Abstract
Here we introduce the multifactor dimensionality reduction (MDR) methodology and software package for detecting and characterizing epistasis in genetic association studies. We provide a general overview of the method and then highlight some of the key functions of the open-source MDR software package that is freely distributed. We end with a few examples of published studies of complex human diseases that have used MDR.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Ritchie MD, Hahn LW, Roodi N et al (2001) Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am J Hum Genet 69:138–147
Ritchie MD, Hahn LW, Moore JH (2003) Power of multifactor dimensionality reduction for detecting gene-gene interactions in the presence of genotyping error, missing data, phenocopy, and genetic heterogeneity. Genet Epidemiol 24:150–157
Hahn LW, Ritchie MD, Moore JH (2003) Multifactor dimensionality reduction software for detecting gene-gene and gene-environment interactions. Bioinformatics (Oxford, England) 19:376–382
Hahn LW, Moore JH (2004) Ideal discrimination of discrete clinical endpoints using multilocus genotypes. In Silico Biol 4:183–194
Moore JH (2010) Detecting, characterizing, and interpreting nonlinear gene-gene interactions using multifactor dimensionality reduction. Adv Genet 72:101–116
Moore JH (2004) Computational analysis of gene-gene interactions using multifactor dimensionality reduction. Expert Rev Mol Diagn 4:795–803
Moore JH (2007) Genome-wide analysis of epistasis using multifactor dimensionality reduction: feature selection and construction in the domain of human genetics. In: Zhu X, Davidson I (eds) Knowledge discovery and data mining: challenges and realities. IGI Global, Hershey, PA, pp 17–30
Moore JH, Gilbert JC, Tsai C-T et al (2006) A flexible computational framework for detecting, characterizing, and interpreting statistical patterns of epistasis in genetic studies of human disease susceptibility. J Theor Biol 241:252–261
Michalski RS (1983) A theory and methodology of inductive learning. Artif Intel 20:111–161
Velez DR, White BC, Motsinger AA et al (2007) A balanced accuracy function for epistasis modeling in imbalanced datasets using multifactor dimensionality reduction. Genet Epidemiol 31:306–315
Pattin KA, White BC, Barney N et al (2009) A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol 33:87–94
Cordell HJ (2009) Detecting gene-gene interactions that underlie human diseases. Nat Rev Genet 10:392–404
Moore JH (2003) The ubiquitous nature of epistasis in determining susceptibility to common human diseases. Hum Hered 56:73–82
Moore JH (2005) A global view of epistasis. Nat Genet 37:13–14
Moore JH, Williams SM (2005) Traversing the conceptual divide between biological and statistical epistasis: systems biology and a more modern synthesis. Bioessays 27:637–646
Moore JH, Williams SM (2009) Epistasis and its implications for personal genetics. Am J Hum Genet 85:309–320
Moore JH, Asselbergs FW, Williams SM (2010) Bioinformatics challenges for genome-wide association studies. Bioinformatics (Oxford, England) 26:445–455
Cordell HJ (2002) Epistasis: what it means, what it doesn’t mean, and statistical methods to detect it in humans. Hum Mol Genet 11:2463–2468
Cowper-Sal lari R, Cole MD, Karagas MR et al (2011) Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies. Wiley Interdiscip Rev Syst Biol Med 3:513–526
Tyler AL, Asselbergs FW, Williams SM et al (2009) Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. Bioessays 31:220–227
Phillips PC (2008) Epistasis–the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet 9:855–867
Phillips PC (1998) The language of gene interaction. Genetics 149:1167–1171
Coffey CS, Hebert PR, Ritchie MD et al (2004) An application of conditional logistic regression and multifactor dimensionality reduction for detecting gene-gene interactions on risk of myocardial infarction: the importance of model validation. BMC Bioinformatics 5:49
Greene CS, Himmelstein DS, Nelson HH et al (2010) Enabling personal genomics with an explicit test of epistasis, Pacific Symposium on Biocomputing. Pac Symp Biocomput:327–336
Lou X-Y, Chen G-B, Yan L et al (2007) A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence. Am J Hum Genet 80:1125–1137
Calle ML, Urrea V, Malats N et al (2010) mbmdr: an R package for exploring gene-gene interactions associated with binary or quantitative traits. Bioinformatics (Oxford, England) 26:2198–2199
Gui J, Andrew AS, Andrews P et al (2011) A robust multifactor dimensionality reduction method for detecting gene-gene interactions with application to the genetic analysis of bladder cancer susceptibility. Ann Hum Genet 75:20–28
Gui J, Andrew AS, Andrews P et al (2010) A simple and computationally efficient sampling approach to covariate adjustment for multifactor dimensionality reduction analysis of epistasis. Hum Hered 70:219–225
Dai H, Charnigo RJ, Becker ML et al (2013) Risk score modeling of multiple gene to gene interactions using aggregated-multifactor dimensionality reduction. BioData Min 6:1
Martin ER, Ritchie MD, Hahn L et al (2006) A novel method to identify gene-gene effects in nuclear families: the MDR-PDT. Genet Epidemiol 30:111–123
Cattaert T, Urrea V, Naj AC et al (2010) FAM-MDR: a flexible family-based multifactor dimensionality reduction technique to detect epistasis using related individuals. PLoS One 5:e10304
Gui J, Moore JH, Kelsey KT et al (2011) A novel survival multifactor dimensionality reduction method for detecting gene-gene interactions with application to bladder cancer prognosis. Hum Genet 129:101–110
Beretta L, Santaniello A, van Riel PLCM et al (2010) Survival dimensionality reduction (SDR): development and clinical application of an innovative approach to detect epistasis in presence of right-censored data. BMC Bioinformatics 11:416
Greene CS, Sinnott-Armstrong NA, Himmelstein DS et al (2010) Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinformatics (Oxford, England) 26:694–695
Sinnott-Armstrong NA, Greene CS, Cancare F et al (2009) Accelerating epistasis analysis in human genetics with consumer graphics hardware. BMC Res Notes 2:149
Gui J, Moore JH, Williams SM et al (2013) A simple and computationally efficient approach to multifactor dimensionality reduction analysis of gene-gene interactions for quantitative traits. PLoS One 8:e66545
Kim NC, Andrews PC, Asselbergs FW et al (2012) Gene ontology analysis of pairwise genetic associations in two genome-wide studies of sporadic ALS. BioData Min 5:9
Wilke RA, Reif DM, Moore JH (2005) Combinatorial pharmacogenetics. Nat Rev Drug Discov 4:911–918
Wilke RA, Mareedu RK, Moore JH (2008) The pathway less traveled: moving from candidate genes to candidate pathways in the analysis of genome-wide data from large scale pharmacogenetic association studies. Curr Pharmacogenomics PersonMed 6:150–159
Andrew AS, Nelson HH, Kelsey KT et al (2006) Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibility. Carcinogenesis 27:1030–1037
Andrew AS, Karagas MR, Nelson HH et al (2008) DNA repair polymorphisms modify bladder cancer risk: a multi-factor analytic strategy. Hum Hered 65:105–118
Winham SJ, Motsinger-Reif AA (2011) An R package implementation of multifactor dimensionality reduction. BioData Min 4:24
Moore JH (2003) Cross validation consistency for the assessment of genetic programming results in microarray studies. In: Cagnoni S, Johnson CG, Cardalda JJR et al (eds) Applications of evolutionary computing. Springer, Berlin, pp 99–106
Winham SJ, Slater AJ, Motsinger-Reif AA (2010) A comparison of internal validation techniques for multifactor dimensionality reduction. BMC Bioinformatics 11:394
Bush WS, Edwards TL, Dudek SM et al (2008) Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction. BMC Bioinformatics 9:238
Fan R, Zhong M, Wang S et al (2011) Entropy-based information gain approaches to detect and to characterize gene-gene and gene-environment interactions/correlations of complex diseases. Genet Epidemiol 35:706–721
Hu T, Sinnott-Armstrong NA, Kiralis JW et al (2011) Characterizing genetic interactions in human disease association studies using statistical epistasis networks. BMC Bioinformatics 12:364
Hu T, Andrew AS, Karagas MR et al (2013) Statistical epistasis networks reduce the computational complexity of searching three-locus genetic models, Pacific Symposium on Biocomputing. Pac Symp Biocomput:397–408
Hu T, Chen Y, Kiralis JW et al (2013) ViSEN: methodology and software for visualization of statistical epistasis networks. Genet Epidemiol 37:283–285
Wong AK, Park CY, Greene CS et al (2012) IMP: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. Nucleic Acids Res 40:W484–W490
Gaertner BE, Parmenter MD, Rockman MV et al (2012) More than the sum of its parts: a complex epistatic network underlies natural variation in thermal preference behavior in Caenorhabditis elegans. Genetics 192:1533–1542
Huang W, Richards S, Carbone MA et al (2012) Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci U S A 109:15553–15559
Lee J-H, Moore JH, Park S-W et al (2008) Genetic interactions model among Eotaxin gene polymorphisms in asthma. J Hum Genet 53:867–875
Bush WS, Dudek SM, Ritchie MD (2006) Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene-gene interactions. Bioinformatics (Oxford, England) 22:2173–2174
Payne JL, Sinnott-Armstrong NA, Moore JH (2010) Exploiting graphics processing units for computational biology and bioinformatics. Interdiscip Sci 2:213–220
Moore JH, White BC (2007) Tuning ReliefF for genome-wide genetic analysis. In: Marchiori E, Moore JH, Rajapakse JC (eds) Evolutionary computation, machine learning and data mining in bioinformatics. Springer, Berlin, pp 166–175
Greene CS, Penrod NM, Kiralis J et al (2009) Spatially uniform relieff (SURF) for computationally-efficient filtering of gene-gene interactions. BioData Min 2:5
Greene CS, Himmelstein DS, Kiralis J et al (2010) The informative extremes: using both nearest and farthest individuals can improve relief algorithms in the domain of human genetics. In: Pizzuti C, Ritchie MD, Giacobini M (eds) Evolutionary computation, machine learning and data mining in bioinformatics. Springer, Berlin, pp 182–193
Pan Q, Hu T, Moore JH (2013) Epistasis, complexity, and multifactor dimensionality reduction. Methods Mol Biol (Clifton, NJ) 1019:465–477
Dai H, Bhandary M, Becker M et al (2012) Global tests of P-values for multifactor dimensionality reduction models in selection of optimal number of target genes. BioData Min 5:3
Bush WS, Dudek SM, Ritchie MD (2009) Biofilter: a knowledge-integration system for the multi-locus analysis of genome-wide association studies, Pacific Symposium on Biocomputing. Pac Symp Biocomput:368–379
Greene CS, White BC, Moore JH (2008) Ant colony optimization for genome-wide genetic analysis. In: Dorigo M, Birattari M, Blum C et al (eds) Ant colony optimization and swarm intelligence. Springer, Berlin, pp 37–47
Gilmore JM, Greene CS, Andrews PC et al (2011) An analysis of new expert knowledge scaling methods for biologically inspired computing. In: Kampis G, Karsai I, Szathmáry E (eds) Advances in artificial life. Darwin meets von Neumann. Springer, Berlin, pp 286–293
Greene CS, Penrod NM, Williams SM et al (2009) Failure to replicate a genetic association may provide important clues about genetic architecture. PLoS One 4:e5639
Acknowledgements
This work was supported by National Institutes of Health (NIH) grants AI59694, EY022300, GM103534, GM103506, LM009012, LM010098, and LM011360.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Moore, J.H., Andrews, P.C. (2015). Epistasis Analysis Using Multifactor Dimensionality Reduction. In: Moore, J., Williams, S. (eds) Epistasis. Methods in Molecular Biology, vol 1253. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2155-3_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2155-3_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2154-6
Online ISBN: 978-1-4939-2155-3
eBook Packages: Springer Protocols