The power of the transmission disequilibrium test in the presence of population stratification

The Transmission Disequilibrium Test (TDT) is a family-based test for association based on the rate of transmission of alleles from heterozygous parents to affected offspring, and has gained popularity as this test preserves the Type I error rate. Population stratification results in a decreased number of heterozygous parents compared to that expected assuming Hardy-Weinberg Equilibrium (Wahlund Effect). We show that population stratification changes the relative proportion of the informative mating types. The decrease in the number of heterozygous parents and the change in the relative proportion of the informative mating types result in significant changes to the sample sizes required to achieve the power desired. We show examples of the changes in sample sizes, and provide an easy method for estimating TDT sample sizes in the presence of population stratification. This method potentially aids in reducing the number of false-negative association studies.