For the CLOZUK + PGC meta-analysis, the LD score intercept was 1.075 ± 0.014 (mean χ2 = 1.960), which supports more than 90% of the signal being driven by polygenic architecture. Both of these figures are in line with those for other well-powered GWAS of complex human traits64, including schizophrenia5. This analysis was also used to calculate SNP-based heritability (h2SNP) for our three datasets (CLOZUK, INDEPENDENT PGC and the CLOZUK + PGC meta-analysis), which we transformed to a liability scale using a population prevalence of 1% (registry-based lifetime prevalence62). For reference and compatibility with epidemiological studies of schizophrenia, prevalence estimates of 0.7% (lifetime morbid risk63) and 0.4% (point prevalence63, more akin to treatment-resistant schizophrenia prevalence (appropriate for CLOZUK)) were used for additional liability-scale h2SNP calculations (Supplementary Table 15).
