Meta-analysis of the CLOZUK and independent PGC datasets, excluding related and overlapping samples (total of 40,675 cases and 64,643 controls; Supplementary Fig. 3) identified 179 independent genome-wide significant SNPs (P < 5 × 108; Supplementary Table 3) mapping to 145 independent loci (Fig. 1, Methods and Supplementary Table 4). The 145 associated loci included 93 of those that were genome-wide significant in the study of the PGC, the majority of which showed a strengthened association (Supplementary Fig. 4 and Supplementary Table 5). This does not imply that the remaining 15 PGC loci were false positives; rather, this reflects the expected inflation of effect sizes for genome-wide significant SNPs in incompletely powered studies and, as we demonstrate, is consistent with all 108 PGC loci representing true positives (Supplementary Note). Of the 52 loci not identified by the PGC, 2 have been reported as genome-wide significant in other studies: the locus at ZEB214 and a locus on chromosome 8 (38.0-38.3 Mb)15.
