On the testing of Hardy‐Weinberg proportions and equality of allele frequencies in males and females at biallelic genetic markers. Issue 1 (25th October 2017)

• Record Type: Journal Article
• Authors: Graffelman, Jan; Weir, Bruce S.
• Is Part Of: Genetic epidemiology. Volume 42:Issue 1(2018)
• Page Start: 34
• Page End: 48
• Publication Date: 2017-10-25
• Subjects: Akaike's information criterion -- exact test -- inbreeding coefficient -- likelihood ratio test -- ternary diagram; Genetic epidemiology -- Periodicals; Heredity -- Periodicals; Medical geography -- Periodicals; 614
• DOI: 10.1002/gepi.22079
• Languages: English
• ISSNs: 0741-0395

Abstract

ABSTRACT: Standard statistical tests for equality of allele frequencies in males and females and tests for Hardy‐Weinberg equilibrium are tightly linked by their assumptions. Tests for equality of allele frequencies assume Hardy‐Weinberg equilibrium, whereas the usual chi‐square or exact test for Hardy‐Weinberg equilibrium assume equality of allele frequencies in the sexes. In this paper, we propose ways to break this interdependence in assumptions of the two tests by proposing an omnibus exact test that can test both hypotheses jointly, as well as a likelihood ratio approach that permits these phenomena to be tested both jointly and separately. The tests are illustrated with data from the 1000 Genomes project.