GADGETS: a genetic algorithm for detecting epistasis using nuclear families.

ABSTRACT:

Motivation

Epistasis may play an etiologic role in complex diseases, but research has been hindered because identification of interactions among sets of single nucleotide polymorphisms (SNPs) requires exploration of immense search spaces. Current approaches using nuclear families accommodate at most several hundred candidate SNPs.

Results

GADGETS detects epistatic SNP-sets by applying a genetic algorithm to case-parent or case-sibling data. To allow for multiple epistatic sets, island subpopulations of SNP-sets evolve separately under selection for evident joint relevance to disease risk. The software evaluates the identified SNP-sets via permutation testing and provides graphical visualization. GADGETS correctly identified epistatic SNP-sets in realistically simulated case-

SUBMITTER: Nodzenski M 

PROVIDER: S-EPMC10060691 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature