GMDR

GMDR: Versatile software for detecting gene-gene and gene-environment interactions underlying complex traits

Xu HM, Xu LF, Hou TT, Luo LF, Chen GB, Sun XW, Lou XY,

Institute of Bioinformatics, Zhejiang University, Hangzhou, China



    Identification of multifactor gene-gene (GxG) and gene-environment (GxE) interactions underlying complex traits poses one of the great challenges to today's genetic study. Development of the generalized multifactor dimensionality reduction (GMDR) method provides a practicable solution to problems in detection of interactions. To exploit the opportunities brought by the availability of diverse data, it is in high demand to develop the corresponding GMDR software that can handle a breadth of phenotypes, such as continuous, count, dichotomous, polytomous nominal, ordinal, survival and multivariate, and various kinds of study designs, such as unrelated case-control, family-based and pooled unrelated and family samples, and also allows adjustment for covariates. We developed a versatile GMDR package to implement this serial of GMDR analyses for various scenarios (e.g., unified analysis of unrelated and family samples) and large-scale (e.g., genome-wide) data. This package includes other desirable features such as data management and preprocessing. Permutation testing strategies are also built in to evaluate the threshold or empirical p values. In addition, its performance is scalable to the computational resources. The software is available at http://www.soph.uab.edu/ssg/software or http://ibi.zju.edu.cn/software.

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Citation
Hou TT, Lin F, Bai S, Cleves MA, Xu HM, Lou XY (2019). Generalized multifactor dimensionality reduction approaches to identification of genetic interactions underlying ordinal traits. Genetic Epidemiology 43 (1): 24-36.
Xu HM, Xu LF, Hou TT, Luo LF, Chen GB, Sun XW, Lou XY (2016). GMDR: Versatile software for detecting gene-gene and gene-environment interactions underlying complex traits. Current Genomics 17 (5): 396-02.
Lou XY (2015). UGMDR: A unified conceptual framework for detection of multifactor interactions underlying complex traits. Heredity 114 (3): 255-261.
Xu HM, Sun XW, Qi T, Lin WY, Liu N, Lou XY (2014). Multivariate dimensionality reduction approaches to identify gene-gene and gene-environment interactions underlying multiple complex traits. PLoS One 9 (9): e108103.
Chen GB, Liu N, Klimentidis YC, Zhu X, Zhi D, Wang X, Lou XY (2014). A unified GMDR method for detecting gene-gene interactions in family and unrelated samples with application to nicotine dependence. Human Genetics 133 (2): 139-150.
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Chen GB, Xu Y, Xu HM, Li MD, Zhu J, Lou XY (2011). Practical and theoretical considerations in study design for detecting gene-gene interactions using MDR and GMDR approaches. PLoS One 6 (2): e16981.
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