The African Genome Variation Project shapes medical genetics in Africa

Deepti Gurdasani (), Tommy Carstensen, Fasil Tekola-Ayele, Luca Pagani, Ioanna Tachmazidou, Konstantinos Hatzikotoulas, Savita Karthikeyan, Louise Iles, Martin O. Pollard, Ananyo Choudhury, Graham R. S. Ritchie, Yali Xue, Jennifer Asimit, Rebecca N. Nsubuga, Elizabeth H. Young, Cristina Pomilla, Katja Kivinen, Kirk Rockett, Anatoli Kamali, Ayo P. Doumatey, Gershim Asiki, Janet Seeley, Fatoumatta Sisay-Joof, Muminatou Jallow, Stephen Tollman, Ephrem Mekonnen, Rosemary Ekong, Tamiru Oljira, Neil Bradman, Kalifa Bojang, Michele Ramsay, Adebowale Adeyemo, Endashaw Bekele, Ayesha Motala, Shane A. Norris, Fraser Pirie, Pontiano Kaleebu (), Dominic Kwiatkowski, Chris Tyler-Smith (), Charles Rotimi (), Eleftheria Zeggini () and Manjinder S. Sandhu ()
Additional contact information
Deepti Gurdasani: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Tommy Carstensen: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, 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
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
Louise Iles: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, 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
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
Cristina Pomilla: Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, 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
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
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
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

Nature, 2015, vol. 517, issue 7534, 327-332

Abstract: 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.

Date: 2015
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DOI: 10.1038/nature13997

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