Margaret Taub, Johns Hopkins School of Public HealthFebruary 29, 2012 @ 3:30 - 4:30 pm
Location: 1412 BRB II/III
Title: Incorporating Genotype Uncertainties into the Genotypic Transmission-Disequilibrium Test
Abstract: Genotype imputation has become a standard option for researchers to expand their genotype datasets to improve signal precision and power in tests of genetic association with disease. In imputations for family based studies however, subjects are often treated as unrelated individuals: currently, only BEAGLE allows for simultaneous imputation for trios of parents and offspring, but only the most likely genotype calls are returned, not estimated genotype probabilities. For population based SNP association studies, it has been shown that incorporating genotype uncertainty can be more powerful than using hard genotype calls. We here investigate this issue in the context of case-parent family data. We present the statistical framework for the genotypic transmission-disequilibrium test (gTDT) using observed genotype calls and imputed genotype probabilities, and illustrate the performance of our method on a set of trios from the International Cleft Consortium.