; D012680:Sensitivity and Specificity
chemical_list: D005492:Folic Acid