title: Genetic algorithm-generated SNP barcodes of the mitochondrial D-loop for chronic dialysis susceptibility.
abstract: OBJECTIVE
  Single nucleotide polymorphism (SNP) interaction analysis can simultaneously evaluate the complex SNP interactions present in complex diseases. However, it is less commonly applied to evaluate the predisposition of chronic dialysis and its computational analysis remains challenging. In this study, we aimed to improve the analysis of SNP-SNP interactions within the mitochondrial D-loop in chronic dialysis.
  
  
  METHODS
  The SNP-SNP interactions between 77 reported SNPs within the mitochondrial D-loop in chronic dialysis study were evaluated in terms of SNP barcodes (different SNP combinations with their corresponding genotypes). We propose a genetic algorithm (GA) to generate SNP barcodes. The χ(2) values were then calculated by the occurrences of the specific SNP barcodes and their non-specific combinations between cases and controls.
  
  
  RESULTS
  Each SNP barcode (2- to 7-SNP) with the highest value in the χ(2) test was regarded as the best SNP barcode (11.304 to 23.310; p < 0.001). The best GA-generated SNP barcodes (2- to 7-SNP) were significantly associated with chronic dialysis (odds ratio [OR] = 1.998 to 3.139; p < 0.001). The order of influence for SNPs was the same as the order of their OR values for chronic dialysis in terms of 2- to 7-SNP barcodes.
  
  
  CONCLUSIONS
  Taken together, we propose an effective algorithm to address the SNP-SNP interactions and demonstrated that many non-significant SNPs within the mitochondrial D-loop may play a role in jointed effects to chronic dialysis susceptibility.
authors.affiliation: Division of Nephrology, Department of Internal Medicine, Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine , Kaohsiung , Taiwan .
authors.forename: Jin-Bor
authors.initials: JB
authors.lastname: Chen
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Yu-Da
authors.initials: YD
authors.lastname: Lin
authors.forename: Chia-Wei
authors.initials: CW
authors.lastname: Liou
authors.forename: Tsu-Kung
authors.initials: TK
authors.lastname: Lin
authors.forename: Wen-Chin
authors.initials: WC
authors.lastname: Lee
authors.forename: Ben-Chung
authors.initials: BC
authors.lastname: Cheng
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D058893:DNA Barcoding, Taxonomic; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics*; D004843:Epistasis, Genetic; D020022:Genetic Predisposition to Disease; D006801:Humans; D008957:Models, Genetic; D009690:Nucleic Acid Conformation; D020641:Polymorphism, Single Nucleotide; D006435:Renal Dialysis; D051436:Renal Insufficiency, Chronic / Q000235:genetics* / Q000628:therapy*; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial
keywords: Chronic dialysis; SNP interaction; genetic algorithm; mitochondrial D-loop; single nucleotide polymorphism