Motivation: Epistasis, which is the phenomenon of genetic interactions, plays a central role in many scientific discoveries. However, due to the combinatorial nature of the problem, it is extremely challenging to decipher the exact combinations of genes that trigger the epistatic effects. Many existing methods only focus on two-way interactions. Some of the most effective methods used machine learning techniques, but many were designed for special case-and-control studies or suffer from overfitting. We propose three new algorithms for multi-effect and multi-way epistases detection, with one guaranteeing global optimality and the other two being local optimization oriented heuristics.

Results: The computational performance of the proposed heuristic algorithm was compared with several state-of-the-art methods using a yeast dataset. Results suggested that searching for the global optimal solution could be extremely time consuming, but the proposed heuristic algorithm was much more effective and efficient than others at finding a close-to-optimal solution. Moreover, it was able to provide biological insight on the exact configurations of epistases, besides achieving a higher prediction accuracy than the state-of-the-art methods.

Availability and implementation: Data source was publicly available and details are provided in the text.

• PMID: 31168598
• DOI full text
• PubMed
• PubTator

Reference Type

Journal Article | Research Support, U.S. Gov't, Non-P.H.S.

Authors

Ansarifar J, Wang L

Primary Lit For

Additional Lit For

Review For