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The African Genome Variation Project shapes medical genetics in Africa

Author

Listed:
  • Deepti Gurdasani

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

  • Tommy Carstensen

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

  • Fasil Tekola-Ayele

    (Centre for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, Maryland 20891-5635, USA)

  • Luca Pagani

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126 Bologna, Italy)

  • Ioanna Tachmazidou

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Konstantinos Hatzikotoulas

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Savita Karthikeyan

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

  • Louise Iles

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK
    University of York, King’s Manor, York YO1 7EP, UK)

  • Martin O. Pollard

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Ananyo Choudhury

    (Sydney Brenner Institute of Molecular Bioscience (SBIMB), University of the Witwatersrand, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, Gauteng, South Africa)

  • Graham R. S. Ritchie

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK)

  • Yali Xue

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Jennifer Asimit

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Rebecca N. Nsubuga

    (Medical Research Council/Uganda Virus Research Institute, Plot 51-57 Nakiwogo Road, Uganda)

  • Elizabeth H. Young

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

  • Cristina Pomilla

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

  • Katja Kivinen

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Kirk Rockett

    (Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK)

  • Anatoli Kamali

    (Medical Research Council/Uganda Virus Research Institute, Plot 51-57 Nakiwogo Road, Uganda)

  • Ayo P. Doumatey

    (Centre for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, Maryland 20891-5635, USA)

  • Gershim Asiki

    (Medical Research Council/Uganda Virus Research Institute, Plot 51-57 Nakiwogo Road, Uganda)

  • Janet Seeley

    (Medical Research Council/Uganda Virus Research Institute, Plot 51-57 Nakiwogo Road, Uganda)

  • Fatoumatta Sisay-Joof

    (Medical Research Council Unit, Atlantic Boulevard, SerrekundaPO Box 273, Banjul, The Gambia)

  • Muminatou Jallow

    (Medical Research Council Unit, Atlantic Boulevard, SerrekundaPO Box 273, Banjul, The Gambia)

  • Stephen Tollman

    (Medical Research Council/Wits Rural Public Health and Health Transitions Unit, School of Public Health, Education Campus, 27 St Andrew’s Road, Parktown 2192, Johannesburg, Gauteng, South Africa
    INDEPTH Network, 38/40 Mensah Wood Street, East Legon, PO Box KD 213, Kanda, Accra, Ghana)

  • Ephrem Mekonnen

    (Institute of Biotechnology, Addis Ababa University, Entoto Avenue, Arat Kilo, 16087 Addis Ababa, Ethiopia)

  • Rosemary Ekong

    (University College, London, Gower Street, London WC1E 6BT, UK)

  • Tamiru Oljira

    (University of Haramaya, PO Box 138, Dire Dawa, Ethiopia)

  • Neil Bradman

    (Henry Stewart Group, 28/30 Little Russell Street, London WC1A 2HN, UK)

  • Kalifa Bojang

    (Medical Research Council Unit, Atlantic Boulevard, SerrekundaPO Box 273, Banjul, The Gambia)

  • Michele Ramsay

    (Sydney Brenner Institute of Molecular Bioscience (SBIMB), University of the Witwatersrand, The Mount, 9 Jubilee Road, Parktown 2193, Johannesburg, Gauteng, South Africa
    National Health Laboratory Service, C/O Hospital and de Korte Streets, Braamfontein 2000, Johannesburg, South Africa
    School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa)

  • Adebowale Adeyemo

    (Centre for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, Maryland 20891-5635, USA)

  • Endashaw Bekele

    (Cellular and Molecular Biology, College of Natural Sciences, Arat Kilo Campus, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia)

  • Ayesha Motala

    (University of KwaZulu-Natal, 719 Umbilo Road, Congella, Durban 4013, South Africa)

  • Shane A. Norris

    (University of Witwatersrand, 7 York Road, Parktown 2198, Johannesburg, Gauteng, South Africa)

  • Fraser Pirie

    (University of KwaZulu-Natal, 719 Umbilo Road, Congella, Durban 4013, South Africa)

  • Pontiano Kaleebu

    (Medical Research Council/Uganda Virus Research Institute, Plot 51-57 Nakiwogo Road, Uganda)

  • Dominic Kwiatkowski

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Headington, Oxford OX3 7BN, UK)

  • Chris Tyler-Smith

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Charles Rotimi

    (Centre for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, 12 South Drive, MSC 5635, Bethesda, Maryland 20891-5635, USA)

  • Eleftheria Zeggini

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK)

  • Manjinder S. Sandhu

    (Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    University of Cambridge, 2 Wort’s Causeway, Cambridge, CB1 8RN, UK)

Abstract

Given the importance of Africa to studies of human origins and disease susceptibility, detailed characterization of African genetic diversity is needed. The African Genome Variation Project provides a resource with which to design, implement and interpret genomic studies in sub-Saharan Africa and worldwide. The African Genome Variation Project represents dense genotypes from 1,481 individuals and whole-genome sequences from 320 individuals across sub-Saharan Africa. Using this resource, we find novel evidence of complex, regionally distinct hunter-gatherer and Eurasian admixture across sub-Saharan Africa. We identify new loci under selection, including loci related to malaria susceptibility and hypertension. We show that modern imputation panels (sets of reference genotypes from which unobserved or missing genotypes in study sets can be inferred) can identify association signals at highly differentiated loci across populations in sub-Saharan Africa. Using whole-genome sequencing, we demonstrate further improvements in imputation accuracy, strengthening the case for large-scale sequencing efforts of diverse African haplotypes. Finally, we present an efficient genotype array design capturing common genetic variation in Africa.

Suggested Citation

  • Deepti Gurdasani & Tommy Carstensen & Fasil Tekola-Ayele & Luca Pagani & Ioanna Tachmazidou & Konstantinos Hatzikotoulas & Savita Karthikeyan & Louise Iles & Martin O. Pollard & Ananyo Choudhury & Gra, 2015. "The African Genome Variation Project shapes medical genetics in Africa," Nature, Nature, vol. 517(7534), pages 327-332, January.
    • Handle: RePEc:nat:nature:v:517:y:2015:i:7534:d:10.1038_nature13997
    DOI: 10.1038/nature13997
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    Cited by:

    1. Sam Tallman & Maria das Dores Sungo & Sílvio Saranga & Sandra Beleza, 2023. "Whole genomes from Angola and Mozambique inform about the origins and dispersals of major African migrations," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    2. Gwenna Breton & Lawrence Barham & George Mudenda & Himla Soodyall & Carina M. Schlebusch & Mattias Jakobsson, 2024. "BaTwa populations from Zambia retain ancestry of past hunter-gatherer groups," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    3. Michel S. Naslavsky & Marilia O. Scliar & Guilherme L. Yamamoto & Jaqueline Yu Ting Wang & Stepanka Zverinova & Tatiana Karp & Kelly Nunes & José Ricardo Magliocco Ceroni & Diego Lima Carvalho & Carlo, 2022. "Whole-genome sequencing of 1,171 elderly admixed individuals from Brazil," Nature Communications, Nature, vol. 13(1), pages 1-11, December.

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