An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity
<p>Abstract</p> <p>Background</p> <p>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 environment...
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BMC
2012-01-01
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| Series: | BMC Genetics |
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| Online Access: | http://www.biomedcentral.com/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 | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-12-12T02:31:49Z |
| publishDate | 2012-01-01 |
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| spelling | doaj.art-2cd207dce06346f29f8b8b3c150112272022-12-22T00:41:22ZengBMCBMC Genetics1471-21562012-01-01131410.1186/1471-2156-13-4An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneityStruchalin Maksim VAmin NajafEilers Paul HCvan Duijn Cornelia MAulchenko Yurii S<p>Abstract</p> <p>Background</p> <p>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.</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusions</p> <p>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.</p>http://www.biomedcentral.com/1471-2156/13/4single-nucleotide polymorphisms (SNPs)genome-wide association (GWA)gene-environment interactions (GxE)gene-gene interactions (GxG)variance heterogeneityenvironmental sensitivityVariABELthe GenABEL project |
| spellingShingle | 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 BMC Genetics single-nucleotide polymorphisms (SNPs) genome-wide association (GWA) gene-environment interactions (GxE) gene-gene interactions (GxG) variance heterogeneity environmental sensitivity VariABEL the GenABEL project |
| 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 | single-nucleotide polymorphisms (SNPs) genome-wide association (GWA) gene-environment interactions (GxE) gene-gene interactions (GxG) variance heterogeneity environmental sensitivity VariABEL the GenABEL project |
| url | http://www.biomedcentral.com/1471-2156/13/4 |
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