Model-specific tests on variance heterogeneity for detection of potentially interacting genetic loci.

ABSTRACT:

Background

Trait variances among genotype groups at a locus are expected to differ in the presence of an interaction between this locus and another locus or environment. A simple maximum test on variance heterogeneity can thus be used to identify potentially interacting single nucleotide polymorphisms (SNPs).

Results

We propose a multiple contrast test for variance heterogeneity that compares the mean of Levene residuals for each genotype group with their average as an alternative to a global Levene test. We applied this test to a Bogalusa Heart Study dataset to screen for potentially interacting SNPs across the whole genome that influence a number of quantitative traits. A user-friendly implementation of this method is available in the R statistical software package multcom

SUBMITTER: Hothorn LA 

PROVIDER: S-EPMC3549778 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature