Chunk #29 — Methods — Genome-wide genotyping array data sets used for evaluation of imputation quality and/or phenotype association analysis — Hispanic Community Health Study/Study of Latinos (HCHS/SOL)
also includes additional exonic, functional, and clinically-relevant variants. Illumina 2.5M array genotypes were available for 12,802 samples, among whom 11,887 samples also had MEGA array genotypes. The Illumina Omni2.5M array was used for imputation to the TOPMed reference panel, with the MEGA array treated as true genotypes for evaluation of imputation quality. For association analysis, imputation was performed on 11,887 samples after merging Omni2.5M array genotypes and MEGA array genotypes (MEGA genotypes were used for variants in both arrays, which resulted in 2,144,214 variants after quality control). Regional background (for evaluation of stratified imputation quality in S8 Table) was defined using both self-identified background and genetic markers, as described in [43]. For the hematological traits association analysis, 11,588 Hispanic/Latino participants were included.
