Testing for goodness rather than lack of fit of an X-chromosomal SNP to the Hardy-Weinberg model

PloS One
Stefan Wellek, Andreas Ziegler

Abstract

The problem of checking the genotype distribution obtained for some diallelic marker for compatibility with the Hardy-Weinberg equilibrium (HWE) condition arises also for loci on the X chromosome. The possible genotypes depend on the sex of the individual in this case: for females, the genotype distribution is trinomial, as in the case of an autosomal locus, whereas a binomial proportion is observed for males. Like in genetic association studies with autosomal SNPs, interest is typically in establishing approximate compatibility of the observed genotype frequencies with HWE. This requires to replace traditional methods tailored for detecting lack of fit to the model with an equivalence testing procedure to be derived by treating approximate compatibility with the model as the alternative hypothesis. The test constructed here is based on an upper confidence bound and a simple to interpret combined measure of distance between true and HWE conforming genotype distributions in female and male subjects. A particular focus of the paper is on the derivation of the asymptotic distribution of the test statistic under null alternatives which is not of the usual Gaussian form. A closed sample size formula is also provided and shown to beh...Continue Reading

References

Aug 1, 1972·Journal of Pharmaceutical Sciences·W J Westlake
Jan 7, 2006·Biometrical Journal. Biometrische Zeitschrift·Stefan Wellek
Jun 6, 2007·Genetic Epidemiology·Gang ZhengNancy L Geller
Apr 23, 2008·Current Protocols in Human Genetics·Kelli Ryckman, Scott M Williams
Feb 25, 2010·The Journal of Clinical Investigation·Stephen Higgs, Sarah A Ziegler
Apr 16, 2010·Biometrical Journal. Biometrische Zeitschrift·Stefan WellekAndreas Ziegler
Dec 25, 2010·Breast Cancer Research and Treatment·Andreas ZieglerStefan Wellek
Dec 31, 2017·Molecular Ecology Resources·Jan Graffelman, Bruce S Weir
Jun 8, 2018·Methods in Molecular Biology·Kalliope Panoutsopoulou, Eleanor Wheeler

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Methods Mentioned

BETA
genotyping

Software Mentioned

SAS
IML script
EQUIVNONINF
gofhwex
IML
R script
R
Hardy
R package

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