Cargando…
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...
Autores principales: | , |
---|---|
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 |
_version_ | 1782504108692865024 |
---|---|
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. |
format | Online Article Text |
id | pubmed-5287119 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Korea Genome Organization |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT lidonghe efficientstrategytoidentifygenegeneinteractionsanditsapplicationtotype2diabetes AT wonsungho efficientstrategytoidentifygenegeneinteractionsanditsapplicationtotype2diabetes |