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Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes

Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide...

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Autores principales: Li, Donghe, Won, Sungho
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Korea Genome Organization 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287119/
https://www.ncbi.nlm.nih.gov/pubmed/28154506
http://dx.doi.org/10.5808/GI.2016.14.4.160
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author Li, Donghe
Won, Sungho
author_facet Li, Donghe
Won, Sungho
author_sort Li, Donghe
collection PubMed
description Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named “BOolean Operation-based Screening and Testing” (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D.
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spelling pubmed-52871192017-02-02 Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes Li, Donghe Won, Sungho Genomics Inform Original Article Over the past decade, the detection of gene-gene interactions has become more and more popular in the field of genome-wide association studies (GWASs). The goal of the GWAS is to identify genetic susceptibility to complex diseases by assaying and analyzing hundreds of thousands of single-nucleotide polymorphisms. However, such tests are computationally demanding and methodologically challenging. Recently, a simple but powerful method, named “BOolean Operation-based Screening and Testing” (BOOST), was proposed for genome-wide gene-gene interaction analyses. BOOST was designed with a Boolean representation of genotype data and is approximately equivalent to the log-linear model. It is extremely fast, and genome-wide gene-gene interaction analyses can be completed within a few hours. However, BOOST can not adjust for covariate effects, and its type-1 error control is not correct. Thus, we considered two-step approaches for gene-gene interaction analyses. First, we selected gene-gene interactions with BOOST and applied logistic regression with covariate adjustments to select gene-gene interactions. We applied the two-step approach to type 2 diabetes (T2D) in the Korea Association Resource (KARE) cohort and identified some promising pairs of single-nucleotide polymorphisms associated with T2D. Korea Genome Organization 2016-12 2016-12-30 /pmc/articles/PMC5287119/ /pubmed/28154506 http://dx.doi.org/10.5808/GI.2016.14.4.160 Text en Copyright © 2016 by the Korea Genome Organization http://creativecommons.org/licenses/by-nc/4.0/ It is identical to the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/).
spellingShingle Original Article
Li, Donghe
Won, Sungho
Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title_full Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title_fullStr Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title_full_unstemmed Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title_short Efficient Strategy to Identify Gene-Gene Interactions and Its Application to Type 2 Diabetes
title_sort efficient strategy to identify gene-gene interactions and its application to type 2 diabetes
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5287119/
https://www.ncbi.nlm.nih.gov/pubmed/28154506
http://dx.doi.org/10.5808/GI.2016.14.4.160
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