Logistic transmission modeling for the simulated data of GAW10 problem 2

A recently developed nonparametric method is a generalization of the transmission disequilibrium test across all alleles of a locus. This approach has been applied to Problem 2 of GAW10 and has been extended to explore the combined contribution of neighboring loci for chromosomes 1, 5, and 8. When applied to the chromosome 5 data of the first replicate of the nuclear pedigrees from Problem 2 of GAW10, the data show that four of the 25 loci obtain a probability less than 0.05. However, when combined models composed of each potentially significant marker (p < 0.05) and its nearest neighbors are considered, the combined contributions of G14 and G15 are the most significant (p = 0.007). Consequently, the region near G14 and G15 is identified as the best candidate region in chromosome 5 for linkage to the common disease.