genome-wide significant SNPs and their weights (bJ) estimated from a conditional/joint COJO analysis (that allows multiple SNPs within an LD block to be selected if they show association additional to the lead SNP).12 For benchmarking comparisons, we also calculated PGS in the 20 cohorts new in this PGC MDD wave 3 using SBayesR, SBayesRC and COJO derived from GWAS summary statistics from previously published PGC MDD GWAS studies in 2018 (Ncase=170,756, Ncont =329,443) by Wray7 and 2019 (PGC2+UKB + 23andMe-1stwave, Ncase=246,363, Ncont=561,190) by Howard,2 omitting the individual-level genotyped studies from PGC MDD2.
