title: An R package "VariABEL" for genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity.
abstract: 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.
authors.affiliation: Department of Epidemiology, Erasmus MC, Rotterdam, 3000 CA, The Netherlands.
authors.forename: Maksim V
authors.initials: MV
authors.lastname: Struchalin
authors.forename: Najaf
authors.initials: N
authors.lastname: Amin
authors.forename: Paul H C
authors.initials: PH
authors.lastname: Eilers
authors.forename: Cornelia M
authors.initials: CM
authors.lastname: van Duijn
authors.forename: Yurii S
authors.initials: YS
authors.lastname: Aulchenko
mesh_terms: D019295:Computational Biology / Q000379:methods*; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D012984:Software