New algorithms for detecting multi-effect and multi-way epistatic interactions

Abstract

AbstractMotivationEpistasis, 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.ResultsThe 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 implementationData source was publicly available and details are provided in the text.