title: An efficiency analysis of high-order combinations of gene-gene interactions using multifactor-dimensionality reduction.
abstract: BACKGROUND
  Multifactor dimensionality reduction (MDR) is widely used to analyze interactions of genes to determine the complex relationship between diseases and polymorphisms in humans. However, the astronomical number of high-order combinations makes MDR a highly time-consuming process which can be difficult to implement for multiple tests to identify more complex interactions between genes. This study proposes a new framework, named fast MDR (FMDR), which is a greedy search strategy based on the joint effect property.
  
  
  RESULTS
  Six models with different minor allele frequencies (MAFs) and different sample sizes were used to generate the six simulation data sets. A real data set was obtained from the mitochondrial D-loop of chronic dialysis patients. Comparison of results from the simulation data and real data sets showed that FMDR identified significant gene-gene interaction with less computational complexity than the MDR in high-order interaction analysis.
  
  
  CONCLUSIONS
  FMDR improves the MDR difficulties associated with the computational loading of high-order SNPs and can be used to evaluate the relative effects of each individual SNP on disease susceptibility. FMDR is freely available at http://bioinfo.kmu.edu.tw/FMDR.rar .
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.affiliation: Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan. e0955767257@yahoo.com.tw.
authors.forename: Yu-Da
authors.initials: YD
authors.lastname: Lin
authors.affiliation: Department of Plastic Surgery, Chia-Yi Christian Hospital, Chiayi, Taiwan. 02150@cych.org.tw.
authors.forename: Cheng-San
authors.initials: CS
authors.lastname: Yang
authors.affiliation: Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan. chuang@isu.edu.tw.
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D004198:Disease Susceptibility; D004843:Epistasis, Genetic; D005787:Gene Frequency; D006801:Humans; D058011:Multifactor Dimensionality Reduction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D012984:Software