There has been considerable debate about the genetic architecture of schizophrenia. We estimated the proportion of variance in liability to schizophrenia explained by SNPs using GCTA. 64 Traditional genetic epidemiological studies use the phenotypic resemblance of relatives to estimate the proportion of variance in liability using theoretic resemblance assumptions. GCTA uses genome-wide SNP genotypes to calculate the heritability in the population from the identity-by-state relationships for each pair of individuals. Using the PGC schizophrenia data, we previously estimated the SNP heritability of schizophrenia at 0.23 (SE 0.01) using HapMap3 imputation and assuming a population risk of 0.01. 7 Using the same imputation reference and population risk, SNP heritability was substantially higher in the Swedish samples (0.32, SE 0.03) possibly due to the greater phenotypic and genetic homogeneity in the Swedish sample compared to the PGC samples of mixed European ancestry. We obtained a similar estimate of SNP heritability using 1000 Genomes imputed data (0.33, SE 0.03, population risk 0.01). For a population risk of 0.004, 4,65 SNP heritability was 0.26 (SE 0.02) using HapMap3 and 0.27 (SE 0.02) using 1000
