We used the sequencing data available through the NHLBI’s Trans-Omics for Precision Medicine (TOPMed) program (https://nhlbiwgs.org ). WGS was performed to an average depth of 38X using DNA isolated from blood, PCR-free library construction, and Illumina HiSeq X technology. Details for variant calling and quality control are described in detail in Taliun et al. [29 (link)]. In brief, variant discovery and genotype calling was performed jointly across all the available TOPMed studies using the GotCloud 6 pipeline, resulting in a single, multi-study, genotype call set. Sample-level quality control was performed to check for pedigree errors, discrepancies between self-reported and genetic sex, and concordance with prior genotyping array data. Among the GeneSTAR samples in TOPMed Freeze 6, 806 EAs in 196 families and 661 AAs in 190 families had complete phenotype data.
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Whole Genome Sequencing of TOPMed Cohort
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Corresponding Organization : Johns Hopkins University
Other organizations : Johns Hopkins Medicine
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Variable analysis
independent variables
- Ancestry (European American (EA), African American (AA))
- Phenotype data
- Sample-level quality control (pedigree errors, discrepancies between self-reported and genetic sex, concordance with prior genotyping array data)
- Variant discovery and genotype calling performed jointly across all the available TOPMed studies using the GotCloud 6 pipeline
- DNA isolated from blood, PCR-free library construction, and Illumina HiSeq X technology used for whole-genome sequencing (WGS) to an average depth of 38X
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