The cohort and ancestry composition of the TOPMed freeze 5b whole genome sequence reference panel used in our study and the samples with array-based genotyping used for imputation and hematological traits association analyses in self-identified AA and Hispanic/Latino individuals are summarized in S1 and S2 Tables, respectively. We first selected two large U.S. minority cohorts—one AA and one Hispanic/Latino—in order to comprehensively evaluate imputation quality: the Jackson Heart Study (JHS, all AA, n = 3,082) and the Hispanic Community Health Study/Study of Latinos (HCHS/SOL, all Hispanic/Latino, n = 11,887). Both the JHS and HCHS/SOL have external sources of dense genotype data available for comparison. JHS is the largest AA general population cohort sequenced in TOPMed freeze 5b. Therefore, we removed JHS samples from the TOPMed freeze 5b reference panel prior to performing imputation into JHS samples using SNPs genotyped on the Affymetrix 6.0 array, treating the TOPMed freeze 5b calls as true genotypes for evaluation of imputation quality in JHS. HCHS/SOL is the largest and most regionally diverse population-based cohort of Hispanic/Latino individuals living in the US. For HCHS/SOL, we
