Significant evidence for linkage of a simulated trait to D1G024-A conclusion reached using multiallelic transmission/disequilibrium tests

We applied three versions of the transmission/disequilibrium test (TDT) for detecting linkage in nuclear families using the a priori information of po ssibly present association. For our analyses we employed all marker data fo r a simulated trait. Results for replicate 11 showed significant linkage to D1G024 using the multiallelic T-mhet statistic and the extended TDT. The T DT for the most frequent parental allele which had been applied successfull y in previous studies failed to detect linkage. This result may have happen ed because the data did not arise from a realistic simulation of the evolut ion of a real population, where mutations might be expected to occur agains t a specific haplotype. Simulation studies are required to elucidate the ap plicability of the TDT for the most frequent parental allele in realistic s ituations. Furthermore, guidelines have to be developed for how to pool cat egories in large, sparse contingency tables to obtain larger cell frequenci es and lower degrees of freedom. (C) 1999 Wiley-Liss, Inc.