The PGC-SCZ includes data from the International Schizophrenia Consortium (ISC)8, the Molecular Genetics of Schizophrenia (MGS) study9 and other samples (OTH) (Supplementary Table 1). Using a linear mixed model (Online Methods) we estimated the proportion of variance in liability to schizophrenia explained by SNPs (h2) in each of these three independent data subsets (Table 1). We use the notation h2 because the estimates represent a lower bound of narrow sense heritability; it is a lower bound because only variation due to association with the SNPs can be estimated. Preliminary analyses were conducted using non-imputed genotypes of the ISC and MGS subsets (Supplementary Table 2). The estimates of h2 for the PGC-SCZ subsets of ISC, MGS and OTH were each greater than the estimate from the total combined PGC-SCZ sample of h2 = 23% (s.e. 1%) (Table 1). We investigated this result by conducting bivariate analyses considering cases and controls from one subset as trait 1 and those from a different subset as trait 2 (Table 2); the two independent subsets are related through the coefficients of genome-wide similarity calculated from
