Abstract
BackgroundThis study is motivated by National Household Surveys that collect genetic data, in which complex samples (e.g. stratified multistage cluster sample), partially from the same family, are selected. In addition to the differential selection probabilities of selecting households and persons within the sampled households, there are two levels of correlations of the collected genetic data in National Genetic Household Surveys (NGHS). The first level of correlation is induced by the hierarchical geographic clustered sampling of households and the second level of correlation is induced by biological inheritances from individuals sampled in the same household.ResultsTo test for Hardy-Weinberg Equilibrium (HWE) in NGHS, two test statistics, the CCS method [1] and the QS method [2], appear to be the only existing methods that take account of both correlations. In this paper, I evaluate both methods in terms of the test size and power under a variety of complex designs with different weighting schemes and varying magnitudes of the two correlation effects. Both methods are applied to a real data example from the Hispanic Health and Nutrition Examination Survey with simulated genotype data.ConclusionsThe QS method maintains the nominal size well and consistently achieves higher power than the CCS method in testing HWE under a variety of sample designs, and therefore is recommended for testing HWE of genetic survey data with complex designs.
Highlights
This study is motivated by National Household Surveys that collect genetic data, in which complex samples, partially from the same family, are selected
This study is motivated by population-based family data collected from National Genetic Household Surveys (NGHS), in which complex samples, partially from the same family, are selected
We examine and compare the performance of two methods, in terms of the sizes and powers, via Monte-Carlo simulation studies under a variety of complex sample designs with differential weighting schemes and varying magnitudes of the correlation effects
Summary
This study is motivated by National Household Surveys that collect genetic data, in which complex samples (e.g. stratified multistage cluster sample), partially from the same family, are selected. In addition to the differential selection probabilities of selecting households and persons within the sampled households, there are two levels of correlations of the collected genetic data in National Genetic Household Surveys (NGHS). This study is motivated by population-based family data collected from National Genetic Household Surveys (NGHS), in which complex samples (i.e. sample collected with stratified multistage cluster sampling), partially from the same family, are selected. There are two levels of correlations of the collected genetic data in NGHS. NHANES III employed a complex sample design, involving stratified multistage cluster sampling, to select participants [6,7]. On average 1.6 persons are sampled per household [8]
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