Efficient test for deviation from Hardy-Weinberg equilibrium with known or ambiguous typing in highly polymorphic loci.

ABSTRACT: The Hardy-Weinberg equilibrium (HWE) assumption is essential to many population genetics models. Multiple tests were developed to test its applicability in observed genotypes. Current methods are divided into exact tests applicable to small populations and a small number of alleles, and approximate goodness-of-fit tests. Existing tests cannot handle ambiguous typing in multi-allelic loci. We here present a novel exact test Unambiguous Multi Allelic Test (UMAT) not limited to the number of alleles and population size, based on a perturbative approach around the current observations. We show its accuracy in the detection of deviation from HWE. We then propose an additional model to handle ambiguous typing using either sampling into UMAT or a goodness-of-fit test test with a variance estimate

SUBMITTER: Shkuri O 

PROVIDER: S-EPMC11414081 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature