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Biostatistics Advance Access published online on April 25, 2008
Biostatistics, doi:10.1093/biostatistics/kxn007
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© The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Testing for association on the X chromosome

David Clayton

Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Addenbrookes's Hospital, Cambridge CB2 0XY, UK david.clayton{at}cimr.cam.ac.uk

The problem of testing for genotype–phenotype association with loci on the X chromosome in mixed-sex samples has received surprisingly little attention. A simple test can be constructed by counting alleles, with males contributing a single allele and females 2. This approach does assume not only Hardy–Weinberg equilibrium in the population from which the study subjects are sampled but also, perhaps, an unrealistic alternative hypothesis. This paper proposes 1 and 2 degree-of-freedom tests for association which do not assume Hardy–Weinberg equilibrium and which treat males as homozygous females. The proposed method remains valid when phenotype varies between sexes, provided the allele frequency does not, and avoids the loss of power resulting from stratification by sex in such circumstances.

Keywords: Genetic association studies

Received November 13, 2007; revised February 21, 2008; accepted for publication February 27, 2008.


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