Premium
A likelihood ratio test of population Hardy‐Weinberg equilibrium for case‐control studies
Author(s) -
Yu Chang,
Zhang Sanguo,
Zhou Chuan,
Sile Saba
Publication year - 2009
Publication title -
genetic epidemiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.301
H-Index - 98
eISSN - 1098-2272
pISSN - 0741-0395
DOI - 10.1002/gepi.20381
Subject(s) - population stratification , hardy–weinberg principle , genotyping , genetic association , population , statistics , feature selection , association (psychology) , type i and type ii errors , biology , econometrics , genetics , genotype , allele frequency , mathematics , computer science , demography , machine learning , psychology , single nucleotide polymorphism , sociology , gene , psychotherapist
Testing Hardy‐Weinberg equilibrium (HWE) in the control group is commonly used to detect genotyping errors in genetic association studies. We propose a likelihood ratio test for testing HWE in the study population using both case and control samples. This test incorporates underlying association models. Another feature is that, when we infer the disease‐genotype association, we explicitly incorporate HWE or a possible departure from Hardy‐Weinberg equilibrium (DHWE) into the model. Our unified framework enables us to infer the disease‐genotype association when a detected DHWE needs to be part of the model after causes for the DHWE are explored. Real data sets are used to illustrate the application of the methodology and its implication in genetic association studies. Our analysis and interpretation touch on issues such as genotyping errors, population selection, population stratification, or the study sampling plan, that all could be the cause of DHWE. Genet. Epidemiol . 2009. Published 2008 Wiley‐Liss, Inc.