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 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.
|Keywords||Environmental sensitivity, Gene-environment interactions (G × E), Gene-gene interactions (G × G), Genome-wide association (GWA), Single-nucleotide polymorphisms (SNPS), The genabel project, Variabel, Variance heterogeneity|
|Persistent URL||dx.doi.org/10.1186/1471-2156-13-4, hdl.handle.net/1765/34946|
Struchalin, M.V., Amin, N., Eilers, P.H., van Duijn, C.M., & Aulchenko, Y.S.. (2012). An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity. BMC Genetics, 13. doi:10.1186/1471-2156-13-4