SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease

Abstract

Detecting SNP-SNP interactions associated with disease is significant in genome-wide association study (GWAS). Owing to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power and long running time. To tackle these drawbacks, a fast self-adaptive memetic algorithm (SAMA) is proposed in this paper. In this method, the crossover, mutation, and selection of standard memetic algorithm are improved to make SAMA adapt to the detection of SNP-SNP interactions associated with disease. Furthermore, a self-adaptive local search algorithm is introduced to enhance the detecting power of the proposed method. SAMA is evaluated on a variety of simulated datasets and a real-world biological dataset, and a comparative study between it and the other four methods (FHSA-SED, AntEpiSeeker, IEACO, and DESeeker) that have been developed recently based on evolutionary algorithms is performed. The results of extensive experiments show that SAMA outperforms the other four compared methods in terms of detection power and running time.

Digenic Analysis Finds Highly Interactive Genetic Variants Underlying Polygenic Traits

“…After removal of five variants with strong main effects, three of our variants (rs1363688, rs7104698, and rs1394608) were found with a search algorithm although some results are not statistically significant 22 . More recently, rs1363688 was found with a method related to genetic algorithms although the search included variants in known risk loci 23 .…”