High-depth African genomes inform human migration and health

Ananyo Choudhury, Shaun Aron, Laura R. Botigué, Dhriti Sengupta, Gerrit Botha, Taoufik Bensellak, Gordon Wells, Judit Kumuthini, Daniel Shriner, Yasmina J. Fakim, Anisah W. Ghoorah, Eileen Dareng, Trust Odia, Oluwadamilare Falola, Ezekiel Adebiyi, Scott Hazelhurst, Gaston Mazandu, Oscar A. Nyangiri, Mamana Mbiyavanga, Alia Benkahla, Samar K. Kassim, Nicola Mulder, Sally N. Adebamowo, Emile R. Chimusa, Donna Muzny, Ginger Metcalf, Richard A. Gibbs, Charles Rotimi, Michèle Ramsay, Adebowale A. Adeyemo (), Zané Lombard () and Neil A. Hanchard ()
Additional contact information
Ananyo Choudhury: University of the Witwatersrand
Shaun Aron: University of the Witwatersrand
Laura R. Botigué: Plant and Animal Genomics Program, CSIC-IRTA-UAB-UB
Dhriti Sengupta: University of the Witwatersrand
Gerrit Botha: IDM, University of Cape Town
Taoufik Bensellak: Abdelmalek Essaadi University, ENSA
Gordon Wells: Centre for Proteomic and Genomic Research (CPGR)
Judit Kumuthini: Centre for Proteomic and Genomic Research (CPGR)
Daniel Shriner: National Human Genome Research Institute, National Institutes of Health
Yasmina J. Fakim: University of Mauritius
Anisah W. Ghoorah: University of Mauritius
Eileen Dareng: University of Cambridge
Trust Odia: Covenant University
Oluwadamilare Falola: Covenant University
Ezekiel Adebiyi: Covenant University
Scott Hazelhurst: University of the Witwatersrand
Gaston Mazandu: IDM, University of Cape Town
Oscar A. Nyangiri: Makerere University
Mamana Mbiyavanga: IDM, University of Cape Town
Alia Benkahla: Institute Pasteur of Tunis
Samar K. Kassim: Ain Shams University, Abbaseya
Nicola Mulder: IDM, University of Cape Town
Sally N. Adebamowo: University of Maryland Baltimore
Emile R. Chimusa: University of Cape Town
Donna Muzny: Baylor College of Medicine
Ginger Metcalf: Baylor College of Medicine
Richard A. Gibbs: Baylor College of Medicine
Charles Rotimi: National Human Genome Research Institute, National Institutes of Health
Michèle Ramsay: University of the Witwatersrand
Adebowale A. Adeyemo: National Human Genome Research Institute, National Institutes of Health
Zané Lombard: University of the Witwatersrand
Neil A. Hanchard: Baylor College of Medicine

Nature, 2020, vol. 586, issue 7831, 741-748

Abstract: Abstract The 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 Bantu-speaking 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.

Date: 2020
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DOI: 10.1038/s41586-020-2859-7

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