We used the subset of all the SNPs (i.e., we did not impose a P value threshold) in the HapMap consortium phase 3 release56 with an imputation quality of more than 0.7 to generate all three scores. For every validation cohort that was also included in the discovery or replication GWAS or in the MTAG analysis, we reran the GWAS and MTAG analyses without the validation cohort to generate the summary statistics we used to construct the scores. Due to data access limitations, the 23andMe cohort could not be included in the meta-analysis whose summary statistics we used to construct the polygenic scores in the NTR, STR, and Zurich cohorts. The second polygenic score (using the MTAG summary statistics) was only constructed for the Add Health, HRS, and UKB-siblings cohorts.
