Browsing by Author "Choudhury, Ananyo"
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Item High-depth African genomes inform human migration and health(Choudhury, A. et al. (2021). Author correction: High-depth African genomes inform human migration and health (nature, (2020), 586, 7831, (741-748), 10.1038/s41586-020-2859-7). Nature, 592(7856), E26. doi:10.1038/s41586-021-03286-9, 2021) Choudhury, Ananyo; Aron, Shaun; Botigué, Laura R; Botha, GerritThe African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals— comprising 50 ethnolinguistic groups, including previously unsampled populations— to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that population from Zambia were a likely intermediate site along the routes of expansion of Bantuspeaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon—but in other genes, variants denoted as ‘likely pathogenic’ in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.Item Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans(Nature Publishing Group, 2017) Choudhury, Ananyo; Christoffels, Alan; Gamieldien, Junaid; Sefid-Dashti, Mahjoubeh J.The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease.