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. 2018:23:548-558.

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

Elisabetta Manduchi  1 , Alessandra Chesi, Molly A Hall, Struan F A Grant, Jason H Moore
Affiliations

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

Elisabetta Manduchi et al. Pac Symp Biocomput. 2018.

Abstract

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.

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Figure 1
Figure 1
Functional genomics data sets of different kinds, for tissues or cells relevant to the trait of interest, are used to identify putative active and interacting enhancer-promoter pairs. Pairs of SNPs harbored in these interacting regions are extracted and analyzed for epistasis in a discovery GWAS. Significant pairs from this analysis are then examined in one or more replication GWAS to identify candidates for subsequent follow-up work.
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