Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene--gene interactions

Authors:
William S. Bush;Scott M. Dudek;Marylyn D. Ritchie
Affiliations:
Center for Human Genetics Research, Vanderbilt University Nashville, TN, USA;Center for Human Genetics Research, Vanderbilt University Nashville, TN, USA;Center for Human Genetics Research, Vanderbilt University Nashville, TN, USA
Venue:
Bioinformatics
Year:
2006

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Abstract

Summary: Parallel multifactor dimensionality reduction is a tool for large-scale analysis of gene--gene and gene--environment interactions. The MDR algorithm was redesigned to allow an unlimited number of study subjects, total variables and variable states, and to remove restrictions on the order of interactions being analyzed. In addition, the algorithm is markedly more efficient, with ∼150-fold decrease in runtime for equivalent analyses. To facilitate the processing of large datasets, the algorithm was made parallel. Availability: Parallel MDR is freely available for non-commercial research institutions. For full details see http://chgr.mc.vanderbilt.edu/ritchielab/pMDR. An open-source version of MDR software is available at http://www.epistasis.org. Contact: ritchie@chgr.mc.vanderbilt.edu