The Pedigree Disequilibrium Test (PDT) (Martin et al., 2001), as implemented in the program UNPHASED (Dudbridge, 2003), was used to test whether the qualitative phenotypes in the extended, multiplex COGA pedigrees were associated with the genotyped SNPs. The PDT-average statistic, which weighs each family equally in computing the overall test statistic, was the statistic of interest for each phenotype.
