Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis.

BMC Bioinformatics
Masao Ueki, Gen Tamiya

Abstract

Genome-wide gene-gene interaction analysis using single nucleotide polymorphisms (SNPs) is an attractive way for identification of genetic components that confers susceptibility of human complex diseases. Individual hypothesis testing for SNP-SNP pairs as in common genome-wide association study (GWAS) however involves difficulty in setting overall p-value due to complicated correlation structure, namely, the multiple testing problem that causes unacceptable false negative results. A large number of SNP-SNP pairs than sample size, so-called the large p small n problem, precludes simultaneous analysis using multiple regression. The method that overcomes above issues is thus needed. We adopt an up-to-date method for ultrahigh-dimensional variable selection termed the sure independence screening (SIS) for appropriate handling of numerous number of SNP-SNP interactions by including them as predictor variables in logistic regression. We propose ranking strategy using promising dummy coding methods and following variable selection procedure in the SIS method suitably modified for gene-gene interaction analysis. We also implemented the procedures in a software program, EPISIS, using the cost-effective GPGPU (General-purpose computing o...Continue Reading

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Citations

Jun 14, 2013·Journal of Human Genetics·Hiroto NarimatsuUNKNOWN Yamagata University Medical Education and Training Program through the Genomic Cohort Study
Sep 10, 2014·Nature Reviews. Genetics·Wen-Hua WeiChris S Haley
Jul 16, 2015·European Journal of Human Genetics : EJHG·Jinying ZhaoMomiao Xiong
Sep 30, 2014·Neurobiology of Aging·Derrek P HibarPaul M Thompson
Jul 22, 2014·Statistics in Medicine·Masao Ueki
Feb 2, 2017·International Journal of Molecular Sciences·Hiroto Narimatsu
Aug 14, 2018·Biometrical Journal. Biometrische Zeitschrift·Dörte Wittenburg, Volkmar Liebscher
Nov 24, 2017·The Plant Journal : for Cell and Molecular Biology·Jingyuan LiuRongling Wu
Aug 15, 2015·Briefings in Bioinformatics·Alex UptonJames Richard Perkins
Aug 13, 2020·Journal of Human Genetics·Akira NaritaGen Tamiya
Jan 1, 2014·The Annals of Applied Statistics·Jiahan LiRongling Wu

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Methods Mentioned

BETA
chip

Software Mentioned

Affymetrix
PLINK
MDR
SIS
BEAM
genomeSIMLA
BOOST
EPISIS
Random Jungle
PADC

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