title: Identification of SNP barcode biomarkers for genes associated with facial emotion perception using particle swarm optimization algorithm.
abstract: BACKGROUND
  Facial emotion perception (FEP) can affect social function. We previously reported that parts of five tested single-nucleotide polymorphisms (SNPs) in the MET and AKT1 genes may individually affect FEP performance. However, the effects of SNP-SNP interactions on FEP performance remain unclear.
  
  
  METHODS
  This study compared patients with high and low FEP performances (n = 89 and 93, respectively). A particle swarm optimization (PSO) algorithm was used to identify the best SNP barcodes (i.e., the SNP combinations and genotypes that revealed the largest differences between the high and low FEP groups).
  
  
  RESULTS
  The analyses of individual SNPs showed no significant differences between the high and low FEP groups. However, comparisons of multiple SNP-SNP interactions involving different combinations of two to five SNPs showed that the best PSO-generated SNP barcodes were significantly associated with high FEP score. The analyses of the joint effects of the best SNP barcodes for two to five interacting SNPs also showed that the best SNP barcodes had significantly higher odds ratios (2.119 to 3.138; P < 0.05) compared to other SNP barcodes. In conclusion, the proposed PSO algorithm effectively identifies the best SNP barcodes that have the strongest associations with FEP performance.
  
  
  CONCLUSIONS
  This study also proposes a computational methodology for analyzing complex SNP-SNP interactions in social cognition domains such as recognition of facial emotion.
authors: Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan.
authors: Li-Yeh
authors: LY
authors: Chuang
authors: Institute of Clinical Medical Science, China Medical University, Taichung 40402, Taiwan ; Department of Psychiatry, China Medical University Hospital, Taichung 40402, Taiwan.
authors: Hsien-Yuan
authors: HY
authors: Lane
authors: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan.
authors: Yu-Da
authors: YD
authors: Lin
authors: Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84001, Taiwan ; Department of Psychiatry, Taipei Veterans General Hospital, Hsinchu Branch, Hsinchu 31064, Taiwan.
authors: Ming-Teng
authors: MT
authors: Lin
authors: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan.
authors: Cheng-Hong
authors: CH
authors: Yang
authors: Cancer Center, Translational Research Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan ; Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan ; Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 80708, Taiwan.
authors: Hsueh-Wei
authors: HW
authors: Chang
keywords: Algorithm; Facial emotion perception; Particle swarm optimization; SNP interaction; Single-nucleotide polymorphism