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An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity
BACKGROUND: Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our unde...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398297/ https://www.ncbi.nlm.nih.gov/pubmed/22272569 http://dx.doi.org/10.1186/1471-2156-13-4 |
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author | Struchalin, Maksim V Amin, Najaf Eilers, Paul HC van Duijn, Cornelia M Aulchenko, Yurii S |
author_facet | Struchalin, Maksim V Amin, Najaf Eilers, Paul HC van Duijn, Cornelia M Aulchenko, Yurii S |
author_sort | Struchalin, Maksim V |
collection | PubMed |
description | BACKGROUND: Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties. We and Pare with colleagues (2010) developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants. RESULTS: In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests. CONCLUSIONS: Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context. |
format | Online Article Text |
id | pubmed-3398297 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-33982972012-07-18 An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity Struchalin, Maksim V Amin, Najaf Eilers, Paul HC van Duijn, Cornelia M Aulchenko, Yurii S BMC Genet Methodology Article BACKGROUND: Hundreds of new loci have been discovered by genome-wide association studies of human traits. These studies mostly focused on associations between single locus and a trait. Interactions between genes and between genes and environmental factors are of interest as they can improve our understanding of the genetic background underlying complex traits. Genome-wide testing of complex genetic models is a computationally demanding task. Moreover, testing of such models leads to multiple comparison problems that reduce the probability of new findings. Assuming that the genetic model underlying a complex trait can include hundreds of genes and environmental factors, testing of these models in genome-wide association studies represent substantial difficulties. We and Pare with colleagues (2010) developed a method allowing to overcome such difficulties. The method is based on the fact that loci which are involved in interactions can show genotypic variance heterogeneity of a trait. Genome-wide testing of such heterogeneity can be a fast scanning approach which can point to the interacting genetic variants. RESULTS: In this work we present a new method, SVLM, allowing for variance heterogeneity analysis of imputed genetic variation. Type I error and power of this test are investigated and contracted with these of the Levene's test. We also present an R package, VariABEL, implementing existing and newly developed tests. CONCLUSIONS: Variance heterogeneity analysis is a promising method for detection of potentially interacting loci. New method and software package developed in this work will facilitate such analysis in genome-wide context. BioMed Central 2012-01-24 /pmc/articles/PMC3398297/ /pubmed/22272569 http://dx.doi.org/10.1186/1471-2156-13-4 Text en Copyright ©2012 Struchalin et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Methodology Article Struchalin, Maksim V Amin, Najaf Eilers, Paul HC van Duijn, Cornelia M Aulchenko, Yurii S An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title | An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title_full | An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title_fullStr | An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title_full_unstemmed | An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title_short | An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
title_sort | r package "variabel" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398297/ https://www.ncbi.nlm.nih.gov/pubmed/22272569 http://dx.doi.org/10.1186/1471-2156-13-4 |
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