For all TOPMed individuals, genetic ancestries were estimated using the top four principal components projected onto the principal component space of 938 Human Genome Diversity Project (HGDP) individuals using verifyBamID2110. For each TOPMed individual, we identified the 10 closest individuals from 2,504 individuals from the 1000 Genomes Project phase 3 based on Euclidean distances in the principal component space estimated by verifyBamID2. If all of the 10 closest individuals from the 1000 Genomes Project phase 3 belonged to the same super-population—among African, admixed American, East Asian, European and South Asian populations—we estimated that the TOPMed individual also belonged to that super-population. Among the 97,256 reference panel individuals, 90,339 (93%) were assigned to a super-population, with the following breakdown: African, 24,267 individuals; admixed American, 17,085 individuals; European, 47,159 individuals; East Asian, 1,184 individuals; South Asian, 644 individuals. We randomly selected 100 individuals from each super-population in the BioMe TOPMed study, and selected markers on chromosome 20 present on the Illumina HumanOmniExpress (8v1-2_A) array. The selected genotypes were phased with Eagle 2.4.181, using the 1000 Genomes Project phase 3 (n = 2,504),
