Binary trait analysis was performed for comparison with the above quantitative trait analysis and also for comparison with the work of other groups. Association of DSM-IIIR and DSMIV AD was examined using the UNPHASED statistical package in two stages. First, for DZ families, a pedigree disequilibrium (PDT) style test was used, in the PDTPHASE module, to test for over-transmission of allele to offspring (a ‘within’ family test that should be robust to any population stratification effects). Second, for MZ families, pairs with discordant phenotypes were set to phenotype unknown while pairs with concordant phenotypes were not changed. Subsequently, one MZ twin per family was included for each trait analyzed in COCAPHASE. Since no parents were genotyped, each MZ twin was treated as unrelated and a case-control test was implemented.
