title: Novel generating protective single nucleotide polymorphism barcode for breast cancer using particle swarm optimization.
abstract: BACKGROUND
  High-throughput single nucleotide polymorphism (SNP) genotyping generates a huge amount of SNP data in genome-wide association studies. Simultaneous analyses for multiple SNP interactions associated with many diseases and cancers are essential; however, these analyses are still computationally challenging.
  
  
  METHODS
  In this study, we propose an odds ratio-based binary particle swarm optimization (OR-BPSO) method to evaluate the risk of breast cancer.
  
  
  RESULTS
  BPSO provides the combinational SNPs with their corresponding genotype, called SNP barcodes, with the maximal difference of occurrence between the control and breast cancer groups. A specific SNP barcode with an optimized fitness value was identified among seven SNP combinations within the space of one minute. The identified SNP barcodes with the best performance between control and breast cancer groups were found to be control-dominant, suggesting that these SNP barcodes may prove protective against breast cancer. After statistical analysis, these control-dominant SNP barcodes were processed for odds ratio analysis for quantitative measurement with regard to the risk of breast cancer.
  
  
  CONCLUSIONS
  This study proposes an effective high-speed method to analyze the SNP-SNP interactions for breast cancer association study.
authors.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan. chyang@cc.kuas.edu.tw
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.forename: Hsueh-Wei
authors.initials: HW
authors.lastname: Chang
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics*; D016022:Case-Control Studies; D001330:Electronic Data Processing / Q000379:methods*; D005260:Female; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D016017:Odds Ratio; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*