Detecting heritable phenotypes without a model using fast permutation testing for heritability and set-tests.

ABSTRACT: Testing for association between a set of genetic markers and a phenotype is a fundamental task in genetic studies. Standard approaches for heritability and set testing strongly rely on parametric models that make specific assumptions regarding phenotypic variability. Here, we show that resulting p-values may be inflated by up to 15 orders of magnitude, in a heritability study of methylation measurements, and in a heritability and expression quantitative trait loci analysis of gene expression profiles. We propose FEATHER, a method for fast permutation-based testing of marker sets and of heritability, which properly controls for false-positive results. FEATHER eliminated 47% of methylation sites found to be heritable by the parametric test, suggesting a substantial inflation of false-positiv

SUBMITTER: Schweiger R 

PROVIDER: S-EPMC6249264 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature