For each of the 127 successfully imputed schizophrenia-associated variants we tested association with each of the 17 endophenotypes. We also conducted single variant tests of all whole-genome-sequenced variants within the 108 PGC-identified loci. In both cases, we used a linear mixed model, EMMAX, that accounts for both family structure and population stratification using an empirical kinship matrix (Kang et al. 2010).
