Our imputation sample used for discovery blood cell trait association analyses included eight cohorts (21,513 AAs and 21,689 Hispanics/Latinos) (S1 Table). These discovery samples do not overlap with individuals sequenced as part of TOPMed freeze 5b (S2 Table). We used the full set of 100,506 phased sequences from TOPMed freeze 5b (including JHS) as the imputation reference panel. We then carried out AA- and Hispanic/Latino-stratified association analyses with quantitative HGB, HCT, and total WBC separately in each cohort genotyping array data set, accounting for ancestry and relatedness. The genome-wide association results for each imputed cohort data set were then meta-analyzed within each ancestry group. S3–S8 Figs show the Manhattan plots from ethnic-specific meta-analyses for each trait. QQ plots (S9–S14 Figs) show no obvious early departure, with genomic control lambda ranging from 1.008 to 1.044, indicating minimal global inflation of test statistics. For replication of any novel associations identified in the imputation-based discovery analysis, we utilized WGS genotype data and hematological trait data from the non-overlapping set of AA individuals within TOPMed freeze 5b (S10 Table) (see Methods for details).
