Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS

We presented this paper at the 2018 Pacific Symposium on Biocomputing. This is an effort to incorporate functional genomics annotations into epistasis analysis in regulatory regions.

Manduchi E, Chesi A, Hall MA, Grant SFA, Moore JH. Leveraging putative enhancer-promoter interactions to investigate two-way epistasis in Type 2 Diabetes GWAS. Pac Symp Biocomput. 2018;23:548-558. [PDF]

We utilized evidence for enhancer-promoter interactions from functional genomics data in order to build biological filters to narrow down the search space for two-way Single Nucleotide Polymorphism (SNP) interactions in Type 2 Diabetes (T2D) Genome Wide Association Studies (GWAS). This has led us to the identification of a reproducible statistically significant SNP pair associated with T2D. As more functional genomics data are being generated that can help identify potentially interacting enhancer-promoter pairs in larger collection of tissues/cells, this approach has implications for investigation of epistasis from GWAS in general.