A systematic analysis of gene–gene interaction in multiple sclerosis

BACKGROUND: For the most part, genome-wide association studies (GWAS) have only partially explained the heritability of complex diseases. One of their limitations is to assume independent contributions of individual variants to the phenotype. Many tools have therefore been developed to investigate the interactions between distant loci, or epistasis. Among them, the recently proposed EpiGWAS models the interactions between a target variant and the rest of the genome. However, applying this approach to studying interactions along all genes of a disease map is not straightforward. Here, we propose a pipeline to that effect, which we illustrate by investigating a multiple sclerosis GWAS dataset from the Wellcome Trust Case Control Consortium 2 through 19 disease maps from the MetaCore pathway database. RESULTS: For each disease map, we build an epistatic network by connecting the genes that are deemed to interact. These networks tend to be connected, complementary to the disease maps and contain hubs. In addition, we report 4 epistatic gene pairs involving missense variants, and 25 gene pairs with a deleterious epistatic effect mediated by eQTLs. Among these, we highlight the interaction of GLI-1 and SUFU, and of IP10 and NF-[Formula: see text] B, as they both match known biological interactions. The latter pair is particularly promising for therapeutic development, as both genes have known inhibitors. CONCLUSIONS: Our study showcases the ability of EpiGWAS to uncover biologically interpretable epistatic interactions that are potentially actionable for the development of combination therapy. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-022-01247-3.