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 used the entire set of 100,506 phased sequences from TOPMed freeze 5b (including JHS) as reference and performed imputation into 11,887 Hispanic/Latino samples genotyped on the Illumina Omni 2.5 SOL custom array (with high quality genotypes at 2,293,536 markers). As the external source of genotype validation in HCHS/SOL, we used genotypes from the Illumina MEGA array genotyping data (containing >1.7 million multi-ethnic global markers, including low frequency coding variants and ancestry-specific variants) available in the same HCHS/SOL samples to assess imputation quality, evaluating 688,189 imputed markers available on MEGA but not on Omni2.5.
