We used risk score profiling14,17 to evaluate the capacity of 130K SNPs derived from the PGC to predict case-control status in the Swedish samples. These SNPs were selected for high-confidence and approximate linkage equilibrium but without regard to association P value. As shown in Figure 2, PGC risk scores had a highly significant capacity to predict case-control status in the independent Swedish samples (P values from 10−26 – 10−114). The increased sample size allowed improved risk profile prediction as more of the SNPs in the lower bins are replicable signals. The threshold at which the explanatory power of these risk profile SNPs plateaus has decreased with increasing sample size: PT=0.1 in Figure 2, 0.2 in the PGC report, and no plateau in the ISC study). 14,17 Although the mean risk profiles were highly significantly different between cases and controls, the distributions overlap substantially (Supplemental Figure 9) and are insufficient for diagnostic purposes (area under the receiver operating characteristic curve 0.65). However, these results strongly support the comparability of the Swedish and PGC samples and the validity of the meta-analysis.
