title: Double-bottom chaotic map particle swarm optimization based on chi-square test to determine gene-gene interactions.
abstract: Gene-gene interaction studies focus on the investigation of the association between the single nucleotide polymorphisms (SNPs) of genes for disease susceptibility. Statistical methods are widely used to search for a good model of gene-gene interaction for disease analysis, and the previously determined models have successfully explained the effects between SNPs and diseases. However, the huge numbers of potential combinations of SNP genotypes limit the use of statistical methods for analysing high-order interaction, and finding an available high-order model of gene-gene interaction remains a challenge. In this study, an improved particle swarm optimization with double-bottom chaotic maps (DBM-PSO) was applied to assist statistical methods in the analysis of associated variations to disease susceptibility. A big data set was simulated using the published genotype frequencies of 26 SNPs amongst eight genes for breast cancer. Results showed that the proposed DBM-PSO successfully determined two- to six-order models of gene-gene interaction for the risk association with breast cancer (odds ratio > 1.0; P value <0.05). Analysis results supported that the proposed DBM-PSO can identify good models and provide higher chi-square values than conventional PSO. This study indicates that DBM-PSO is a robust and precise algorithm for determination of gene-gene interaction models for breast cancer.
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan.
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan.
authors.forename: Yu-Da
authors.identifier: 0000-0001-5100-6072
authors.initials: YD
authors.lastname: Lin
authors.affiliation: Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan.
authors.forename: Li-Yeh
authors.identifier: 0000-0002-9817-5102
authors.initials: LY
authors.lastname: Chuang
authors.affiliation: Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung, 80708, Taiwan ; Department of Biomedical Science and Environmental Biology, Translational Research Center, Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D016022:Case-Control Studies; D016009:Chi-Square Distribution; D016001:Confidence Intervals; D030541:Databases, Genetic; D004843:Epistasis, Genetic; D005260:Female; D052138:Genes, Neoplasm; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics; D008957:Models, Genetic; D016017:Odds Ratio; D020641:Polymorphism, Single Nucleotide; D012307:Risk Factors
chemical_list: D036341:Intercellular Signaling Peptides and Proteins