A Comparative Study on Multifactor Dimensionality Reduction Methods for Detecting Gene-Gene Interactions with the Survival Phenotype.
Genome-wide association studies (GWAS) have extensively analyzed single SNP effects on a wide variety of common and complex diseases and found many genetic variants associated with diseases. However, there is still a large portion of the genetic variants left unexplained. This missing heritability problem might be due to the analytical strategy that limits analyses to only single SNPs. One of possible approaches to the missing heritability problem is to consider identifying multi-SNP effects or gene-gene interactions. The multifactor dimensionality reduction method has been widely used to detect gene-gene interactions based on the constructive induction by classifying high-dimensional genotype combinations into one-dimensional variable with two attributes of high risk and low risk for the case-control study. Many modifications of MDR have been proposed and also extended to the survival phenotype. In this study, we propose several extensions of MDR for the survival phenotype and compare the proposed extensions with earlier MDR through comprehensive simulation studies.
Department of Mathematics and Statistics, Sejong University, Seoul 143-747, Republic of Korea.
Seungyeoun
S
Lee
Department of Statistics, Seoul National University, Seoul 151-747, Republic of Korea.
Yongkang
Y
Kim
Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Republic of Korea.
Min-Seok
MS
Kwon
Department of Statistics, Seoul National University, Seoul 151-747, Republic of Korea ; Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747, Republic of Korea.
Taesung
T
Park
D000465:Algorithms; D003198:Computer Simulation; D004843:Epistasis, Genetic; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D058011:Multifactor Dimensionality Reduction; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics