GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes

With the development of genome-wide association studies, how to gain information from a large scale of data has become an issue of common concern, since traditional methods are not fully developed to solve problems such as identifying loci-to-loci interactions (also known as epistasis). Previous epistatic studies mainly focused on local information with a single outcome (phenotype), while in this paper, we developed a two-stage global search algorithm, Greedy Equivalence Search with Local Modification (GESLM), to implement a global search of directed acyclic graph in order to identify genome-wide epistatic interactions with multiple outcome variables (phenotypes) in a case-control design. GESLM integrates the advantages of score-based methods and constraint-based methods to learn the phenotype-related Bayesian network and is powerful and robust to find the interaction structures that display both genetic associations with phenotypes and gene interactions. We compared GESLM with some common phenotype-related loci detecting methods in simulation studies. The results showed that our method improved the accuracy and efficiency compared with others, especially in an unbalanced case-control study. Besides, its application on the UK Biobank dataset suggested that our algorithm has great performance when handling genome-wide association data with more than one phenotype.