<abstract xmlns="http://www.w3.org/1999/xhtml"> Detecting genetic association models between single nucleotide polymorphisms (SNPs) in various disease-related genes can help to understand susceptibility to disease. Statistical tools have been widely used to detect significant genetic association models, according to their related statistical values, including odds ratio (OR), chi-square test (χ2), p-value, etc. However, the high number of computations entailed in such operations may limit the capacity of such statistical tools to detect high-order genetic associations. In this study, we propose lsGA algorithm, a genetic algorithm based on local search method, to detect significant genetic association models amongst large numbers of SNP combinations. We used two disease models to simulate the large data sets considering the minor allele frequency (MAF), number of SNPs, and number of samples. The three-order epistasis models were evaluated by chi-square test (χ2) to evaluate the significance (P-value &lt; 0.05). Analysis results showed that lsGA provided higher chi-square test values than that of GA. Simple linear regression indicated that lsGA provides a significant advantage over GA, providing the highest β values and significant p-value. </abstract>

Detecting genetic association models between single nucleotide polymorphisms (SNPs) in various disease-related genes can help to understand susceptibility to disease. Statistical tools have been widely used to detect significant genetic association models, according to their related statistical values, including odds ratio (OR), chi-square test (χ2), p-value, etc. However, the high number of computations entailed in such operations may limit the capacity of such statistical tools to detect high-order genetic associations. In this study, we propose lsGA algorithm, a genetic algorithm based on local search method, to detect significant genetic association models amongst large numbers of SNP combinations. We used two disease models to simulate the large data sets considering the minor allele frequency (MAF), number of SNPs, and number of samples. The three-order epistasis models were evaluated by chi-square test (χ2) to evaluate the significance (P-value < 0.05). Analysis results showed that lsGA provided higher chi-square test values than that of GA. Simple linear regression indicated that lsGA provides a significant advantage over GA, providing the highest β values and significant p-value.

Genetic Algorithm Combined with a Local Search Method for Identifying Susceptibility Genes

Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan

Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan

Journal of Artificial Intelligence and Soft Computing Research

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Detecting genetic association models between single nucleotide polymorphisms (SNPs) in various disease-related genes can help to understand susceptibility to...

Genetic Algorithm Combined with a Local Search Method for Identifying Susceptibility Genes

Published Online: Jun 10, 2016

Page range: 203 - 212

DOI: https://doi.org/10.1515/jaiscr-2016-0015

Keywords
Genetic algorithms, identifying susceptibility genes, local search algorithm

© 2016

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Genetic Algorithm Combined with a Local Search Method for Identifying Susceptibility Genes

Published Online: Jun 10, 2016

Page range: 203 - 212

DOI: https://doi.org/10.1515/jaiscr-2016-0015

KeywordsGenetic algorithms, identifying susceptibility genes, local search algorithm

© 2016

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Keywords
Genetic algorithms, identifying susceptibility genes, local search algorithm