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A robustness study of parametric and non-parametric tests in model-based multifactor dimensionality reduction for epistasis detection

Jestinah M Mahachie John, François Van Lishout, Elena S Gusareva, Kristel Van Steen
2013 BioData Mining  
Model-Based Multifactor Dimensionality Reduction (MB-MDR) for epistasis detection relies on association testing between a trait and a factor consisting of multilocus genotype information.  ...  In this study, we assess through simulations, the cumulative effect of deviations from normality and homoscedasticity on the overall performance of quantitative Model-Based Multifactor Dimensionality Reduction  ...  Model-Based Multifactor Dimensionality Reduction (MB-MDR) originated as such a unified dimensionality reduction approach.  ... 
doi:10.1186/1756-0381-6-9 pmid:23618370 pmcid:PMC3668290 fatcat:xbz2zvc34jf4zfyfj54kn77zjm

Multifactor dimensionality reduction reveals a three-locus epistatic interaction associated with susceptibility to pulmonary tuberculosis

Ryan L Collins, Ting Hu, Christian Wejse, Giorgio Sirugo, Scott M Williams, Jason H Moore
2013 BioData Mining  
Multifactor dimensionality reduction (MDR) is a machine learning method that was designed specifically for this problem.  ...  Identifying high-order genetics associations with non-additive (i.e. epistatic) effects in population-based studies of common human diseases is a computational challenge.  ...  Acknowledgements This work was supported by NIH R01 grants LM010098, LM009012 and AI59694.  ... 
doi:10.1186/1756-0381-6-4 pmid:23418869 pmcid:PMC3618340 fatcat:i6obij7o55gzrn2evmriew5nva

Gene-gene interaction: the curse of dimensionality

Amrita Chattopadhyay, Tzu-Pin Lu
2019 Annals of Translational Medicine  
With the immense popularity of multifactor dimensionality reduction (MDR), a non-parametric method, proposed in 2001, that classifies multi-dimensional genotypes into one- dimensional binary approaches  ...  An avenue, to account for a part of this "missingness" is to evaluate gene-gene interactions (epistasis) thereby elucidating their effect on complex diseases.  ...  Acknowledgments We thank Melissa Stauffer, PhD, for editing the manuscript.  ... 
doi:10.21037/atm.2019.12.87 pmid:32042829 pmcid:PMC6989881 fatcat:kfgkttrktvd6ndkx6qmqre6zsu

Travelling the world of gene-gene interactions

K. Van Steen
2011 Briefings in Bioinformatics  
The purpose of this work is to give a perspective view on a selection of currently active analysis strategies and concerns in the context of epistasis detection, and to provide an eye to the future of  ...  These include the inclusion of several genetic inheritance assumptions in model development, the consideration of different sources of information, and the acknowledgement of disease underlying pathways  ...  reduction (MDR, [59] ) and model-based multifactor dimensionality reduction (MB-MDR).  ... 
doi:10.1093/bib/bbr012 pmid:21441561 fatcat:3kojyhlvfrgjrjbjtrovmg2aaa

Kernel Methods and Applications in Bioinformatics [chapter]

Yan Fu
2014 Springer Handbook of Bio-/Neuroinformatics  
The four presented algorithms, including ANNs (Artificial Neural Networks), SVM (Support Vector Machines), MDR (Multifactor Dimensionality Reduction) and RF (Random Forrest) are used to address some problems  ...  Bioinformatics, or computational biology, is an interdisciplinary field of study for interpreting biological data using computer science.  ...  Multifactor Dimensionality Reduction (MDR): MDR was method impact upon its reliability as a predictor of one of the first ML methods developed to detect and disease-genotype interactions.  ... 
doi:10.1007/978-3-642-30574-0_18 fatcat:ghta2jsk7jcyheujnktp5xetxe

Power of grammatical evolution neural networks to detect gene-gene interactions in the presence of error

Alison A Motsinger-Reif, Theresa J Fanelli, Anna C Davis, Marylyn D Ritchie
2008 BMC Research Notes  
Additionally, we compare the performance of GENN to that of another computational method -Multifactor Dimensionality Reduction (MDR).  ...  Findings: GENN is extremely robust to missing data and genotyping error. Phenocopy in a dataset reduces the power of both GENN and MDR.  ...  Acknowledgements The work for this project was supported by National Institutes of Health grants HL65962, GM62758, and AG20135.  ... 
doi:10.1186/1756-0500-1-65 pmid:18710518 pmcid:PMC2531119 fatcat:el3jgaag2bcxtf5se3jkzhhuky

Lower-Order Effects Adjustment in Quantitative Traits Model-Based Multifactor Dimensionality Reduction

Jestinah M. Mahachie John, Tom Cattaert, François Van Lishout, Elena S. Gusareva, Kristel Van Steen, Yun Li
2012 PLoS ONE  
Via simulations, we assess the performance of different corrective measures for lower-order genetic effects in Model-Based Multifactor Dimensionality Reduction epistasis detection, using additive and co-dominant  ...  The same is true for procedures that adjust for lower-order effects prior to Model-Based Multifactor Dimensionality Reduction and involve using residuals as the new trait.  ...  It has been suggested that Model-Based Multifactor Dimensionality Reduction is a useful method for identifying genegene interactions in case-control or family-based design for both dichotomous and quantitative  ... 
doi:10.1371/journal.pone.0029594 pmid:22242176 pmcid:PMC3252336 fatcat:dlvinjer65hitcnjmjhtivyeym

FAM-MDR: A Flexible Family-Based Multifactor Dimensionality Reduction Technique to Detect Epistasis Using Related Individuals

Tom Cattaert, Víctor Urrea, Adam C. Naj, Lizzy De Lobel, Vanessa De Wit, Mao Fu, Jestinah M. Mahachie John, Haiqing Shen, M. Luz Calle, Marylyn D. Ritchie, Todd L. Edwards, Kristel Van Steen (+1 others)
2010 PLoS ONE  
We propose a novel multifactor dimensionality reduction method for epistasis detection in small or extended pedigrees, FAM-MDR.  ...  When comparing FAM-MDR with Pedigree-based Generalized MDR (PGMDR), which is a generalization of Multifactor Dimensionality Reduction (MDR) to continuous traits and related individuals, FAM-MDR was found  ...  Acknowledgments Interesting discussions with Yurii Aulchenko and Florence Demenais are gratefully acknowledged. Author Contributions FAM-MDR Epistasis Screening PLoS ONE | www.plosone.org  ... 
doi:10.1371/journal.pone.0010304 pmid:20421984 pmcid:PMC2858665 fatcat:qc7u2yrt7jdmlekid7dqq2mxnq

Model-Based Multifactor Dimensionality Reduction to detect epistasis for quantitative traits in the presence of error-free and noisy data

Jestinah M Mahachie John, François Van Lishout, Kristel Van Steen
2011 European Journal of Human Genetics  
In this study, we evaluate the power of Model-Based Multifactor Dimensionality Reduction for quantitative traits to detect gene-gene interactions (epistasis) in the presence of error-free and noisy data  ...  One of these methods, Model-Based Multifactor Dimensionality Reduction, has so far mainly been applied to case-control studies.  ...  One of these methods is the Multifactor Dimensionality Reduction (MDR) method, 1 which nicely tackles the dimensionality problem involved in interaction detection by pooling multi-locus genotypes into  ... 
doi:10.1038/ejhg.2011.17 pmid:21407267 pmcid:PMC3110049 fatcat:esolu7zrujgjvgeflylocuiddi

Weighted Risk Score-Based Multifactor Dimensionality Reduction to Detect Gene-Gene Interactions in Nasopharyngeal Carcinoma

Chao-Feng Li, Fu-Tian Luo, Yi-Xin Zeng, Wei-Hua Jia
2014 International Journal of Molecular Sciences  
Multifactor dimensionality reduction (MDR) has been proven to be capable of effectively detecting the statistical patterns of epistasis, although classification accuracy is required for this approach.  ...  Zhang and Liu proposed a Bayesian epistasis association mapping (BEAM) algorithm for identifying both single-marker and epistasis associations in population-based case-control studies [27] .  ...  The work was supported by the National Natural Science Foundation of China (81325018, 81220108022) and the National Basic Research Program of China (2011CB504303).  ... 
doi:10.3390/ijms150610724 pmid:24933637 pmcid:PMC4100176 fatcat:jc2x6wy2hrduhoh7ylji26brye

A Robust Multifactor Dimensionality Reduction Method for Detecting Gene-Gene Interactions with Application to the Genetic Analysis of Bladder Cancer Susceptibility

Jiang Gui, Angeline S. Andrew, Peter Andrews, Heather M. Nelson, Karl T. Kelsey, Margaret R. Karagas, Jason H. Moore
2010 Annals of Human Genetics  
The multifactor dimensionality reduction (MDR) method was developed as machine learning alternative to parametric logistic regression for detecting interactions in absence of significant marginal effects  ...  Here, we propose a Robust Multifactor Dimensionality Reduction (RMDR) method that performs constructive induction using a Fisher's Exact Test rather than a predetermined threshold.  ...  Acknowledgments This work was funded by grant #IRG-82-003-22 from the American Cancer Society and NIH grants LM009012, LM010098, AI59694, CA57494 and ES007373.  ... 
doi:10.1111/j.1469-1809.2010.00624.x pmid:21091664 pmcid:PMC3057873 fatcat:2j6idasae5dkvdgbfdivex4gci

Gene–Gene and Gene-Sex Epistatic Interactions of MiR146a, IRF5, IKZF1, ETS1 and IL21 in Systemic Lupus Erythematosus

Rui-Xue Leng, Wei Wang, Han Cen, Mo Zhou, Chen-Chen Feng, Yan Zhu, Xiao-Ke Yang, Mei Yang, Yu Zhai, Bao-Zhu Li, Xiao-Song Wang, Rui Li (+5 others)
2012 PLoS ONE  
Epistasis was tested by additive model, multiplicative model and multifactor dimensionality reduction (MDR) method.  ...  The aim of this study was to test for gene-gene/gene-sex epistasis (interactions) in these known lupus susceptibility loci.  ...  Acknowledgments We wish to thank Xiang-Pei Li, Jin-Hui Tao (Anhui Provincial Hospital) and Jian-Hua Xu (the First Affiliated Hospital of Anhui Medical University) for assistance in sample preparation and  ... 
doi:10.1371/journal.pone.0051090 pmid:23236436 pmcid:PMC3517573 fatcat:t37d4powkrcnlivahsnheintni

A survey about methods dedicated to epistasis detection

Clément Niel, Christine Sinoquet, Christian Dina, Ghislain Rocheleau
2015 Frontiers in Genetics  
Some of these methods are exhaustive, such as multifactor dimensionality reduction, likelihood ratio-based tests or receiver operating characteristic curve analysis; some are non-exhaustive, such as machine  ...  Statistical analysis typically looks for association between a phenotype and a SNP taken individually via single-locus tests.  ...  We also thank two anonymous reviewers for very helpful comments and valuable improvement of the manuscript.  ... 
doi:10.3389/fgene.2015.00285 pmid:26442103 pmcid:PMC4564769 fatcat:5e5bqfpcbjbchf5n7mhurtejny

Log-linear model-based multifactor dimensionality reduction method to detect gene gene interactions

S. Yeoun Lee, Y. Chung, R. C. Elston, Y. Kim, T. Park
2007 Bioinformatics  
Results: In this article, we propose the log-linear model-based multifactor dimensionality reduction (LM MDR) method to improve the MDR in classifying sparse or empty cells.  ...  To address this problem, the multifactor dimensionality reduction (MDR) method has been proposed by Ritchie et al. to detect gene-gene interactions or gene-environment interactions.  ...  ACKNOWLEDGEMENTS The work was supported by the National Research Laboratory Program of Korea Science and Engineering Foundation (M10500000126) and a US Public Health Service Research grant (GM28356) from  ... 
doi:10.1093/bioinformatics/btm396 pmid:17872915 fatcat:hth2gl5znvfq3pm27odr6kgr44

An overview of SNP interactions in genome-wide association studies

P. Li, M. Guo, C. Wang, X. Liu, Q. Zou
2014 Briefings in Functional Genomics  
In this article, we review the two main aspects of SNP interaction studies in recent yearsçthe simulation and identification of SNP interactionsçand then discuss the principles, efficiency and differences  ...  devising new diagnostic tests and treatments.  ...  SNP interaction detection Method/tools Advantage/implement Source Reference MDR Non-parametric and model free http://ritchielab.psu.edu/ritchielab/current-research/ [53] multifactor-dimensionality-reduction-mdr  ... 
doi:10.1093/bfgp/elu036 pmid:25241224 fatcat:m6ceiikvofaohewiljs5yheqom
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