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Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions

Title
Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions
Author
정혜영
Keywords
Gene-gene interaction; Fuzzy-set theory; FGMDR; Multifactor dimensionality reduction
Issue Date
2018-04
Publisher
BioMed Central Ltd.
Citation
BMC Medical Genomics, v. 11, Article no. 32
Abstract
Gene-gene interactions (GGIs) are a known cause of missing heritability. Multifactor dimensionality reduction (MDR) is one of most commonly used methods for GGI detection. The generalized multifactor dimensionality reduction (GMDR) method is an extension of MDR method that is applicable to various types of traits, and allows covariate adjustments. Our previous Fuzzy MDR (FMDR) is another extension for overcoming simple binary classification. FMDR uses continuous member-ship values instead of binary membership values 0 and 1, improving power for detecting causal SNPs and more intuitive interpretations in real data analysis. Here, we propose the fuzzy generalized multifactor dimensionality reduction (FGMDR) method, as a combined analysis of fuzzy set-based analysis and GMDR method, to detect GGIs associated with diseases using fuzzy set theory. Results Through simulation studies for different types of traits, the proposed FGMDR showed a higher detection ratio of causal SNPs, compared to GMDR. We then applied FGMDR to two real data: Crohn’s disease (CD) data from the Wellcome Trust Case Control Consortium (WTCCC) with a binary phenotype and the Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) data from Korean population with a continuous phenotype. The interactions derived by our method include the pre-reported interactions associated with phenotypes. Conclusions The proposed FGMDR performs well for GGI detection with covariate adjustments. The program written in R for FGMDR is available at http://statgen.snu.ac.kr/software/FGMDR.
URI
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-018-0343-0https://repository.hanyang.ac.kr/handle/20.500.11754/126352
ISSN
1755-8794
DOI
10.1186/s12920-018-0343-0
Appears in Collections:
COLLEGE OF SCIENCE AND CONVERGENCE TECHNOLOGY[E](과학기술융합대학) > APPLIED MATHEMATICS(응용수학과) > Articles
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2018.04_정혜영_Fuzzy set-based generalized multifactor dimensionality reduction analysis of gene-gene interactions.pdfDownload
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