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Team Compares Reference Panels for Sub-Saharan African Population Imputation

For a paper appearing in Cell Genomics, a University of Witwatersrand-led team compares genotype imputation across five reference panels comprised of roughly 10,900 samples from sub-Saharan African (SSA) populations. As part of the "Africa-Wits INDEPTH Partnership for Genomics Studies in African populations," or AWI-Gen, study, the team imputed data from the African Genome Resource (AGR), 1000 Genomes (Sanger), 1000 Genomes (Michigan), Haplotype Reference Consortium, and Trans-Omics for Precision Medicine (TOPMed), looking at SNP numbers and quality across the available panels. Along with differences in the number of SNPs found in data generated in different parts of the continent, the analyses highlighted efforts with enhanced imputation performance on datasets from SSA, particularly TOPMed and AGR. Likewise, the AGR panel compared favorably to other panels when directly compared to whole-genome sequences from 95 individuals from SSA. Even so, the "level of concordance between imputed and WGS datasets was strongly influenced by the extent of Khoe-San ancestry in a genome," they write, "highlighting the need for integration of not only geographically but also ancestrally diverse WGS data in reference panels for further improvement in imputation of SSA datasets."

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