For studies where the PGC analyst had genotype data access, ancestry was determined using a global reference panel11 using SNPweights87. The ancestry pipeline was shared with external sites to be utilized where possible. Participants were placed into three large groupings: European and European Americans (EA; individuals with ≥90% European ancestry), African and African-Americans (AA; individuals with ≥5% African ancestry, <90% European ancestry, <5% East Asian, Native American, Oceanian, and Central-South Asian ancestry; and individuals with ≥50% African ancestry, <5% Native American, Oceanian, and <1% Asian ancestry), and Latin Americans (LAT; individuals with ≥5% Native American ancestry, <90% European, <5% African, East Asian, Oceanian, and Central-South Asian ancestry). Native Americans (individuals with ≥60% Native American ancestry, <20% East Asian, <15% Central-South Asian, and <5% African and Oceanian ancestry) were grouped together with LAT. All other individuals were excluded from the current analyses. For the MVP cohort, ancestry was determined using standard principal components analysis approach where MVP samples were projected onto a PC space made from 1000 Genomes Phase 3 (KGP3) samples with known population origins (EUR, AFR, EAS, SAS, and AMR populations). EHR cohorts followed their own site-specific ancestry classification protocols.
