Testing for linkage and Hardy-Weinberg disequilibrium

Kulinskaya, E. and Lewin, A. (2009) Testing for linkage and Hardy-Weinberg disequilibrium. Annals of Human Genetics, 72 (2). pp. 253-262. ISSN 1469-1809

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Abstract

This paper concerns several important points when testing for Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) in genetics. First, we challenge the necessity of using exclusively two-sided tests for LD. Next, we show that the exact 2-sided tests based on the most popular measures of LD are not equivalent, and neither are the standard statistical tests even though the 1-sided tests are equivalent. We show how this results in different inference about LD for two data sets consisting of small groups of markers. Finally, we advocate the use of the conditional p-value for both LD and HWE testing. An important advantage of this p-value is that equivalent 1-sided tests are transformed into equivalent 2-sided tests.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Data Science and Statistics Faculty of Medicine and Health Sciences > Research Centres > Business and Local Government Data Research Centre Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Depositing User:	Vishal Gautam
Date Deposited:	11 Mar 2011 16:23
Last Modified:	22 Apr 2023 00:46
URI:	https://ueaeprints.uea.ac.uk/id/eprint/23073
DOI:	10.1111/j.1469-1809.2008.00501.x

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