Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data
Qiong Li, Hélène Massam and Xin Gao*
Department of Mathematics and Statistics, York University, Toronto, ON, M3J 1P3, Canada
- Corresponding Author:
- Xin Gao
Department of Mathematics and Statistics
York University, Toronto, ON, M3J 1P3, Canada
Tel: 416-736-2100, ext: 66097
E-mail: [email protected]
Received date: August 22, 2013; Accepted date: November 18, 2013; Published date: November 26, 2013
Citation: Li Q, Massam H, Gao X (2013) Likelihood Ratio Test of Hardy-Weinberg Equilibrium Using Uncertain Genotypes for Sibship Data. Int J Biomed Data Min 3:104. doi: 10.4172/2090-4924.1000104
Copyright: © 2013 Li Q, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Testing for Hardy-Weinberg equilibrium of genotype frequencies is a crucial first step in the study of population genetics. In this paper, we develop an Expectation-Maximization algorithm to estimate the genotype frequencies for sibship data with genotype uncertainty. We also develop a likelihood ratio test of Hardy-Weinberg equilibrium for sibships with no parental genotypes available and with possible genotyping errors. Simulations show that our likelihood ratio test maintains valid control of the type I error rate and good statistical power. Finally, the likelihood ratio test is extended across strata when a sample is stratified by multiple ethnic populations with different genotype frequencies.