title: Particle swarm optimization algorithm for analyzing SNP-SNP interaction of renin-angiotensin system genes against hypertension.
abstract: Most non-significant individual single nucleotide polymorphisms (SNPs) were undiscovered in hypertension association studies. Their possible SNP-SNP interactions were usually ignored and leaded to missing heritability. In present study, we proposed a particle swarm optimization (PSO) algorithm to analyze the SNP-SNP interaction associated with hypertension. Genotype dataset of eight SNPs of renin-angiotensin system genes for 130 non-hypertension and 313 hypertension subjects were included. Without SNP-SNP interaction, most individual SNPs were non-significant difference between the hypertension and non-hypertension groups. For SNP-SNP interaction, PSO can select the SNP combinations involving different SNP numbers, namely the best SNP barcodes, to show the maximum frequency difference between non-hypertension and hypertension groups. After computation, the best PSO-generated SNP barcodes were dominant in non-hypertension in terms of the occurrences of frequency differences between non-hypertension and hypertension groups. The OR values of the best SNP barcodes involving 2-8 SNPs were 0.705-0.334, suggesting that these SNP barcodes were protective against hypertension. In conclusion, this study demonstrated that non-significant SNPs may generate the joint effect in association study. Our proposed PSO algorithm is effective to identify the best protective SNP barcodes against hypertension.
authors.affiliation: Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan.
authors.forename: Shyh-Jong
authors.initials: SJ
authors.lastname: Wu
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Yu-Da
authors.initials: YD
authors.lastname: Lin
authors.forename: Wen-Hsien
authors.initials: WH
authors.lastname: Ho
authors.forename: Fu-Tien
authors.initials: FT
authors.lastname: Chiang
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004843:Epistasis, Genetic; D020022:Genetic Predisposition to Disease; D005838:Genotype; D006801:Humans; D006973:Hypertension / Q000235:genetics*; D008954:Models, Biological; D016017:Odds Ratio; D020641:Polymorphism, Single Nucleotide; D012084:Renin-Angiotensin System / Q000235:genetics*; D015203:Reproducibility of Results