This project involved analysis of a simulated dataset from the Genetic Analysis Workshop 12. A set of data for a complex qualitative trait was simulated by the data organizing committee of the GAW12. We used these data to compare the power of two new family-based tests of linkage disequilibrium that are being developed by me and my collaborators to several other implementations of the published Transmission Disequilibrium Test (TDT). We showed that none of these tests had adequate power in the small samples originally supplied, but that when all the replicates were combined to yield a large dataset, then all the methods had good power to detect loci with very small effects on the trait at genome-wide significance levels. One of our new methods was particularly successful in that we were able to show that it yields good estimates of both the recombination fraction and a generalized measure of association, something that the TDT does not accomplish. These results were recently presented at the GAW12 workshop and a paper is in preparation.
