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

Pac Symp Biocomput. 2018;23:548-558.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • Databases, Genetic / statistics & numerical data
  • Diabetes Mellitus, Type 2 / genetics*
  • Enhancer Elements, Genetic
  • Epistasis, Genetic*
  • Genome-Wide Association Study / statistics & numerical data
  • Genomics / statistics & numerical data
  • Humans
  • Models, Genetic
  • Polymorphism, Single Nucleotide
  • Promoter Regions, Genetic