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. DoumateyGershim 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, Manjinder S. Sandhu

Research output: Contribution to journalArticlepeer-review

390 Scopus citations

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.

Original languageEnglish
Pages (from-to)327-332
Number of pages6
JournalNature
Volume517
Issue number7534
DOIs
StatePublished - 15 Jan 2015
Externally publishedYes

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