The reference panel used for imputation was obtained from deep-coverage whole genome sequences derived from NHLBI’s TOPMed program (www.nhlbiwgs.org), freeze 5b (September 2017). This release included 54,035 non-duplicated, dbGaP released samples, of whom 50,253 have consent to be part of an imputation reference panel. The parent studies that contributed these 50,253 samples are listed in S2 Table. Specific to our analyses, freeze 5b includes 3,082 individuals from the Jackson Heart Study, who were removed from the reference panel for our analysis of imputation quality in this particular cohort. Overall, freeze 5b included 54% European ancestry, 26% AA, 10% Hispanic/Latino, 7% Asian, and 3% other ancestry samples. Detailed sequencing methods used in TOPMed are available at https://www.nhlbiwgs.org/topmed-whole-genome-sequencing-project-freeze-5b-phases-1-and-2. In brief, WGS with mean genome coverage ≥30x was completed at six sequencing centers (New York Genome Center, the Broad Institute of MIT and Harvard, the University of Washington Northwest Genomics Center, Illumina Genomic Services, Macrogen Corp., and Baylor Human Genome Sequencing Center). Sequence data files were transferred from sequencing centers to the TOPMed Informatics Research Center (IRC), where reads were aligned to human
