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Ndiaye R. Planting the milestones of human genetics in Senegal. Nat Genet 2024; 56:2-3. [PMID: 37985821 DOI: 10.1038/s41588-023-01581-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Affiliation(s)
- Rokhaya Ndiaye
- Division of Human Genetics, Faculty of Medicine, Pharmacy and Odonto-stomatology, University Cheikh Anta Diop, Dakar, Senegal.
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2
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Abstract
To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and global governance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Ambroise Wonkam
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; , , .,Current affiliation: McKusick-Nathans Institute of Genetic Medicine and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA;
| | - Nchangwi S Munung
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; , ,
| | - Collet Dandara
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; , ,
| | - Kevin K Esoh
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa; , ,
| | - Neil A Hanchard
- Center for Precision Health Research, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA;
| | - Guida Landoure
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques, and Technology of Bamako, Bamako, Mali;
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3
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Pereira L, Mutesa L, Tindana P, Ramsay M. African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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Abstract
Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda.,Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda.,The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Disease Institute, Makerere University, P.O. Box 22418, Kampala, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda
| | - Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
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Alimohamed MZ, Mwakilili AD, Mbwanji K, Manji ZK, Kaywang F, Mwaikono KS, Adolf I, Makani J, Hamel B, Masimirembwa C, Ishengoma DS, Nkya S. Inauguration of the Tanzania Society of Human Genetics: Biomedical Research in Tanzania with Emphasis on Human Genetics and Genomics. Am J Trop Med Hyg 2020; 104:474-477. [PMID: 33350369 DOI: 10.4269/ajtmh.20-0861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 11/16/2020] [Indexed: 11/07/2022] Open
Abstract
Human genetics research and applications are rapidly growing areas in health innovations and services. African populations are reported to be highly diverse and carry the greatest number of variants per genome. Exploring these variants is key to realize the genomic medicine initiative. However, African populations are grossly underrepresented in various genomic databases, which has alerted scientists to address this issue with urgency. In Tanzania, human genetics research and services are conducted in different institutions on both communicable and noncommunicable diseases. However, there is poor coordination of the research activities, often leading to limited application of the research findings and poor utilization of available resources. In addition, contributions from Tanzanian human genetics research and services are not fully communicated to the government, national, and international communities. To address this scientific gap, the Tanzania Society of Human Genetics (TSHG) has been formed to bring together all stakeholders of human genetics activities in Tanzania and to formally bring Tanzania as a member to the African Society of Human Genetics. This article describes the inauguration event of the TSHG, which took place in November 2019. It provides a justification for its establishment and discusses presentations from invited speakers who took part in the inauguration of the TSHG.
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Affiliation(s)
- Mohamed Zahir Alimohamed
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania.,Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Aneth David Mwakilili
- Plant Protection Department, Swedish University of Agricultural Sciences, Alnarp, Sweden.,Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania
| | | | - Zainab Karim Manji
- Department of Clinical Nursing, School of Nursing, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frida Kaywang
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Kilaza Samson Mwaikono
- Department of Science and Laboratory Technology, Dar es Salaam Institute of Technology, Dar es Salaam, Tanzania
| | - Ismael Adolf
- Mbeya College of Health and Allied Sciences, University of Dar es Salaam, Mbeya, Tanzania
| | - Julie Makani
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
| | - Ben Hamel
- Kilimanjaro Christian Medical University College, Moshi, Tanzania.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Collen Masimirembwa
- African Institute of Biomedical Science and Technology, Wilkins Hospital, Harare, Zimbabwe
| | - Deus Simon Ishengoma
- Harvard T. H. Chan School of Public Health, Harvard University, Boston, Massachusetts.,Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia.,National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Siana Nkya
- Dar es Salaam University College of Education, UDSM, Dar es Salaam, Tanzania.,Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.,Department of Haematology and Blood Transfusion, Muhimbili University of Health and Allied Sciences, Dar-es-Salaam, Tanzania
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6
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Musanabaganwa C, Mihigo B, Tumusime R, Uwanyirigira M, da Rocha J, Hayat M, Govender M, Buto P, Nyunga T, Ramesar RS, Rotimi C, Souopgui J, Wonkam A, Williams SM, Jansen S, Ramsay M, Mutesa L. Building Skills and Resources for Genomics, Epigenetics, and Bioinformatics Research for Africa: Report of the Joint 11th Conference of the African Society of Human Genetics and 12th H3Africa Consortium, 2018. Am J Trop Med Hyg 2020; 102:1417-1424. [PMID: 32207403 PMCID: PMC7253097 DOI: 10.4269/ajtmh.19-0837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 11th Congress of the African Society of Human Genetics (AfSHG) was held from September 16, 2018 to September 21, 2018, in conjunction with the 12th Human Heredity and Health in Africa (H3Africa) Consortium meeting in Kigali, Rwanda. The event was organized by the AfSHG in partnership with the Rwanda Society of Human Genetics and the University of Rwanda. A 2-day workshop on the application of next-generation sequencing technologies for analyzing monogenic disease in African populations was organized as part of the conference (September 22, 2018−September 23, 2018, Kigali, Rwanda). The theme of the conference was “Building skills and resources for genomics, epigenetics and bioinformatics research for Africa.” The conference served as a platform to bring together members from country-specific Societies of Human Genetics, including Rwanda, Cameroon, Democratic Republic of Congo, Egypt, Mali, Senegal, and South Africa, and included 435 delegates from 38 countries, including 29 African countries that attended the conference. A major topic of discussion was how to bridge the gap between the emerging knowledge on genomics and Omics in African populations. The importance of understanding the role of genetic variation in disease causation and susceptibility among Africans was a constant theme during the meeting, as was the need to develop research infrastructure and resources to enhance healthcare systems, so that they are not left behind in the genomic revolution. It was concluded that there is a need to inspire more African scientists to train and work as investigators, clinicians, and genetic counselors in the field of human genetics in Africa. Local investments, and South–South and South–North collaboration were identified as the key drivers for the successful implementation of research and development on the continent.
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Affiliation(s)
- Clarisse Musanabaganwa
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Bonaventure Mihigo
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Robert Tumusime
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Mediatrice Uwanyirigira
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience and Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahtaab Hayat
- Sydney Brenner Institute for Molecular Bioscience and Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Melanie Govender
- Sydney Brenner Institute for Molecular Bioscience and Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Peace Buto
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Tina Nyunga
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Raj S Ramesar
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Charles Rotimi
- National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland
| | - Jacob Souopgui
- Laboratory of Embryology and Biotechnology DBM-IBMM, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Scott M Williams
- Department of Epidemiology and Biostatistics, Institute of Computational Biology, Case Western Reserve University, Cleveland, Ohio
| | - Stefan Jansen
- Center for Mental Health, Directorate of Research and Innovation, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience and Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Leon Mutesa
- Centre for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
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7
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Bope CD, Chimusa ER, Nembaware V, Mazandu GK, de Vries J, Wonkam A. Dissecting in silico Mutation Prediction of Variants in African Genomes: Challenges and Perspectives. Front Genet 2019; 10:601. [PMID: 31293624 PMCID: PMC6603221 DOI: 10.3389/fgene.2019.00601] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/05/2019] [Indexed: 12/20/2022] Open
Abstract
Genomic medicine is set to drastically improve clinical care globally due to high throughput technologies which enable speedy in silico detection and analysis of clinically relevant mutations. However, the variability in the in silico prediction methods and categorization of functionally relevant genetic variants can pose specific challenges in some populations. In silico mutation prediction tools could lead to high rates of false positive/negative results, particularly in African genomes that harbor the highest genetic diversity and that are disproportionately underrepresented in public databases and reference panels. These issues are particularly relevant with the recent increase in initiatives, such as the Human Heredity and Health (H3Africa), that are generating huge amounts of genomic sequence data in the absence of policies to guide genomic researchers to return results of variants in so-called actionable genes to research participants. This report (i) provides an inventory of publicly available Whole Exome/Genome data from Africa which could help improve reference panels and explore the frequency of pathogenic variants in actionable genes and related challenges, (ii) reviews available in silico prediction mutation tools and the criteria for categorization of pathogenicity of novel variants, and (iii) proposes recommendations for analyzing pathogenic variants in African genomes for their use in research and clinical practice. In conclusion, this work proposes criteria to define mutation pathogenicity and actionability in human genetic research and clinical practice in Africa and recommends setting up an African expert panel to oversee the proposed criteria.
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Affiliation(s)
- Christian Domilongo Bope
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Departments of Mathematics and Computer Sciences, Faculty of Sciences, University of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Emile R. Chimusa
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Victoria Nembaware
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gaston K. Mazandu
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jantina de Vries
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ambroise Wonkam
- Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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Abstract
This review highlights molecular genetic studies of monogenic traits where common pathogenic mutations occur in black families from sub-Saharan Africa. Examples of founder mutations have been identified for oculocutaneous albinism, cystic fibrosis, Fanconi anemia, and Gaucher disease. Although there are few studies from Africa, some of the mutations traverse populations across the continent, and they are almost all different from the common mutations observed in non-African populations. Myotonic dystrophy is curiously absent among Africans, and nonsyndromic deafness does not arise from mutations in GJB2 and GJB7. Locus heterogeneity is present for Huntington disease, with two common triplet expansion loci in Africa, HTT and JPH3. These findings have important clinical consequences for diagnosis, treatment, and genetic counseling in affected families. We currently have just a glimpse of the molecular etiology of monogenic diseases in sub-Saharan Africa, a proverbial “ears of the hippo” situation.
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Affiliation(s)
- Amanda Krause
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service, and Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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