An efficiency analysis of high-order combinations of gene-gene interactions using multifactor-dimensionality reduction.

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An efficiency analysis of high-order combinations of gene-gene interactions using multifactor-dimensionality reduction.

BMC Genomics. 2015;16:489

Authors: Yang CH, Lin YD, Yang CS, Chuang LY

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.
CONCLUSION: 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 .

PMID: 26126977 [PubMed - in process]