Journal
CURRENT GENOMICS
Volume 17, Issue 5, Pages 396-402Publisher
BENTHAM SCIENCE PUBL LTD
DOI: 10.2174/1389202917666160513102612
Keywords
Generalized multifactor dimensionality reduction; Gene-gene interactions; Gene-environment interactions; Complex; traits; Unrelated sample; Family sample; Computer software
Funding
- National Institute of Health Grant [R01 DA025095]
- National Science Foundation [DMS1462990]
- National Basic Research Programs of China (973 Programs) [2011CB109306]
- National Natural Science Foundation [31271608, 31470083]
- NATIONAL INSTITUTE ON DRUG ABUSE [R01DA025095] Funding Source: NIH RePORTER
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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.
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