All estimates of h2SNP were computed with the PCGC66 approach implemented with PCGC-ss33, using 5,276,842 common SNPs (MAF > 5% in all 337,198 White-British unrelated samples). LD scores at SNPs were computed with LDSC34 in 10,000 random samples drawn from the White-British samples in the UK Biobank as an LD reference, as well as the MAF at all 5,276,842 common SNPs in all 337,198 White-British samples as a MAF reference. Covariates were genotyping array and 20 principal components computed using samples in each definition of MDD with flashPCA67. Where we stratified each definition of MDD in the UK Biobank into two strata by risk factors such as sex (Supplementary Note), we computed specific principal components for each definition and stratum (see also the Supplementary Note and Supplementary Table 13).
