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Sudi SM, Kabbashi S, Roomaney IA, Aborass M, Chetty M. The genetic determinants of oral diseases in Africa: The gaps should be filled. FRONTIERS IN ORAL HEALTH 2022; 3:1017276. [PMID: 36304994 PMCID: PMC9593064 DOI: 10.3389/froh.2022.1017276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/16/2022] [Indexed: 11/07/2022] Open
Abstract
Oral diseases are a major health concern and are among the most prevalent diseases globally. This problem is becoming more prominent in the rapidly growing populations of Africa. It is well documented that Africa exhibits the most diverse genetic make-up in the world. However, little work has been conducted to understand the genetic basis of oral diseases in Africans. Oral health is often neglected and receives low prioritisation from funders and governments. The genetic determinants of highly prevalent oral diseases such as dental caries and periodontal disease, and regionally prevalent conditions such as oral cancer and NOMA, are largely under-researched areas despite numerous articles alluding to a high burden of these diseases in African populations. Therefore, this review aims to shed light on the significant gaps in research on the genetic and genomic aspects of oral diseases in African populations and highlights the urgent need for evidence-based dentistry, in tandem with the development of the dentist/scientist workforce.
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Raga SV, Wilmshurst JM, Smuts I, Meldau S, Bardien S, Schoonen M, van der Westhuizen FH. A case for genomic medicine in South African paediatric patients with neuromuscular disease. Front Pediatr 2022; 10:1033299. [PMID: 36467485 PMCID: PMC9713312 DOI: 10.3389/fped.2022.1033299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
Paediatric neuromuscular diseases are under-recognised and under-diagnosed in Africa, especially those of genetic origin. This may be attributable to various factors, inclusive of socioeconomic barriers, high burden of communicable and non-communicable diseases, resource constraints, lack of expertise in specialised fields and paucity of genetic testing facilities and biobanks in the African population, making access to and interpretation of results more challenging. As new treatments become available that are effective for specific sub-phenotypes, it is even more important to confirm a genetic diagnosis for affected children to be eligible for drug trials and potential treatments. This perspective article aims to create awareness of the major neuromuscular diseases clinically diagnosed in the South African paediatric populations, as well as the current challenges and possible solutions. With this in mind, we introduce a multi-centred research platform (ICGNMD), which aims to address the limited knowledge on NMD aetiology and to improve genetic diagnostic capacities in South African and other African populations.
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Affiliation(s)
- Sharika V Raga
- Department of Neurophysiology, Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Jo Madeleine Wilmshurst
- Department of Neurophysiology, Department of Paediatric Neurology, Red Cross War Memorial Children's Hospital, Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Izelle Smuts
- Department of Paediatrics, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Surita Meldau
- Division of Chemical Pathology, Department of Pathology, National Health Laboratory Service and University of Cape Town, Cape Town, South Africa
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.,South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town, South Africa
| | - Maryke Schoonen
- Human Metabolomics, North-West University, Potchefstroom, South Africa
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Wudil UJ, Aliyu MH, Prigmore HL, Ingles DJ, Ahonkhai AA, Musa BM, Muhammad H, Sani MU, Nalado AM, Abdu A, Abdussalam K, Shepherd BE, Dankishiya FS, Burgner AM, Ikizler TA, Wyatt CM, Kopp JB, Kimmel PL, Winkler CA, Wester CW. Apolipoprotein-1 risk variants and associated kidney phenotypes in an adult HIV cohort in Nigeria. Kidney Int 2021; 100:146-154. [PMID: 33901548 PMCID: PMC8487768 DOI: 10.1016/j.kint.2021.03.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/17/2022]
Abstract
HIV-positive adults are at risk for various kidney diseases, and apolipoprotein 1 (APOL1) high-risk genotypes increase this risk. This study aimed to determine the prevalence and ethnic distribution of APOL1 risk genotypes among a cohort of HIV-positive Nigerian adults and explore the relationship between APOL1 risk variant status with albuminuria and estimated glomerular filtration rate (eGFR). We conducted a cross-sectional study among 2 458 persons living with HIV who attended an HIV clinic in northern Nigeria and had received antiretroviral therapy for a minimum of six months. We collected two urine samples four-eight weeks apart to measure albumin excretion, and blood samples to measure eGFR and determine APOL1 genotype. The frequency of APOL1 high-risk genotype was 6.2%, which varied by ethnic group: Hausa/Fulani (2.1%), Igbo (49.1%), and Yoruba (14.5%). The prevalence of microalbuminuria (urine/albumin creatinine ratio 30- 300 mg/g) was 37%, and prevalence of macroalbuminuria (urine/albumin creatinine ratio over 300 mg/g) was 3%. The odds of microalbuminuria and macroalbuminuria were higher for participants with the APOL1 high-risk genotype compared to those carrying the low-risk genotype ([adjusted odds ratio 1.97, 95% confidence interval 1.37-2.82] and [3.96, 1.95-8.02] respectively). APOL1 high-risk genotype participants were at higher risk of having both an eGFR under 60 ml/min/1.73m2 and urine/albumin creatinine ratio over 300 mg/g (5.56, 1.57-19.69). Thus, we found a high proportion of HIV-positive, antiretroviral therapy-experienced, and largely virologically suppressed adults had microalbuminuria. Hence, although the high-risk APOL1 genotype was less prevalent than expected, it was strongly associated with some level of albuminuria.
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Affiliation(s)
- Usman J Wudil
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Muktar H Aliyu
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Heather L Prigmore
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Donna J Ingles
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Aima A Ahonkhai
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Baba M Musa
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria; Africa Center of Excellence for Population Health and Policy, Bayero University, Kano, Nigeria
| | - Hamza Muhammad
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Mahmoud U Sani
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Aisha M Nalado
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Aliyu Abdu
- Department of Medicine, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Kabiru Abdussalam
- Department of Chemical Pathology, Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Bryan E Shepherd
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Anna M Burgner
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - T Alp Ikizler
- Department of Medicine, Division of Nephrology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christina M Wyatt
- Department of Medicine, Division of Nephrology, Duke University School of Medicine, Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Jeffrey B Kopp
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Paul L Kimmel
- Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - C William Wester
- Vanderbilt Institute for Global Health, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA.
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Tshabalala S, Choudhury A, Beeton-Kempen N, Martinson N, Ramsay M, Mancama D. Targeted ultra-deep sequencing of a South African Bantu-speaking cohort to comprehensively map and characterize common and novel variants in 65 pharmacologically-related genes. Pharmacogenet Genomics 2019; 29:167-178. [PMID: 31162291 PMCID: PMC6675649 DOI: 10.1097/fpc.0000000000000380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/16/2019] [Indexed: 01/11/2023]
Abstract
BACKGROUND African populations are characterised by high genetic diversity, which provides opportunities for discovering and elucidating novel variants of clinical importance, especially those affecting therapeutic outcome. Significantly more knowledge is however needed before such populations can take full advantage of the advances in precision medicine. Coupled with the need to concisely map and better understand the pharmacological implications of genetic diversity in populations of sub-Sharan African ancestry, the aim of this study was to identify and characterize known and novel variants present within 65 important absorption, distribution, metabolism and excretion genes. PATIENTS AND METHODS Targeted ultra-deep next-generation sequencing was used to screen a cohort of 40 South African individuals of Bantu ancestry. RESULTS We identified a total of 1662 variants of which 129 are novel. Moreover, out of the 1662 variants 22 represent potential loss-of-function variants. A high level of allele frequency differentiation was observed for variants identified in this study when compared with other populations. Notably, on the basis of prior studies, many appear to be pharmacologically important in the pharmacokinetics of a broad range of drugs, including antiretrovirals, chemotherapeutic drugs, antiepileptics, antidepressants, and anticoagulants. An in-depth analysis was undertaken to interrogate the pharmacogenetic implications of this genetic diversity. CONCLUSION Despite the new insights gained from this study, the work illustrates that a more comprehensive understanding of population-specific differences is needed to facilitate the development of pharmacogenetic-based interventions for optimal drug therapy in patients of African ancestry.
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Affiliation(s)
- Sibongile Tshabalala
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences
- CSIR Biosciences Unit, Pretoria, South Africa
| | - Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences
| | | | - Neil Martinson
- Perinatal HIV Research Unit, Baragwanath Hospital and Faculty of Health Sciences
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg
| | - Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service, School of Pathology, Faculty of Health Sciences
- Sydney Brenner Institute for Molecular Bioscience (SBIMB), Faculty of Health Sciences
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Butali A, Mossey PA, Adeyemo WL, Eshete MA, Gowans LJJ, Busch TD, Jain D, Yu W, Huan L, Laurie CA, Laurie CC, Nelson S, Li M, Sanchez-Lara PA, Magee WP, Magee KS, Auslander A, Brindopke F, Kay DM, Caggana M, Romitti PA, Mills JL, Audu R, Onwuamah C, Oseni GO, Owais A, James O, Olaitan PB, Aregbesola BS, Braimah RO, Oginni FO, Oladele AO, Bello SA, Rhodes J, Shiang R, Donkor P, Obiri-Yeboah S, Arthur FKN, Twumasi P, Agbenorku P, Plange-Rhule G, Oti AA, Ogunlewe OM, Oladega AA, Adekunle AA, Erinoso AO, Adamson OO, Elufowoju AA, Ayelomi OI, Hailu T, Hailu A, Demissie Y, Derebew M, Eliason S, Romero-Bustillous M, Lo C, Park J, Desai S, Mohammed M, Abate F, Abdur-Rahman LO, Anand D, Saadi I, Oladugba AV, Lachke SA, Amendt BA, Rotimi CN, Marazita ML, Cornell RA, Murray JC, Adeyemo AA. Genomic analyses in African populations identify novel risk loci for cleft palate. Hum Mol Genet 2019; 28:1038-1051. [PMID: 30452639 PMCID: PMC6400042 DOI: 10.1093/hmg/ddy402] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 11/07/2018] [Accepted: 11/11/2018] [Indexed: 12/13/2022] Open
Abstract
Orofacial clefts are common developmental disorders that pose significant clinical, economical and psychological problems. We conducted genome-wide association analyses for cleft palate only (CPO) and cleft lip with or without palate (CL/P) with ~17 million markers in sub-Saharan Africans. After replication and combined analyses, we identified novel loci for CPO at or near genome-wide significance on chromosomes 2 (near CTNNA2) and 19 (near SULT2A1). In situ hybridization of Sult2a1 in mice showed expression of SULT2A1 in mesenchymal cells in palate, palatal rugae and palatal epithelium in the fused palate. The previously reported 8q24 was the most significant locus for CL/P in our study, and we replicated several previously reported loci including PAX7 and VAX1.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
| | - Peter A Mossey
- Department of Orthodontics, University of Dundee, Dundee, UK
| | - Wasiu L Adeyemo
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Mekonen A Eshete
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lord J J Gowans
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Tamara D Busch
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Deepti Jain
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Wenjie Yu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Liu Huan
- State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST, Ministry of Science and Technology) and Key Laboratory for Oral Biomedicine of Ministry of Education, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Cecelia A Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Cathy C Laurie
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Sarah Nelson
- Department of Biostatistics, Genetic Analysis Center, University of Washington, Seattle, WA, USA
| | - Mary Li
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Pedro A Sanchez-Lara
- Department of Pediatrics, Cedars-Sinai Medical Center, David Geffen School of Medicine at University of California, Los Angeles (UCLA), Los Angeles, CA, USA
| | - William P Magee
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Kathleen S Magee
- Operation Smile, 3641 Faculty Boulevard, Virginia Beach, VA, USA
| | - Allyn Auslander
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Frederick Brindopke
- Division of Plastic and Maxillofacial Surgery, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Denise M Kay
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Michele Caggana
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Paul A Romitti
- Department of Epidemiology, College of Public Health, University of Iowa, Iowa, IA, USA
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Rosemary Audu
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chika Onwuamah
- Department of Virology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Ganiyu O Oseni
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Arwa Owais
- Department of Pediatric Dentistry, University of Iowa, Iowa, IA, USA
| | - Olutayo James
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Peter B Olaitan
- Department of Plastic Surgery, Ladoke Akintola University of Science and Technology, Osogbo, Oyo, Nigeria
| | - Babatunde S Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ramat O Braimah
- Department of Oral and Maxillofacial Surgery, Usmanu Danfodiyo University Teaching Hospital, Sokoto, Nigeria
| | - Fadekemi O Oginni
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | - Ayodeji O Oladele
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife, Osun, Nigeria
| | | | - Jennifer Rhodes
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Rita Shiang
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Peter Donkor
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Peter Twumasi
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | - Pius Agbenorku
- Kwame Nkrumah University of Science and Technology, Kumasi, Ashanti, Ghana
| | | | | | - Olugbenga M Ogunlewe
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Afisu A Oladega
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Adegbayi A Adekunle
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Akinwunmi O Erinoso
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Olatunbosun O Adamson
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Abosede A Elufowoju
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Oluwanifemi I Ayelomi
- Department of Oral and Maxillofacial Surgery, University of Lagos, Akoka, Lagos, Nigeria
| | - Taiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abiye Hailu
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Yohannes Demissie
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Miliard Derebew
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Steve Eliason
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Cynthia Lo
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - James Park
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Shaan Desai
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Muiawa Mohammed
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA, USA
| | - Firke Abate
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lukman O Abdur-Rahman
- Division of Pediatric Surgery, Department of Surgery, University of Ilorin, Ilorin, Kwara, Nigeria
| | - Deepti Anand
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Irfaan Saadi
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas, KS, USA
| | | | - Salil A Lachke
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, USA
| | - Brad A Amendt
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine; Department of Human Genetics, Graduate School of Public Health, and Clinical and Translational Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Robert A Cornell
- Department of Anatomy and Cell Biology, University of Iowa, Iowa, IA, USA
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD, USA,To whom correspondence should be addressed at: Azeez Butali, Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa, IA 52242, USA. Tel:+319 3358980; Fax: 319-384-1169; ; or Adebowale A. Adeyemo, Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. Tel: (301) 594-7501; Fax: (301) 451-5426;
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Munung NS, Mayosi BM, de Vries J. Genomics research in Africa and its impact on global health: insights from African researchers. Glob Health Epidemiol Genom 2018; 3:e12. [PMID: 30263136 PMCID: PMC6152488 DOI: 10.1017/gheg.2018.3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/19/2018] [Accepted: 03/01/2018] [Indexed: 12/27/2022] Open
Abstract
Africa may be heading for an era of genomics medicine. There are also expectations that genomics may play a role in reducing global health inequities. However, the near lack of genomics studies on African populations has led to concerns that genomics may widen, rather than close, the global health inequity gap. To prevent a possible genomics divide, the genomics 'revolution' has been extended to Africa. This is motivated, in part, by Africa's rich genetic diversity and high disease burden. What remains unclear, however, are the prospects of using genomics technology for healthcare in Africa. In this qualitative study, we explored the views of 17 genomics researchers in Africa on the prospects and challenges of genomics medicine in Africa. Interviewees were researchers in Africa who were involved in genomics research projects in Africa. Analysis of in-depth interviews suggest that genomics medicine may have an impact on disease surveillance, diagnosis, treatment and prevention. However, Africa's capacity for genomics medicine, current research priorities in genomics and the translation of research findings will be key defining factors impacting on the ability of genomics medicine to improve healthcare in Africa.
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Affiliation(s)
- N. S. Munung
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
| | - B. M. Mayosi
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
- Dean's Office, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - J. de Vries
- Department of Medicine, University of Cape Town and Groote Schuur Hospital, Cape Town, South Africa
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Quansah E, McGregor NW. Towards diversity in genomics: The emergence of neurogenomics in Africa? Genomics 2018; 110:1-9. [PMID: 28774809 DOI: 10.1016/j.ygeno.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/11/2022]
Abstract
There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent. Further, most of the individuals in the African ancestry category were identified to be African-Americans/Afro-Caribbeans, highlighting the huge under-representation of homogenous African populations in large-scale neurogenomic studies. Efforts geared at establishing strong collaborative ties with European/American researchers, maintaining freely accessible biobanks and establishing comprehensive African genome data repositories to track African genome variations are critical for propelling neurogenomics/precision medicine in Africa.
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Affiliation(s)
- Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK.
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa; Department of Psychiatry, Stellenbosch University, Tygerberg Medical Campus, Tygerberg, South Africa.
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8
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Whole-genome sequencing for an enhanced understanding of genetic variation among South Africans. Nat Commun 2017; 8:2062. [PMID: 29233967 PMCID: PMC5727231 DOI: 10.1038/s41467-017-00663-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 07/17/2017] [Indexed: 11/08/2022] Open
Abstract
The Southern African Human Genome Programme is a national initiative that aspires to unlock the unique genetic character of southern African populations for a better understanding of human genetic diversity. In this pilot study the Southern African Human Genome Programme characterizes the genomes of 24 individuals (8 Coloured and 16 black southeastern Bantu-speakers) using deep whole-genome sequencing. A total of ~16 million unique variants are identified. Despite the shallow time depth since divergence between the two main southeastern Bantu-speaking groups (Nguni and Sotho-Tswana), principal component analysis and structure analysis reveal significant (p < 10−6) differentiation, and FST analysis identifies regions with high divergence. The Coloured individuals show evidence of varying proportions of admixture with Khoesan, Bantu-speakers, Europeans, and populations from the Indian sub-continent. Whole-genome sequencing data reveal extensive genomic diversity, increasing our understanding of the complex and region-specific history of African populations and highlighting its potential impact on biomedical research and genetic susceptibility to disease. African populations show a high level of genetic diversity and extensive regional admixture. Here, the authors sequence the whole genomes of 24 South African individuals of different ethnolinguistic origin and find substantive genomic divergence between two southeastern Bantu-speaking groups.
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Genomic Research Data Generation, Analysis and Sharing – Challenges in the African Setting. DATA SCIENCE JOURNAL 2017. [DOI: 10.5334/dsj-2017-049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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10
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Roberts L, Ratnapriya R, du Plessis M, Chaitankar V, Ramesar RS, Swaroop A. Molecular Diagnosis of Inherited Retinal Diseases in Indigenous African Populations by Whole-Exome Sequencing. Invest Ophthalmol Vis Sci 2017; 57:6374-6381. [PMID: 27898983 PMCID: PMC5132076 DOI: 10.1167/iovs.16-19785] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Purpose A majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts. Methods Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics). Variants in reported IRD genes were identified using WES and validated by Sanger sequencing. Custom TaqMan assays were used to screen for identified mutations in 193 unrelated indigenous Africans with IRDs. Results A total of 3494 variants were identified in 217 known IRD genes, leading to the identification of seven different mutations (including six novel) in six genes (RHO, PRPF3, PRPF31, ABCA4, CERKL, and PDE6B) in six distinct families. TaqMan screening in additional probands revealed identical homozygous CERKL and PDE6B variants in four more patients. Conclusions This is the first report of WES of patients with IRDs in indigenous African populations. Our study identified genetic defects in almost 40% of the families analyzed, significantly enhancing the molecular diagnosis of IRD in South Africa. Thus, WES of understudied cohorts seems to present an effective strategy for determining novel mutations in heterogeneous retinal diseases.
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Affiliation(s)
- Lisa Roberts
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Rinki Ratnapriya
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Morné du Plessis
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Vijender Chaitankar
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Raj S Ramesar
- University of Cape Town/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anand Swaroop
- Neurobiology, Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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11
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RICH2 is implicated in viraemic control of HIV-1 in black South African individuals. INFECTION GENETICS AND EVOLUTION 2017; 49:78-87. [PMID: 28069446 DOI: 10.1016/j.meegid.2017.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/22/2016] [Accepted: 01/05/2017] [Indexed: 11/22/2022]
Abstract
An intronic single nucleotide polymorphism (SNP) in RICH2 (rs2072255; 255i), in complete linkage disequilibrium (LD) with an exonic SNP (rs2072254; 254e), has been identified in a genome wide association study to be associated with progression to AIDS in Caucasian individuals. RICH2 links tetherin to the cortical actin network and the RICH2/tetherin interaction has been shown to be important for the downstream activation of NF-κβ and the consequential promotion of proinflammatory responses. We investigated the role of these two SNPs in natural control of HIV-1 in black South Africans including healthy controls (HCs; N=102) and antiretroviral-naive HIV-1-infected controllers (HICs; N=52) and progressors (N=74). HICs were stratified as elite controllers (ECs; N=11), viraemic controllers (VCs; N=30), high viral load (VL) long term non-progressors (HVL LTNPs; N=11) and also according to VL<400RNA copies/ml (HICs VL<400; N=20) and VL>400RNA copies/ml (HICs VL>400; N=32). Results showed that in contrast to Caucasians who had very strong LD between these SNPs (r2=0.97), black populations exhibited low LD (r2=0.11-0.27), however a 254e minor allele was always present with a 255i minor allele but not vice versa. The SNPs did not show significant over- or underrepresentation in any particular group, however the combination of 254e major allele homozygosity and 255i heterozygosity (254eAA/255iGA) was underrepresented in HICs (OR=3.26; P=0.04) and VCs (OR=7.77; P=0.02) compared to HCs, and in HICs VL>400 compared to both HCs (P=0.002) and progressors (P=0.02). A lower CD4+ T-cell count was associated with 254eAA/255iGA and 255i (GA+AA) in the total HIV-1-infected group (P=0.043) and progressors (P=0.017), respectively. In silico analysis predicted loss of an exonic splice enhancer site with the 254e-G allele. We postulate that altered splicing of RICH2 will affect levels of RICH2 expression and consequently NF-κβ activation. These findings point to a role for RICH2 and tetherin in viraemic natural control of HIV-1.
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Embracing an "African Ethos" to facilitate African immigrants participation in medical genetics and genomics research. Nurs Outlook 2016; 65:9-17. [PMID: 27687163 DOI: 10.1016/j.outlook.2016.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 08/02/2016] [Accepted: 08/21/2016] [Indexed: 12/25/2022]
Abstract
BACKGROUND Limited published research exists on perceptions and potentials for black African immigrants' participation in medical genetics and genomics research. PURPOSE This study explores the inclination and disinclination of African immigrants to be involved in genetics and genomics research. METHODS In-depth qualitative interviews were employed in which a sample of black African immigrants 18 years and older (n = 34) were interviewed. DISCUSSION Barriers included contrary beliefs and customs about disease and the human body that differs from Western conceptions, and lack of genuine connection to the health care system. Facilitators included promotion of an "African ethos," wherein Africans unite with one another in a communal extension of self and robust community involvement across the life span of genetic studies. CONCLUSION It is important for researchers and genetic counselors to understand the sociocultural underpinnings of African immigrants about genetics and genomics research as an initial step to encouraging their participation.
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13
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Akinyemi RO, Ovbiagele B, Akpalu A, Jenkins C, Sagoe K, Owolabi L, Sarfo F, Obiako R, Gebreziabher M, Melikam E, Warth S, Arulogun O, Lackland D, Ogunniyi A, Tiwari H, Kalaria RN, Arnett D, Owolabi MO. Stroke genomics in people of African ancestry: charting new paths. Cardiovasc J Afr 2016; 26:S39-49. [PMID: 25962947 PMCID: PMC4557488 DOI: 10.5830/cvja-2015-039] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
One in six people worldwide will experience a stroke in his/her lifetime. While people in Africa carry a disproportionately higher burden of poor stroke outcomes, compared to the rest of the world, the exact contribution of genomic factors to this disparity is unknown. Despite noteworthy research into stroke genomics, studies exploring the genetic contribution to stroke among populations of African ancestry in the United States are few. Furthermore, genomics data in populations living in Africa are lacking. The wide genomic variation of African populations offers a unique opportunity to identify genomic variants with causal relationships to stroke across different ethnic groups. The Stroke Investigative Research and Educational Network (SIREN), a component of the Human Health and Heredity in Africa (H3Africa) Consortium, aims to explore genomic and environmental risk factors for stroke in populations of African ancestry in West Africa and the United States. In this article, we review the literature on the genomics of stroke with particular emphasis on populations of African origin.
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Affiliation(s)
- R O Akinyemi
- Division of Neurology, Federal Medical Centre Abeokuta, Nigeria; Institute of Neuroscience, Newcastle University, UK
| | - B Ovbiagele
- Department of Neurosciences, Medical University of South Carolina, USA
| | - A Akpalu
- College of Health Sciences, University of Ghana, Accra, Ghana
| | | | - K Sagoe
- College of Health Sciences, University of Ghana, Accra, Ghana
| | - L Owolabi
- Department of Medicine, Bayero University, Kano, Nigeria
| | - F Sarfo
- School of Medical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - R Obiako
- Department of Medicine, Ahmadu Bello University, Zaria, Nigeria
| | - M Gebreziabher
- Department of Neurosciences, Medical University of South Carolina, USA
| | - E Melikam
- College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - S Warth
- Department of Neurosciences, Medical University of South Carolina, USA
| | - O Arulogun
- College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - D Lackland
- Department of Neurosciences, Medical University of South Carolina, USA
| | - A Ogunniyi
- College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - H Tiwari
- Department of Public Health, University of Alabama at Birmingham, USA
| | - R N Kalaria
- Institute of Neuroscience, Newcastle University, UK
| | - D Arnett
- Department of Public Health, University of Alabama at Birmingham, USA
| | - M O Owolabi
- College of Medicine, University of Ibadan, Ibadan, Nigeria
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14
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Mulder NJ, Christoffels A, de Oliveira T, Gamieldien J, Hazelhurst S, Joubert F, Kumuthini J, Pillay CS, Snoep JL, Tastan Bishop Ö, Tiffin N. The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. PLoS Comput Biol 2016; 12:e1004395. [PMID: 26845152 PMCID: PMC4742231 DOI: 10.1371/journal.pcbi.1004395] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bioinformatics is now a critical skill in many research and commercial environments as biological data are increasing in both size and complexity. South African researchers recognized this need in the mid-1990s and responded by working with the government as well as international bodies to develop initiatives to build bioinformatics capacity in the country. Significant injections of support from these bodies provided a springboard for the establishment of computational biology units at multiple universities throughout the country, which took on teaching, basic research and support roles. Several challenges were encountered, for example with unreliability of funding, lack of skills, and lack of infrastructure. However, the bioinformatics community worked together to overcome these, and South Africa is now arguably the leading country in bioinformatics on the African continent. Here we discuss how the discipline developed in the country, highlighting the challenges, successes, and lessons learnt.
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Affiliation(s)
- Nicola J. Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Alan Christoffels
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Tulio de Oliveira
- Africa Centre for Health and Population Studies, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Junaid Gamieldien
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Scott Hazelhurst
- School of Electrical & Information Engineering, and Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Judit Kumuthini
- Centre for Proteomic and Genomic Research, Cape Town, South Africa
| | - Ché S. Pillay
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Jacky L. Snoep
- Department of Biochemistry, Stellenbosch University, Stellenbosch, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa
| | - Nicki Tiffin
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
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15
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Mulder NJ, Adebiyi E, Alami R, Benkahla A, Brandful J, Doumbia S, Everett D, Fadlelmola FM, Gaboun F, Gaseitsiwe S, Ghazal H, Hazelhurst S, Hide W, Ibrahimi A, Jaufeerally Fakim Y, Jongeneel CV, Joubert F, Kassim S, Kayondo J, Kumuthini J, Lyantagaye S, Makani J, Mansour Alzohairy A, Masiga D, Moussa A, Nash O, Ouwe Missi Oukem-Boyer O, Owusu-Dabo E, Panji S, Patterton H, Radouani F, Sadki K, Seghrouchni F, Tastan Bishop Ö, Tiffin N, Ulenga N. H3ABioNet, a sustainable pan-African bioinformatics network for human heredity and health in Africa. Genome Res 2015; 26:271-7. [PMID: 26627985 PMCID: PMC4728379 DOI: 10.1101/gr.196295.115] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/25/2015] [Indexed: 11/24/2022]
Abstract
The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants, and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The Human Heredity and Health in Africa (H3Africa) initiative was established to drive the development of genomic research for human health in Africa, and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. Although pockets of high-quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and supervise bioinformatics students. H3ABioNet aims to address this dire need, specifically in the area of human genetics and genomics, but knock-on effects are ensuring this extends to other areas of bioinformatics. Here, we describe the emergence of genomics research and the development of bioinformatics in Africa through H3ABioNet.
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Affiliation(s)
- Nicola J Mulder
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe) and Department of Computer and Information Sciences, Covenant University, Ota, Ogun State, Nigeria, P.M.B. 1023
| | - Raouf Alami
- Centre National de Transfusion Sanguine, Rabat, Morocco 10100
| | | | - James Brandful
- Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana, LG
| | - Seydou Doumbia
- University of Sciences, Techniques and Technology of Bamako, Bamako, Mali BPE 3206
| | - Dean Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi, 3/Institute of Infection and Global Health, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Faisal M Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum/Future University of Sudan, Khartoum, Sudan 11115
| | - Fatima Gaboun
- Institut National de Recherche Agronomique, Rabat, Morocco 10000
| | | | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa 2193
| | - Winston Hide
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA/Sheffield Institute for Translational Neuroscience, Department of Neuroscience, University of Sheffield, Sheffield S10 2HQ, United Kingdom
| | - Azeddine Ibrahimi
- Faculté de Médecine et de Pharmacie de Rabat, Université Mohammed V Souissi, Rabat, Morocco 10100
| | | | - C Victor Jongeneel
- National Center for Supercomputing Applications and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Fourie Joubert
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa 0083
| | - Samar Kassim
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Cairo, Egypt 11566
| | | | - Judit Kumuthini
- Centre for Proteomic and Genomic Research, Cape Town, South Africa 7925
| | | | - Julie Makani
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania 00255
| | | | - Daniel Masiga
- International Centre of Insect Physiology and Ecology, Nairobi, Kenya 00100
| | - Ahmed Moussa
- Abdelmalek Essaadi University, ENSA, Tangier, Morocco 90000
| | - Oyekanmi Nash
- National Biotechnology Development Agency, Abuja, Nigeria 10099
| | | | - Ellis Owusu-Dabo
- Kumasi Centre for Collaborative Research in Tropical Medicine/Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, PMB
| | - Sumir Panji
- Computational Biology Group, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa 7925
| | - Hugh Patterton
- University of the Free State, Bloemfontein, South Africa 9300
| | | | - Khalid Sadki
- Faculty of Sciences of Rabat, University Mohammed V of Rabat, Rabat, Morocco 10000
| | | | - Özlem Tastan Bishop
- Research Unit in Bioinformatics, Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, South Africa 6140
| | - Nicki Tiffin
- South African National Bioinformatics Institute/Medical Research Council of South Africa Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa 7530
| | - Nzovu Ulenga
- Management and Development for Health, Dar es Salaam, Tanzania, 61
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16
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Butali A, Mossey P, Tiffin N, Adeyemo W, Eshete M, Mumena C, Audu R, Onwuamah C, Agbenorku P, Ogunlewe M, Adebola A, Olasoji H, Aregbesola B, Braimah R, Oladugba A, Onah I, Adebiyi E, Olaitan P, Abdur-Rahman L, Adeyemo A. Multidisciplinary approach to genomics research in Africa: the AfriCRAN model. Pan Afr Med J 2015; 21:229. [PMID: 26523171 PMCID: PMC4607986 DOI: 10.11604/pamj.2015.21.229.7380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 07/23/2015] [Indexed: 01/01/2023] Open
Abstract
This article is an outcome of the African Craniofacial Anomalies Research Network (AfriCRAN) Human Hereditary and Health (H3A) grant planning meeting in 2012 in Lagos, Nigeria. It describes the strengths of a multidisciplinary team approach to solving complex genetic traits in the craniofacial region. It also highlights the different components and argues for the composition of similar teams to fast track the discovery of disease genes, diagnostic tools, improved clinical treatment and ultimately prevention of diseases.
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Affiliation(s)
- Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, College of Dentistry, University of Iowa, Iowa City, IA. U.S.A
| | - Peter Mossey
- Department of Orthodontics, University of Dundee, Scotland. UK
| | - Nikki Tiffin
- South African National Bioinformatics Institute, University of the Western Cape, Private Bag, X17, Bellville 7535, South Africa
| | - Wasiu Adeyemo
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos. Nigeria
| | - Mekonen Eshete
- Department of surgery School of Medicine Faculty of health sciences Addis Ababa University, Addis Ababa. Ethiopia
| | - Chrispinanus Mumena
- Department of Oral and Maxillofacial Surgery, Kigali Health Institute, P.O. Box 3286, Kigali, Rwanda
| | - Rosemary Audu
- Human Virology Laboratory, Nigerian Institute of Medical Research, 6, Edmond Crescent, P.M.B. 2013, Yaba, Lagos, Nigeria
| | - Chika Onwuamah
- Human Virology Laboratory, Nigerian Institute of Medical Research, 6, Edmond Crescent, P.M.B. 2013, Yaba, Lagos, Nigeria
| | - Pius Agbenorku
- Department of Plastic Surgery, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana, P.O. Box 448, KNUST, Kumasi, Ghana
| | - Mobolanle Ogunlewe
- Department of Oral and Maxillofacial Surgery, College of Medicine, University of Lagos, Lagos. Nigeria
| | - Adetokunbo Adebola
- Department of Oral and Maxillofacial Surgery, Aminu Kano University Teaching Hospital, Kano. Nigeria
| | - Hecto Olasoji
- Department of Oral and Maxillofacial Surgery, University of Maiduguri Teaching Hospital, Maiduguri. Nigeria
| | - Babatunde Aregbesola
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife. Nigeria
| | - Ramat Braimah
- Department of Oral and Maxillofacial Surgery, Obafemi Awolowo University, Ile-Ife. Nigeria
| | | | - Ifeanyichukwu Onah
- Department of Plastic Surgery, National Orthopedic hospital, Enugu. Nigeria
| | - Ezekiel Adebiyi
- Department of Computer and Information Sciences and Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Peter Olaitan
- Department of Plastic and Reconstructive Surgery, Ladoke Akintola University Ogbomosho. Nigeria
| | | | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, U.S.A
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de Vries J, Tindana P, Littler K, Ramsay M, Rotimi C, Abayomi A, Mulder N, Mayosi BM. The H3Africa policy framework: negotiating fairness in genomics. Trends Genet 2015; 31:117-9. [PMID: 25601285 PMCID: PMC4471134 DOI: 10.1016/j.tig.2014.11.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 11/30/2014] [Indexed: 12/25/2022]
Abstract
Human Heredity and Health in Africa (H3Africa) research seeks to promote fair collaboration between scientists in Africa and those from elsewhere. Here, we outline how concerns over inequality and exploitation led to a policy framework that places a firm focus on African leadership and capacity building as guiding principles for African genomics research.
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Affiliation(s)
- Jantina de Vries
- Department of Medicine, University of Cape Town, UCT Centre for Clinical Research, Old Main Building, Groote Schuur Hospital, Observatory, Cape Town 7925, South Africa.
| | - Paulina Tindana
- Navrongo Health Research Centre, Ghana Health Service, PO Box 114, Navrongo, Ghana
| | | | - Michèle Ramsay
- Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, PO Box 1038, Johannesburg 2000, South Africa
| | - Charles Rotimi
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, Parktown 2193, South Africa
| | - Akin Abayomi
- Center for Research on Genomics and Global Health, MSC 5635, Bethesda, MD 20892-5635, USA
| | - Nicola Mulder
- NSB-H3A Biobank, National Health Laboratory Services of South Africa, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town 7505, South Africa
| | - Bongani M Mayosi
- Institute of Infectious Disease and Molecular Medicine, UCT Faculty of Health Sciences, Observatory 7925, South Africa
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Olaitan PB, Odesina V, Ademola S, Fadiora SO, Oluwatosin OM, Reichenberger EJ. Recruitment of Yoruba families from Nigeria for genetic research: experience from a multisite keloid study. BMC Med Ethics 2014; 15:65. [PMID: 25182071 PMCID: PMC4158348 DOI: 10.1186/1472-6939-15-65] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 08/22/2014] [Indexed: 12/21/2022] Open
Abstract
Background More involvement of sub-Saharan African countries in biomedical studies, specifically in genetic research, is needed to advance individualized medicine that will benefit non-European populations. Missing infrastructure, cultural and religious beliefs as well as lack of understanding of research benefits can pose a challenge to recruitment. Here we describe recruitment efforts for a large genetic study requiring three-generation pedigrees within the Yoruba homelands of Nigeria. The aim of the study was to identify genes responsible for keloids, a wound healing disorder. We also discuss ethical and logistical considerations that we encountered in preparation for this research endeavor. Methods Protocols for this bi-national intercultural study were approved by the Institutional Review Board (IRB) in the US and the ethics committees of the Nigerian institutions for consideration of cultural differences. Principles of community based participatory research were employed throughout the recruitment process. Keloid patients (patient advisors), community leaders, kings/chiefs and medical directors were engaged to assist the research teams with recruitment strategies. Community meetings, church forums, and media outlets (study flyers, radio and TV announcements) were utilized to promote the study in Nigeria. Recruitment of research participants was conducted by trained staff from the local communities. Pedigree structures were re-analyzed on a regular basis as new family members were recruited and recruitment challenges were documented. Results Total recruitment surpassed 4200 study participants over a 7-year period including 79 families with complete three-generation pedigrees. In 9 families more than 20 family members participated, however, in 5 of these families, we encountered issues with pedigree structure as members from different branches presented inconsistent family histories. These issues were due to the traditional open family structure amongst the Yoruba and by beliefs in voodoo or in juju. In addition, family members living in other parts of the country or abroad complicated timely and complete family recruitment. Conclusions Organizational, logistics and ethics challenges can be overcome by additional administrative efforts, good communication, community involvement and education of staff members. However, recruitment challenges due to infrastructural shortcomings or cultural and religious beliefs can lead to significant delays, which may negatively affect study time lines and expectations of funding agencies.
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Affiliation(s)
| | | | | | | | | | - Ernst J Reichenberger
- Department of Reconstructive Sciences, Center for Regenerative Medicine and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT 06030-3705, USA.
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Limou S, Nelson GW, Kopp JB, Winkler CA. APOL1 kidney risk alleles: population genetics and disease associations. Adv Chronic Kidney Dis 2014; 21:426-33. [PMID: 25168832 DOI: 10.1053/j.ackd.2014.06.005] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 06/09/2014] [Accepted: 06/09/2014] [Indexed: 01/13/2023]
Abstract
APOL1 kidney disease is a unique case in the field of the genetics of common disease: 2 variants (termed G1 and G2) with high population frequency have been repeatedly associated with nondiabetic CKDs, with very strong effect size (odds ratios 3-29) in populations of sub-Saharan African descent. This review provides an update on the spectrum of APOL1 kidney disease and on the worldwide distribution of these kidney risk variants. We also summarize the proper way to run a recessive analysis on joint and independent effects of APOL1 G1 and G2 kidney risk variants.
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de Vries J, Williams TN, Bojang K, Kwiatkowski DP, Fitzpatrick R, Parker M. Knowing who to trust: exploring the role of 'ethical metadata' in mediating risk of harm in collaborative genomics research in Africa. BMC Med Ethics 2014; 15:62. [PMID: 25124199 PMCID: PMC4146449 DOI: 10.1186/1472-6939-15-62] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/22/2014] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The practice of making datasets publicly available for use by the wider scientific community has become firmly integrated in genomic science. One significant gap in literature around data sharing concerns how it impacts on scientists' ability to preserve values and ethical standards that form an essential component of scientific collaborations. We conducted a qualitative sociological study examining the potential for harm to ethnic groups, and implications of such ethical concerns for data sharing. We focused our empirical work on the MalariaGEN Consortium, one of the first international collaborative genomics research projects in Africa. METHODS We conducted a study in three MalariaGEN project sites in Kenya, the Gambia, and the United Kingdom. The study entailed analysis of project documents and 49 semi-structured interviews with fieldworkers, researchers and ethics committee members. RESULTS Concerns about how best to address the potential for harm to ethnic groups in MalariaGEN crystallised in discussions about the development of a data sharing policy. Particularly concerning for researchers was how best to manage the sharing of genomic data outside of the original collaboration. Within MalariaGEN, genomic data is accompanied by information about the locations of sample collection, the limitations of consent and ethics approval, and the values and relations that accompanied sample collection. For interviewees, this information and context were of important ethical value in safeguarding against harmful uses of data, but is not customarily shared with secondary data users. This challenged the ability of primary researchers to protect against harmful uses of 'their' data. CONCLUSION We identified three protective mechanisms--trust, the existence of a shared morality, and detailed contextual understanding--which together might play an important role in preventing the use of genomic data in ways that could harm the ethnic groups included in the study. We suggest that the current practice of sharing of datasets as isolated objects rather than as embedded within a particular scientific culture, without regard for the normative context within which samples were collected, may cause ethical tensions to emerge that could have been prevented or addressed had the 'ethical metadata' that accompanies genomic data also been shared.
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Affiliation(s)
- Jantina de Vries
- Department of Medicine, University of Cape Town, Anzio Road Observatory, Cape Town 7925, South Africa.
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Ramsay M. Africa: continent of genome contrasts with implications for biomedical research and health. FEBS Lett 2012; 586:2813-9. [PMID: 22858376 DOI: 10.1016/j.febslet.2012.07.061] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Accepted: 07/23/2012] [Indexed: 10/28/2022]
Abstract
The genomic architecture of African populations is poorly understood and there is considerable variation between ethno-linguistic groups. Genome-wide approaches have been extensively applied to search for genetic associations to complex traits in Europeans, but rarely in Africans. This is largely attributed to lower levels of funding, poor infrastructure and public health systems, and to the small pool of trained scientists. High levels of genetic variation and underlying population structure in Africans present significant challenges, but lower levels of linkage disequilibrium provide an opportunity for more effective localisation of causal variants. High throughput technologies, including dense genotyping arrays, genome sequencing and epigenome studies, together with plummeting costs, are making research more affordable, even for African scientists. Understanding the interactions between genome structure and environmental influences is essential to interpreting their contributions to the increase in infectious diseases and non-communicable diseases, exacerbated by adverse environments and lifestyle choices. The unique genome dynamics in African populations have an important role to play in understanding human health and susceptibility to disease.
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Affiliation(s)
- Michèle Ramsay
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences and the Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
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