We then conducted a meta-analysis of the Swedish and independent PGC schizophrenia samples using the same quality control, imputation, and analysis pipeline. This GWAS meta-analysis of 13,833 schizophrenia cases and 18,310 controls (Table 1) afforded power to detect genotypic relative risks of 1.10-1.14 for reference allele frequencies 0.15-0.85 (power=0.8, α=5×10−8, log-additive model). We evaluated the comparability of the Swedish and PGC studies using sign tests: of 608 SNPs selected from the PGC results with P < 0.0001 and in approximate linkage equilibrium, 62.6% had logistic regression beta coefficients with the same sign in the Swedish results, an observation highly inconsistent with the null (P=2.2×10−10). λGC was 1.186 and λ1000 was 1.012, values consistent with a polygenic pattern of association but not gross inflation due to technical artifacts. 20 Quantile-quantile and Manhattan plots are shown in Supplemental Figure 11 and Figure 1, and genome-wide significance was exceeded by 3,538 SNPs in 12 genomic regions.
