For the Genomic SEM analyses, we conducted a total of 10 GWAS in UKB (listed in Supplementary Table 1). These GWAS were conducted for two reasons: (1) to generate summary statistics for phenotypes that had not yet been studied in the full genetic data release, or (2) to generate hold-out summary statistics that excluded participants for follow-up analyses. The hold-out summary statistics were used to replace, in our Genomic SEM analyses, summary statistics from existing studies that had included UKB. With respect to (1), summary statistics for “age at first sexual intercourse” and “Alcohol Use Disorder Identification Test problem items” (AUDIT-P) were later included in the final Genomic SEM specification (the latter as a meta-analysis with a GWAS on alcohol dependence by the PGC). With respect to (2), the final specification included replacement summary statistics on “lifetime cannabis use”, “general risk tolerance”, and “lifetime smoking initiation”, and “number of sexual partners”. The seventh phenotype in the final specification—ADHD by the PGC—did not include analyses from UKB. For a detailed description, see Supplementary Information section 2.2–2.3.
