Extended Data Fig. 6 ∣. Out-of-sample prediction in PGC cohorts.

a, This figure shows the Nagelkerke’s r² of polygenic risk scores (PRS) calculated for each definition of depression in UK Biobank and MDD status indicated in 19 PGC29-MDD cohorts, while controlling for cohort specific effects. PRS were calculated using effect sizes at independent (LD r² < 0.1) SNPs passing P-value thresholds 10⁻⁴, 0.001, 0.01, 0.05, 0.01, 0.2, 0.5 and 1 respectively, in GWAS performed on all definitions of depression in UK Biobank. b, This figure shows the same analysis performed on down-sampled data (7,500 cases, 42,500 controls) for each definition of depression.