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The African Genome Variation Project shapes medical genetics in Africa.

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.

SUBMITTER: Gurdasani D

PROVIDER: S-EPMC4297536 | biostudies-literature | 2015 Jan

REPOSITORIES: biostudies-literature

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The African Genome Variation Project shapes medical genetics in Africa.

Gurdasani Deepti D Carstensen Tommy T Tekola-Ayele Fasil F Pagani Luca L Tachmazidou Ioanna I Hatzikotoulas Konstantinos K Karthikeyan Savita S Iles Louise L Pollard Martin O MO Choudhury Ananyo A Ritchie Graham R S GR Xue Yali Y Asimit Jennifer J Nsubuga Rebecca N RN Young Elizabeth H EH Pomilla Cristina C Kivinen Katja K Rockett Kirk K Kamali Anatoli A Doumatey Ayo P AP Asiki Gershim G Seeley Janet J Sisay-Joof Fatoumatta F Jallow Muminatou M Tollman Stephen S Mekonnen Ephrem E Ekong Rosemary R Oljira Tamiru T Bradman Neil N Bojang Kalifa K Ramsay Michele M Adeyemo Adebowale A Bekele Endashaw E Motala Ayesha A Norris Shane A SA Pirie Fraser F Kaleebu Pontiano P Kwiatkowski Dominic D Tyler-Smith Chris C Rotimi Charles C Zeggini Eleftheria E Sandhu Manjinder S MS

Nature 20141203 7534

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 ...[more]

PMID: 25470054

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Project description:BackgroundKey discoveries and innovations in the field of human genetics have led to the foundation of molecular and personalized medicine. Here, we present the Genome Tunisia Project, a two-phased initiative (2022-2035) which aims to deliver the reference sequence of the Tunisian Genome and to support the implementation of personalized medicine in Tunisia, a North African country that represents a central hub of population admixture and human migration between African, European, and Asian populations. The main goal of this initiative is to develop a healthcare system capable of incorporating omics data for use in routine medical practice, enabling medical doctors to better prevent, diagnose, and treat patients.MethodsA multidisciplinary partnership involving Tunisian experts from different institutions has come to discern all requirements that would be of high priority to fulfill the project's goals. One of the most urgent priorities is to determine the reference sequence of the Tunisian Genome. In addition, extensive situation analysis and revision of the education programs, community awareness, appropriate infrastructure including sequencing platforms and biobanking, as well as ethical and regulatory frameworks, have been undertaken towards building sufficient capacity to integrate personalized medicine into the Tunisian healthcare system.ResultsIn the framework of this project, an ecosystem with all engaged stakeholders has been implemented including healthcare providers, clinicians, researchers, pharmacists, bioinformaticians, industry, policymakers, and advocacy groups. This initiative will also help to reinforce research and innovation capacities in the field of genomics and to strengthen discoverability in the health sector.ConclusionsGenome Tunisia is the first initiative in North Africa that seeks to demonstrate the major impact that can be achieved by Human Genome Projects in low- and middle-income countries to strengthen research and to improve disease management and treatment outcomes, thereby reducing the social and economic burden on healthcare systems. Sharing this experience within the African scientific community is a chance to turn a major challenge into an opportunity for dissemination and outreach. Additional efforts are now being made to advance personalized medicine in patient care by educating consumers and providers, accelerating research and innovation, and supporting necessary changes in policy and regulation.

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The African Genome Variation Project shapes medical genetics in Africa.

Publications

The African Genome Variation Project shapes medical genetics in Africa.

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