Routine discovery of complex genetic models using genetic algorithms

Jason H. Moore, Lance W. Hahn, Marylyn D. Ritchie, Tricia A. Thornton, Bill C. White

Research output: Contribution to journalArticle

40 Scopus citations

Abstract

Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the effects of other genes (i.e. epistasis or gene-gene interaction). Despite this need, the development of complex genetic models that can be used to simulate data is not always intuitive. In fact, only a few such models have been published. We previously developed a genetic algorithm (GA) approach to discovering complex genetic models in which two single nucleotide polymorphisms (SNPs) influence disease risk solely through nonlinear interactions. In this paper, we extend this approach for the discovery of high-order epistasis models involving three to five SNPs. We demonstrate that the genetic algorithm is capable of routinely discovering interesting high-order epistasis models in which each SNP influences risk of disease only through interactions with the other SNPs in the model. This study opens the door for routine simulation of complex gene-gene interactions among SNPs for the development and evaluation of new statistical and computational approaches for identifying common, complex multifactorial disease susceptibility genes.

Original languageEnglish (US)
Pages (from-to)79-86
Number of pages8
JournalApplied Soft Computing Journal
Volume4
Issue number1
DOIs
StatePublished - Feb 2004

All Science Journal Classification (ASJC) codes

  • Software

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