The ENIGMA Center of Excellence, based at the University of Southern California, will work with the KnowEnG Center as part of an ambitious new collaboration funded by the NIH Big Data to Knowledge (BD2K) Commons Pilots Projects. BD2K Centers Commons pilots will develop and test elements of the Commons framework that will facilitate interoperability between and amongst different BD2K centers.

Drawing upon recent advances in genome sequencing, genome-wide association studies (GWAS) have led to a wealth of discoveries by mining the human genome for common variants in our genetic sequence that relate to our risk for a range of diseases. A major challenge for GWAS, however, is that the number of SNPs – locations in DNA where people differ in their genetic make-up – is much larger than the number of subjects who can be assessed in a study.

As part of this collaboration, the ENIGMA and KnowEnG centers will mine existing databases of biological pathways and genetic perturbation screening datasets to discover important new genetic interactions and construct networks of gene interactions, called “epistasis networks”. These novel epistasis networks will provide prior information needed to expand sparse learning models and enhance the power of future genome-wide genetic analyses.

This collaborative project will leverage the strengths of the KnowEng center (knowledge of gene-gene interactions) with those of the ENIGMA Center (ongoing development of sparse learning models) to improve our ability to identify causal single nucleotide polymorphisms (SNPs). The project will be coordinated by Jieping Ye and Paul Thompson (ENIGMA) and Sihai Dave Zhao, Jiawei Han & Jun S. Song (KnowEnG).