title: Identification of SNP-SNP interaction for chronic dialysis patients.
abstract: Analyses of interactions between single nucleotide polymorphisms (SNPs) have reported significant associations between mitochondrial displacement loops (D-loops) and chronic dialysis diseases. However, the method used to detect potential SNP-SNP interaction still requires improvement. This study proposes an effective algorithm named dynamic center particle swarm optimization k-nearest neighbors (DCPSO-KNN) to detect the SNP-SNP interaction. DCPSO-KNN uses dynamic center particle swarm optimization (DCPSO) to generate SNP combinations with a fitness function designed using the KNN method and statistical verification. A total of 77 SNPs in the mitochondrial D-loop were used to detect the SNP-SNP interactions and the search ability was compared against that of other methods. The detected SNP-SNP interactions were statistically evaluated. Experimental results showed that DCPSO-KNN successfully detects SNP-SNP interactions in two-to-seven-order combinations (positive predictive value (PPV)+negative predictive value (NPV)=1.154 to 1.310; odds ratio (OR)=1.859 to 4.015; 95% confidence interval (95% CI)=1.151 to 4.265; p-value <0.001). DCPSO-KNN can improve the detection ability of SNP-SNP associations between mitochondrial D-loops and chronic dialysis diseases, thus facilitating the development of biomedical applications.
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, No. 1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City 84001, Taiwan. Electronic address: chyang@cc.kuas.edu.tw.
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, No. 1, Sec. 1, Syuecheng Rd., Dashu District, Kaohsiung City 84001, Taiwan. Electronic address: dsa0543@hotmail.com.
authors.forename: Zi-Jie
authors.initials: ZJ
authors.lastname: Weng
authors.affiliation: Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-ShouI-Shou University, No. 415, Jiangong Rd., Sanmin Dist., Kaohsiung City 807, Taiwan. Electronic address: chuang@isu.edu.tw.
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.affiliation: Department of Plastic Surgery, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi 60002, Taiwan.
authors.forename: Cheng-San
authors.initials: CS
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D020022:Genetic Predisposition to Disease / Q000453:epidemiology / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods*; D006801:Humans; D008957:Models, Genetic; D005810:Multigene Family / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D006435:Renal Dialysis / Q000706:statistics & numerical data*; D051436:Renal Insufficiency, Chronic / Q000453:epidemiology / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
keywords: Dynamic center SNP-SNP interaction; Genome-wide association studies; Particle swarm optimization; k-nearest neighbors