Robustness of case-control studies to population stratification

What to make of it? The (Re)emergence of a biological conceptualization of race in health disparities research

The debate over the role of race/ethnicity in determining disease susceptibility has re-emerged since it was declared that race was arbitrary biological fiction more than 50 years ago. Partly due to advancements in the Human Genome Project and related technologies, the idea that race/ethnicity does have a genetic basis is enjoying a resurgence. A rise in the use of race in genetic studies has left many researchers who are committed to a social conceptualization of race at a loss regarding how to evaluate these developments. The commentary attempts to correct the problem by providing a critical review of the state of research on race, genetics and health. This review aims to bring social health disparities researchers up-to-date on developments in the genetic literature and to facilitate a more critical engagement of research that purports to find a genetic basis to racial disparities in health.

Association methods in human genetics

Genetic association studies are increasingly used in the search for susceptibility variants for human traits. While many of the statistical tools available for such studies are well established, the field is advancing rapidly, as biological and technological developments allow investigators to generate vast amounts of detailed genetic data. This chapter gives an overview of the statistical evaluation of genetic data in both unrelated individuals and families. A brief introduction to fundamental population genetics concepts is followed by detailed examinations of measures of linkage disequilibrium and single-marker and haplotype association tests. Emphasis is given to the historical development of family-based tests to provide the context for more recent advancements. The chapter concludes with a discussion of design strategies for genetic association studies with dense genotyping of hundreds or thousands of markers, such as those planned for follow up of a linkage-candidate region or genome-wide association studies.

An evaluation of power and type I error of single-nucleotide polymorphism transmission/disequilibrium-based statistical methods under different family structures, missing parental data, and population stratification

Researchers conducting family-based association studies have a wide variety of transmission/disequilibrium (TD)-based methods to choose from, but few guidelines exist in the selection of a particular method to apply to available data. Using a simulation study design, we compared the power and type I error of eight popular TD-based methods under different family structures, frequencies of missing parental data, genetic models, and population stratifications. No method was uniformly most powerful under all conditions, but type I error was appropriate for nearly every test statistic under all conditions. Power varied widely across methods, with a 46.5% difference in power observed between the most powerful and the least powerful method when 50% of families consisted of an affected sib pair and one parent genotyped under an additive genetic model and a 35.2% difference when 50% of families consisted of a single affection-discordant sibling pair without parental genotypes available under an additive genetic model. Methods were generally robust to population stratification, although some slightly less so than others. The choice of a TD-based test statistic should be dependent on the predominant family structure ascertained, the frequency of missing parental genotypes, and the assumed genetic model.