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Desalegn Z, Smith A, Yohannes M, Cao X, Anberber E, Bekuretsion Y, Assefa M, Bauer M, Vetter M, Kantelhardt EJ, Abebe T, Starlard-Davenport A. Human Breast Tissue Microbiota Reveals Unique Microbial Signatures that Correlate with Prognostic Features in Adult Ethiopian Women with Breast Cancer. Cancers (Basel) 2023; 15:4893. [PMID: 37835588 PMCID: PMC10571711 DOI: 10.3390/cancers15194893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023] Open
Abstract
Breast cancer (BC) is the leading cause of cancer mortality among women in Ethiopia. Overall, women of African ancestry have the highest death toll due to BC compared to other racial/ethnic groups. The cause of the disparity in mortality is unclear. Recently, studies conducted in the United States and other high-income countries highlighted the role of microbial dysbiosis in BC initiation, tumor growth, and treatment outcome. However, the extent to which inter-individual differences in the makeup of microbiota are associated with clinical and histopathological outcomes in Ethiopian women has not been studied. The goal of our study was to profile the microbiome in breast tumor and normal adjacent to tumor (NAT) tissues of the same donor and to identify associations between microbial composition and abundance and clinicopathological factors in Ethiopian women with BC. We identified 14 microbiota genera in breast tumor tissues that were distinct from NAT tissues, of which Sphingobium, Anaerococcus, Corynebacterium, Delftia, and Enhydrobacter were most significantly decreased in breast tumors compared to NAT tissues. Several microbial genera significantly differed by clinicopathological factors in Ethiopian women with BC. Specifically, the genus Burkholderia more strongly correlated with aggressive triple negative (TNBC) and basal-like breast tumors. The genera Alkanindiges, Anoxybacillus, Leifsonia, and Exiguobacterium most strongly correlated with HER2-E tumors. Luminal A and luminal B tumors also correlated with Anoxybacillus but not as strongly as HER2-E tumors. A relatively higher abundance of the genus Citrobacter most significantly correlated with advanced-stage breast tumors compared to early-stage tumors. This is the first study to report an association between breast microbial dysbiosis and clinicopathological factors in Ethiopian women.
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Affiliation(s)
- Zelalem Desalegn
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences Addis Ababa University, Addis Ababa 9086, Ethiopia; (Z.D.); (M.Y.); (T.A.)
- Global Health Working Group, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
| | - Alana Smith
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Meron Yohannes
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences Addis Ababa University, Addis Ababa 9086, Ethiopia; (Z.D.); (M.Y.); (T.A.)
- Global Health Working Group, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
- School of Medical Laboratory Sciences, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, College of Nursing, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Endale Anberber
- Department of Surgery, School of Medicine, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Yonas Bekuretsion
- Department of Pathology, School of Medicine, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Mathewos Assefa
- Department of Oncology, School of Medicine, Addis Ababa University, Addis Ababa 9086, Ethiopia;
| | - Marcus Bauer
- Institute of Pathology, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
| | - Martina Vetter
- Department of Gynecology, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
| | - Eva Johanna Kantelhardt
- Global Health Working Group, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
- Department of Gynecology, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
- Institute of Medical Epidemiology, Biostatistics, and Informatics, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany
| | - Tamrat Abebe
- Department of Microbiology, Immunology, and Parasitology, School of Medicine, College of Health Sciences Addis Ababa University, Addis Ababa 9086, Ethiopia; (Z.D.); (M.Y.); (T.A.)
- Global Health Working Group, Martin Luther University Halle-Wittenberg, 06097 Halle (Saale), Germany;
| | - Athena Starlard-Davenport
- Department of Genetics, Genomics and Informatics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
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Magnier J, Druet T, Naves M, Ouvrard M, Raoul S, Janelle J, Moazami-Goudarzi K, Lesnoff M, Tillard E, Gautier M, Flori L. The genetic history of Mayotte and Madagascar cattle breeds mirrors the complex pattern of human exchanges in Western Indian Ocean. G3 GENES|GENOMES|GENETICS 2022; 12:6523972. [PMID: 35137043 PMCID: PMC8982424 DOI: 10.1093/g3journal/jkac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 11/16/2022]
Abstract
Despite their central economic and cultural role, the origin of cattle populations living in Indian Ocean islands still remains poorly documented. Here, we unravel the demographic and adaptive histories of the extant Zebus from the Mayotte and Madagascar islands using high-density SNP genotyping data. We found that these populations are very closely related and both display a predominant indicine ancestry. They diverged in the 16th century at the arrival of European people who transformed the trade network in the area. Their common ancestral cattle population originates from an admixture between an admixed African zebu population and an Indian zebu that occurred around the 12th century at the time of the earliest contacts between human African populations of the Swahili corridor and Austronesian people from Southeast Asia in Comoros and Madagascar. A steep increase in the estimated population sizes from the beginning of the 16th to the 17th century coincides with the expansion of the cattle trade. By carrying out genome scans for recent selection in the two cattle populations from Mayotte and Madagascar, we identified sets of candidate genes involved in biological functions (cancer, skin structure, and UV-protection, nervous system and behavior, organ development, metabolism, and immune response) broadly representative of the physiological adaptation to tropical conditions. Overall, the origin of the cattle populations from Western Indian Ocean islands mirrors the complex history of human migrations and trade in this area.
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Affiliation(s)
- Jessica Magnier
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Tom Druet
- Unit of Animal Genomics, GIGA-R, Faculty of Veterinary Medicine, University of Liège, Liège 4000, Belgium
| | | | | | | | - Jérôme Janelle
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | | | - Matthieu Lesnoff
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Montpellier 34398, France
| | - Emmanuel Tillard
- SELMET, University of Montpellier, CIRAD, INRAE, L’Institut Agro, Montpellier 34398, France
- CIRAD, UMR SELMET, Saint-Pierre 97410, France
| | - Mathieu Gautier
- CBGP, INRAE, CIRAD, IRD, L’Institut Agro, University of Montpellier, Montferrier sur Lez 34988, France
| | - Laurence Flori
- SELMET, INRAE, CIRAD, L’Institut Agro, University of Montpellier, Montpellier 34398, France
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Motshwari DD, George C, Matshazi DM, Weale CJ, Davids SFG, Zemlin AE, Erasmus RT, Kengne AP, Matsha TE. Expression of whole blood miR-126-3p, -30a-5p, -1299, -182-5p and -30e-3p in chronic kidney disease in a South African community-based sample. Sci Rep 2022; 12:4107. [PMID: 35260775 PMCID: PMC8904505 DOI: 10.1038/s41598-022-08175-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/04/2022] [Indexed: 12/30/2022] Open
Abstract
The burden of chronic kidney disease (CKD) in Africa remains poorly characterized, due partly to the lack of appropriate diagnostic strategies. Although in recent years the diagnostic and prognostic utility of microRNAs (miRNAs) have gained prominence in the context of CKD, its value has not been evaluated in African populations. We investigated the expression of whole blood miRNAs (miR-126-3p, -30a-5p, -1299, -182-5p and -30e-3p) in a total sample of 1449 comprising of 13.3% individuals with CKD (stage 1-5) and 26.4% male participants, as well as the association of these miRNAs with prevalent CKD, in a community-based sample of South African adults. We used Reverse Transcription Quantitative Real-Time PCR (RT-qPCR) to analyze miRNA expression. There was an increased expression in whole blood miR-126-3p, -30a-5p, -1299 and -182-5p in individuals with CKD, compared to those without (all p ≤ 0.036), whereas miR-30e-3p showed no significant difference between the groups (p = 0.482). Only miR-126-3p, -182-5p and -30e-3p were independently associated with increased risk of CKD (all p ≤ 0.022). This study showed for the first time that there is a dysregulation of whole blood miR-126-3p, -30a-5p, -1299 and -182-5p in South Africans of mixed-ancestry with CKD. More research is needed to ascertain their role in CKD risk screening in African populations.
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Affiliation(s)
- Dipuo D Motshwari
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Cindy George
- Non-Communicable Disease Research Unit, South African Medical Research Council, Parow, Francie van Zijl Drive, Parow Valley, Cape Town, South Africa.
| | - Don M Matshazi
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Cecil J Weale
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Saarah F G Davids
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
| | - Annalise E Zemlin
- Division of Chemical Pathology, Faculty of Medicine and Health Sciences, National Health Laboratory Service (NHLS) and University of Stellenbosch, Cape Town, South Africa
| | - Rajiv T Erasmus
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
- Division of Chemical Pathology, Faculty of Medicine and Health Sciences, National Health Laboratory Service (NHLS) and University of Stellenbosch, Cape Town, South Africa
| | - Andre P Kengne
- Non-Communicable Disease Research Unit, South African Medical Research Council, Parow, Francie van Zijl Drive, Parow Valley, Cape Town, South Africa
- Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Tandi E Matsha
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health and Wellness Science, Cape Peninsula University of Technology, Cape Town, South Africa
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Fernandez PW. Prostate Cancer Genomics Research Disparities in Africa: Advancing Knowledge in Resource Constrained Settings. Cancer Control 2022; 29:10732748221095952. [PMID: 35475404 PMCID: PMC9087236 DOI: 10.1177/10732748221095952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Prostate cancer disproportionately affects men of African descent and it is
estimated that Africa will bear the highest disease burden in the next decade.
Underlying genomic factors may contribute to prostate cancer disparities;
however, it is unclear whether Africa has prioritised genomics research toward
addressing these disparities. A Pubmed review was performed of publications
spanning a 15-year period, with specific focus on prostate cancer genomics
research that included samples from Africa and investigators in Africa. Data are
presented on research publications from Africa relative to similar publications
from different geographical regions, and more specifically, the extent of
disparities and the contributions to prostate cancer knowledge as a result of
genomics research that included African samples and African institutions.
Limited publication output may reflect the infrastructure and funding challenges
in Africa. Widespread cooperation should be fostered by sharing capacity and
leveraging existing expertise to address the growing cancer burden facing the
continent.
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Affiliation(s)
- Pedro W Fernandez
- Division of Urology, 26697Stellenbosch University, Cape Town, South Africa
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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Ghoorah AW, Chaplain T, Rindra R, Goorah S, Chinien G, Jaufeerally-Fakim Y. Population Structure of the South West Indian Ocean Islands: Implications for Precision Medicine. Front Genet 2021; 12:758563. [PMID: 34899843 PMCID: PMC8653818 DOI: 10.3389/fgene.2021.758563] [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: 08/14/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022] Open
Abstract
Precision medicine has brought new hopes for patients around the world with the applications of novel technologies for understanding genetics of complex diseases and their translation into clinical services. Such applications however require a foundation of skills, knowledge and infrastructure to translate genetics for health care. The crucial element is no doubt the availability of genomics data for the target populations, which is seriously lacking for most parts of Africa. We discuss here why it is vital to prioritize genomics data for the South West Indian Ocean region where a mosaic of ethnicities co-exist. The islands of the SWIO, which comprise Madagascar, La Reunion, Mauritius, Seychelles and Comoros, have been the scene for major explorations and trade since the 17th century being on the route to Asia. This part of the world has lived through active passage of slaves from East Africa to Arabia and further. Today’s demography of the islands is a diverse mix of ancestries including European, African and Asian. The extent of admixtures has yet to be resolved. Except for a few studies in Madagascar, there is very little published data on human genetics for these countries. Isolation and small population sizes have likely resulted in reduced genetic variation and possible founder effects. There is a significant prevalence of diabetes, particularly in individuals of Indian descent, while breast and prostate cancers are on the rise. The island of La Reunion is a French overseas territory with a high standard of health care and close ties to Mauritius. Its demography is comparable to that of Mauritius but with a predominantly mixed population and a smaller proportion of people of Indian descent. On the other hand, Madagascar’s African descendants inhabit mostly the lower coastal zones of the West and South regions, while the upper highlands are occupied by peoples of mixed African-Indonesian ancestries. Historical records confirm the Austronesian contribution to the Madagascar genomes. With the rapid progress in genomic medicine, there is a growing demand for sequencing services in the clinical settings to explore the incidence of variants in candidate disease genes and other markers. Genome sequence data has become a priority in order to understand the population sub-structures and to identify specific pathogenic variants among the different groups of inhabitants on the islands. Genomic data is increasingly being used to advise families at risk and propose diagnostic screening measures to enhance the success of therapies. This paper discusses the complexity of the islands’ populations and argues for the needs for genotyping and understanding the genetic factors associated with disease risks. The benefits to patients and improvement in health services through a concerted regional effort are depicted. Some private patients are having recourse to external facilities for molecular profiling with no return of data for research. Evidence of disease variants through sequencing represents a valuable source of medical data that can guide policy decisions at the national level. There are presently no such records for future implementation of strategies for genomic medicine.
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Affiliation(s)
| | - Toto Chaplain
- University of Toamasina, Barikadimy, Toamasina, Madagascar
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Ruchman SG, Delong AK, Kamano JH, Bloomfield GS, Chrysanthopoulou SA, Fuster V, Horowitz CR, Kiptoo P, Matelong W, Mugo R, Naanyu V, Orango V, Pastakia SD, Valente TW, Hogan JW, Vedanthan R. Egocentric social network characteristics and cardiovascular risk among patients with hypertension or diabetes in western Kenya: a cross-sectional analysis from the BIGPIC trial. BMJ Open 2021; 11:e049610. [PMID: 34475172 PMCID: PMC8413931 DOI: 10.1136/bmjopen-2021-049610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/11/2021] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES Management of cardiovascular disease (CVD) is an urgent challenge in low-income and middle-income countries, and interventions may require appraisal of patients' social networks to guide implementation. The purpose of this study is to determine whether egocentric social network characteristics (SNCs) of patients with chronic disease in western Kenya are associated with overall CVD risk and individual CVD risk factors. DESIGN Cross-sectional analysis of enrollment data (2017-2018) from the Bridging Income Generation with GrouP Integrated Care trial. Non-overlapping trust-only, health advice-only and multiplex (trust and health advice) egocentric social networks were elicited for each participant, and SNCs representing social cohesion were calculated. SETTING 24 communities across four counties in western Kenya. PARTICIPANTS Participants (n=2890) were ≥35 years old with diabetes (fasting glucose ≥7 mmol/L) or hypertension. PRIMARY AND SECONDARY OUTCOMES We hypothesised that SNCs would be associated with CVD risk status (QRISK3 score). Secondary outcomes were individual CVD risk factors. RESULTS Among the 2890 participants, 2020 (70%) were women, and mean (SD) age was 60.7 (12.1) years. Forty-four per cent of participants had elevated QRISK3 score (≥10%). No relationship was observed between QRISK3 level and SNCs. In unadjusted comparisons, participants with any individuals in their trust network were more likely to report a good than a poor diet (41% vs 21%). SNCs for the trust and multiplex networks accounted for a substantial fraction of variation in measures of dietary quality and physical activity (statistically significant via likelihood ratio test, adjusted for false discovery rate). CONCLUSION SNCs indicative of social cohesion appear to be associated with individual behavioural CVD risk factors, although not with overall CVD risk score. Understanding how SNCs of patients with chronic diseases relate to modifiable CVD risk factors could help inform network-based interventions. TRIAL REGISTRATION NUMBER ClinicalTrials.gov identifier: NCT02501746; https://clinicaltrials.gov/ct2/show/NCT02501746.
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Affiliation(s)
- Samuel G Ruchman
- Department of Medicine, Department of Pediatrics, University of Colorado, Aurora, Colorado, USA
| | - Allison K Delong
- Department of Biostatistics, School of Public Health, Brown University, Providence, Rhode Island, USA
| | - Jemima H Kamano
- Department of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | | | | | - Valentin Fuster
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Carol R Horowitz
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Peninah Kiptoo
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Winnie Matelong
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Richard Mugo
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Violet Naanyu
- Department of Sociology, Psychology and Anthropology, School of Arts and Social Sciences, Moi University, Eldoret, Kenya
| | - Vitalis Orango
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - Sonak D Pastakia
- Department of Pharmacy Practice, Purdue University, West Lafayette, Indiana, USA
| | - Thomas W Valente
- Department of Preventive Medicine, University of Southern California, Los Angeles, California, USA
| | - Joseph W Hogan
- Department of Biostatistics, School of Public Health, Brown University, Providence, Rhode Island, USA
| | - Rajesh Vedanthan
- Department of Population Health, NYU Grossman School of Medicine, New York City, New York, USA
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Zhou DT, Mudhluli TE, Madhombiro M, Nyamhunga A, Matekaire-Chirimo R, Mudzviti T, Manasa J, Ma Q, Maponga CC, Morse GD. Emerging role for pharmacogenomics in HIV research in Africa. Future Virol 2021. [DOI: 10.2217/fvl-2020-0388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Tweetable abstract Pharmacogenomics (Pgx); the study of how genes affect drug response may optimize treatment by improving effectiveness and safety of medications. To apply current guidelines for African HIV-infected patients Pgx research is key.
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Affiliation(s)
- Danai Tavonga Zhou
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Medical Laboratory Sciences Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Taona Emmah Mudhluli
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Munyaradzi Madhombiro
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Primary Health Care, Psychiatry Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Albert Nyamhunga
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Oncology, Radiology Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Ratidzo Matekaire-Chirimo
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Primary Health Care, Paediatrics Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Tinashe Mudzviti
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Box A 178, Avondale, Harare, Zimbabwe
| | - Justen Manasa
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Microbiology Unit, Box A 178, Avondale, Harare, Zimbabwe
| | - Qing Ma
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
| | - Charles Chiedza Maponga
- University of Zimbabwe, Faculty of Medicine & Health Sciences, Department of Pharmacy & Pharmaceutical Sciences, Box A 178, Avondale, Harare, Zimbabwe
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
| | - Gene D Morse
- University at Buffalo, School of Pharmacy and Pharmaceutical Sciences, Center for Integrated Global Biomedical Sciences, NYS Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, NY 14203-1101, USA
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Anyigba CA, Awandare GA, Paemka L. Breast cancer in sub-Saharan Africa: The current state and uncertain future. Exp Biol Med (Maywood) 2021; 246:1377-1387. [PMID: 33926257 DOI: 10.1177/15353702211006047] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Breast cancer is the commonest cause of global cancer-related deaths in women and a public health burden in sub-Saharan Africa (SSA). Although the disease incidence in SSA seems lower, mortality rates are disproportionately high in comparison to high-income countries. The global disease burden is growing, with SSA reporting the majority of cases; however, the dearth of information results in insufficient data which is barely representative of the actual disease burden in this population. Future incidence predictions assign the subregion with a majority of the cases and associated deaths. Breast cancer presents with racial and ethnic variations, and available evidence suggests geographical diversity and persistent risk factors that have barely been explored in SSA. Breast cancer is a complex genetic disease, but the genetic risk factors in the extant African population, which is the most genetically diverse population, is scant and of low quality. This review focuses on the burden, prevalence, detection, treatment, survival, biology, as well as risk factors, and reinforces the need for breast cancer-associated risk factor investigation and population-specific studies in SSA.
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Affiliation(s)
- Claudia A Anyigba
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, 58835University of Ghana, Accra, GH 00233, Ghana
| | - Gordon A Awandare
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, 58835University of Ghana, Accra, GH 00233, Ghana
| | - Lily Paemka
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, 58835University of Ghana, Accra, GH 00233, Ghana
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10
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Choudhury A, Sengupta D, Ramsay M, Schlebusch C. Bantu-speaker migration and admixture in southern Africa. Hum Mol Genet 2021; 30:R56-R63. [PMID: 33367711 PMCID: PMC8117461 DOI: 10.1093/hmg/ddaa274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 01/16/2023] Open
Abstract
The presence of Early and Middle Stone Age human remains and associated archeological artifacts from various sites scattered across southern Africa, suggests this geographic region to be one of the first abodes of anatomically modern humans. Although the presence of hunter-gatherer cultures in this region dates back to deep times, the peopling of southern Africa has largely been reshaped by three major sets of migrations over the last 2000 years. These migrations have led to a confluence of four distinct ancestries (San hunter-gatherer, East-African pastoralist, Bantu-speaker farmer and Eurasian) in populations from this region. In this review, we have summarized the recent insights into the refinement of timelines and routes of the migration of Bantu-speaking populations to southern Africa and their admixture with resident southern African Khoe-San populations. We highlight two recent studies providing evidence for the emergence of fine-scale population structure within some South-Eastern Bantu-speaker groups. We also accentuate whole genome sequencing studies (current and ancient) that have both enhanced our understanding of the peopling of southern Africa and demonstrated a huge potential for novel variant discovery in populations from this region. Finally, we identify some of the major gaps and inconsistencies in our understanding and emphasize the importance of more systematic studies of southern African populations from diverse ethnolinguistic groups and geographic locations.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Michele Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2193, South Africa
| | - Carina Schlebusch
- Palaeo-Research Institute, University of Johannesburg, Auckland Park 2006, South Africa
- Human Evolution, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18C, SE-752 36 Uppsala 75326, Sweden
- SciLifeLab, Uppsala 75237, Sweden
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11
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Campbell MC, Ranciaro A. Human adaptation, demography and cattle domestication: an overview of the complexity of lactase persistence in Africa. Hum Mol Genet 2021; 30:R98-R109. [PMID: 33847744 DOI: 10.1093/hmg/ddab027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/13/2021] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
Lactase persistence (LP) is a genetically-determined trait that is prevalent in African, European and Arab populations with a tradition of animal herding and milk consumption. To date, genetic analyses have identified several common variants that are associated with LP. Furthermore, data have indicated that these functional alleles likely have been maintained in pastoralist populations due to the action of recent selection, exemplifying the ongoing evolution of anatomically modern humans. Additionally, demographic history has also played a role in the geographic distribution of LP and associated alleles in Africa. In particular, the migration of ancestral herders and their subsequent admixture with local populations were integral to the spread of LP alleles and the culture of pastoralism across the continent. The timing of these demographic events was often correlated with known major environmental changes and/or the ability of domesticated cattle to resist/avoid infectious diseases. This review summarizes recent advances in our understanding of the genetic basis and evolutionary history of LP, as well as the factors that influenced the origin and spread of pastoralism in Africa.
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Affiliation(s)
- Michael C Campbell
- Department of Biology, Howard University, EE Just Hall Biology Building, 415 College Street NW, Washington, DC 20059, USA
| | - Alessia Ranciaro
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, 415 Curie Boulevard, Philadelphia, PA 19104, USA
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12
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Hamdi Y, Zass L, Othman H, Radouani F, Allali I, Hanachi M, Okeke CJ, Chaouch M, Tendwa MB, Samtal C, Mohamed Sallam R, Alsayed N, Turkson M, Ahmed S, Benkahla A, Romdhane L, Souiai O, Tastan Bishop Ö, Ghedira K, Mohamed Fadlelmola F, Mulder N, Kamal Kassim S. Human OMICs and Computational Biology Research in Africa: Current Challenges and Prospects. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:213-233. [PMID: 33794662 DOI: 10.1089/omi.2021.0004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Fouzia Radouani
- Chlamydiae and Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
| | - Mariem Hanachi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Chiamaka Jessica Okeke
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Maureen Bilinga Tendwa
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Chaimae Samtal
- Laboratory of Biotechnology, Environment, Agri-food and Health, Faculty of Sciences Dhar El Mahraz-Sidi Mohammed Ben Abdellah University, Fez, Morocco.,University of Mohamed Premier, Oujda, Morocco
| | - Reem Mohamed Sallam
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt.,Department of Basic Medical Sciences, Faculty of Medicine, Galala University, Suez, Egypt
| | - Nihad Alsayed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Michael Turkson
- The National Institute for Mathematical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Samah Ahmed
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia.,Faculty of Science of Bizerte, Zarzouna, University of Carthage, Tunis, Tunisia
| | - Oussema Souiai
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, South Africa
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Faisal Mohamed Fadlelmola
- Centre for Bioinformatics and Systems Biology, Faculty of Science, University of Khartoum, Khartoum, Sudan
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, CIDRI Africa Wellcome Trust Centre, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Samar Kamal Kassim
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
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13
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Chikowore T, Kamiza AB, Oduaran OH, Machipisa T, Fatumo S. Non-communicable diseases pandemic and precision medicine: Is Africa ready? EBioMedicine 2021; 65:103260. [PMID: 33639396 PMCID: PMC7921515 DOI: 10.1016/j.ebiom.2021.103260] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 01/12/2021] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Non-communicable diseases (NCDs) kill more than 41 million people every year, accounting for 71% of all deaths globally. The prevalence of NCDs is estimated to be higher than that of infectious diseases in Africa by 2030. Precision medicine may help with early identification of cases, resulting in timely prevention and improvement in the efficacy of treatments. However, Africa has been lagging behind in genetic research, a key component of the precision medicine initiative. A number of genomic research initiatives which could lead to translational genomics are emerging on the African continent which includes the Non-communicable Diseases Genetic Heritage Study (NCDGHS) and the Men of African Descent and Carcinoma of the Prostate (MADCaP) Network. These offer a promise that precision medicine can be applied in African countries. This review evaluates the advances of genetic studies for cancer, hypertension, type 2 diabetes and body mass index (BMI) in Africa.
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Affiliation(s)
- Tinashe Chikowore
- MRC/Wits Developmental Pathways for Health Research Unit, Department of Paediatrics, 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.
| | - Abram Bunya Kamiza
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Ovokeraye H Oduaran
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tafadzwa Machipisa
- Hatter Institute for Cardiovascular Diseases Research in Africa (HICRA), Department of Medicine, University of Cape Town, Cape Town, South Africa; Population Health Research Institute, David Braley Cardiac, Vascular and Stroke Research Institute, 237 Barton Street East, Hamilton, ON L8L 2 × 2, Canada
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research group, MRC/UVRI and LSHTM, Uganda; London School of Hygiene and Tropical Medicine London UK; H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria.
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14
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Pedro N, Pinto RJ, Cavadas B, Pereira L. Sub-Saharan African information potential to unveil adaptations to infectious disease. Hum Mol Genet 2021; 30:R138-R145. [PMID: 33461217 DOI: 10.1093/hmg/ddab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/10/2020] [Accepted: 01/05/2021] [Indexed: 12/09/2022] Open
Abstract
Sub-Saharan Africa is the most promising region of the world to conduct high-throughput studies to unveil adaptations to infectious diseases due to several reasons, namely, the longest evolving time-depth in the Homo sapiens phylogenetic tree (at least two-third older than any other worldwide region); the continuous burden of infectious diseases (still number one in health/life threat); and the coexistence of populations practising diverse subsistence modes (nomadic or seminomadic hunter-gatherers and agropastoralists, and sedentary agriculturalists, small urban and megacity groups). In this review, we will present the most up-to-date results that shed light on three main hypotheses related with this adaptation. One is the hypothesis of coevolution between host and pathogen, given enough time for the establishment of this highly dynamic relationship. The second hypothesis enunciates that the agricultural transition was responsible for the increase of the infectious disease burden, due to the huge expansion of the sedentary human population and the cohabitation with domesticates as main reservoirs of pathogens. The third hypothesis states that the boosting of our immune system against pathogens by past selection may have resulted in maladaptation of the developed hygienic societies, leading to an increase of allergic, inflammatory and autoimmune disorders. Further work will enlighten the biological mechanisms behind these main adaptations, which can be insightful for translation into diagnosis, prognosis and treatment interventions.
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Affiliation(s)
- Nicole Pedro
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Ricardo J Pinto
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,IPATIMUP - Instituto de Patologia e Imunologia Molecular, Universidade do Porto, 4200-135 Porto, Portugal
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15
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Mathuba B, Koromina M, Mitropoulou C, Patrinos GP. Catalyzing clinical implementation of pharmacogenomics and personalized medicine interventions in Africa. Pharmacogenomics 2020; 22:115-122. [PMID: 33353428 DOI: 10.2217/pgs-2020-0101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pharmacogenomics is considered to be the low-hanging fruit in the tree of genomic medicine with numerous examples of its successful implementation in the clinic. In this perspective, we provide details about the potential clinical application of pharmacogenomics in African populations by using relevant drug cases and high-throughput genomics approaches; involving numerous countries and stakeholders; and most importantly exploiting the existing knowledge of respective large-scale initiatives. We emphasize on the necessity of constructing appropriate frameworks for government policies in African countries. We also provide input about different initiatives in the field of genomics medicine implementation in Africa, not only for their potential for synergy and collaboration among them, but also as models for replication in other regions worldwide, aiming for healthcare improvement.
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Affiliation(s)
- Bathusi Mathuba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Maria Koromina
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, 26503, Greece
| | | | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, 26503, Greece.,Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, UAE.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, UAE
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16
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Ingram CJE, Ekong R, Ansari-Pour N, Bradman N, Swallow DM. Group-based pharmacogenetic prediction: is it feasible and do current NHS England ethnic classifications provide appropriate data? THE PHARMACOGENOMICS JOURNAL 2020; 21:47-59. [PMID: 32683419 DOI: 10.1038/s41397-020-0175-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Inter-individual variation of drug metabolising enzymes (DMEs) leads to variable efficacy of many drugs and even adverse drug responses. Consequently, it would be desirable to test variants of many DMEs before drug treatment. Inter-ethnic differences in frequency mean that the choice of SNPs to test may vary across population groups. Here we examine the utility of testing representative groups as a way of assessing what variants might be tested. We show that publicly available population information is potentially useful for determining loci for pre-treatment genetic testing, and for determining the most prevalent risk haplotypes in defined groups. However, we also show that the NHS England classifications have limitations for grouping for these purposes, in particular for people of African descent. We conclude: (1) genotyping of hospital patients and people from the hospital catchment area confers no advantage over using samples from appropriate existing ethnic group collections or publicly available data, (2) given the current NHS England Black African grouping, a decision as to whether to test, would have to apply to all patients of recent Black African ancestry to cover reported risk alleles and (3) the current scarcity of available genome and drug effect data from Africans is a problem for both testing and treatment decisions.
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Affiliation(s)
- Catherine J E Ingram
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Rosemary Ekong
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LF, UK
| | - Neil Bradman
- Henry Stewart Group, 40-41 Museum Street, London, WC1A 1LT, UK
| | - Dallas M Swallow
- Research Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK.
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17
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Sonographic Assessment of Fetal Neck Circumference (NC) As a Predictor of Gestational Age. JOURNAL OF FETAL MEDICINE 2020. [DOI: 10.1007/s40556-020-00256-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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18
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Hurley CK, Kempenich J, Wadsworth K, Sauter J, Hofmann JA, Schefzyk D, Schmidt AH, Galarza P, Cardozo MBR, Dudkiewicz M, Houdova L, Jindra P, Sorensen BS, Jagannathan L, Mathur A, Linjama T, Torosian T, Freudenberger R, Manolis A, Mavrommatis J, Cereb N, Manor S, Shriki N, Sacchi N, Ameen R, Fisher R, Dunckley H, Andersen I, Alaskar A, Alzahrani M, Hajeer A, Jawdat D, Nicoloso G, Kupatawintu P, Cho L, Kaur A, Bengtsson M, Dehn J. Common, intermediate and well-documented HLA alleles in world populations: CIWD version 3.0.0. HLA 2020; 95:516-531. [PMID: 31970929 PMCID: PMC7317522 DOI: 10.1111/tan.13811] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 12/25/2022]
Abstract
A catalog of common, intermediate and well-documented (CIWD) HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1 and -DPB1 alleles has been compiled from over 8 million individuals using data from 20 unrelated hematopoietic stem cell volunteer donor registries. Individuals are divided into seven geographic/ancestral/ethnic groups and data are summarized for each group and for the total population. P (two-field) and G group assignments are divided into one of four frequency categories: common (≥1 in 10 000), intermediate (≥1 in 100 000), well-documented (≥5 occurrences) or not-CIWD. Overall 26% of alleles in IPD-IMGT/HLA version 3.31.0 at P group resolution fall into the three CIWD categories. The two-field catalog includes 18% (n = 545) common, 17% (n = 513) intermediate, and 65% (n = 1997) well-documented alleles. Full-field allele frequency data are provided but are limited in value by the variations in resolution used by the registries. A recommended CIWD list is based on the most frequent category in the total or any of the seven geographic/ancestral/ethnic groups. Data are also provided so users can compile a catalog specific to the population groups that they serve. Comparisons are made to three previous CWD reports representing more limited population groups. This catalog, CIWD version 3.0.0, is a step closer to the collection of global HLA frequencies and to a clearer view of HLA diversity in the human population as a whole.
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Affiliation(s)
- Carolyn K. Hurley
- Department of OncologyGeorgetown UniversityWashingtonDistrict of Columbia
| | | | | | | | | | | | | | | | | | - Malgorzata Dudkiewicz
- Central Unrelated Potential Bone Marrow Donor and Cord Blood Registry POLTRANSPLANTWarsawPoland
| | - Lucie Houdova
- University of West Bohemia, New Technologies for the Information SocietyPilsenCzech Republic
| | - Pavel Jindra
- Czech National Marrow Donors Registry and University Hospital PilsenPilsenCzech Republic
| | | | - Latha Jagannathan
- DKMS BMST Foundation IndiaBangaloreIndia
- Bangalore Medical Services TrustBangaloreIndia
| | | | | | | | | | | | | | - Nezih Cereb
- DATRI Blood Stem Cell Donor RegistryChennaiIndia
| | - Sigal Manor
- Israel‐Ezer Mizion Bone Marrow Donor RegistryBnei BrakIsrael
| | - Nira Shriki
- Israel‐Ezer Mizion Bone Marrow Donor RegistryBnei BrakIsrael
| | | | - Reem Ameen
- Kuwait National Stem Cell RegistryJabriyaKuwait
| | - Raewyn Fisher
- New Zealand Bone Marrow Donor RegistryAucklandNew Zealand
| | | | | | - Ahmed Alaskar
- Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, RiyadhMinistry of National Guard Health AffairsRiyadhSaudi Arabia
| | - Mohsen Alzahrani
- Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, RiyadhMinistry of National Guard Health AffairsRiyadhSaudi Arabia
| | - Ali Hajeer
- Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, RiyadhMinistry of National Guard Health AffairsRiyadhSaudi Arabia
| | - Dunia Jawdat
- Saudi Stem Cell Donor Registry, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, RiyadhMinistry of National Guard Health AffairsRiyadhSaudi Arabia
| | | | | | - Louise Cho
- The Bone Marrow Donor ProgrammeSingapore
| | | | - Mats Bengtsson
- Tobias Registry of Swedish Bone Marrow Donors and Department of Immunology, Genetics and PathologyUppsala UniversityUppsalaSweden
| | - Jason Dehn
- National Marrow Donor ProgramMinneapolisMinnesota
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19
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Prospective avenues for human population genomics and disease mapping in southern Africa. Mol Genet Genomics 2020; 295:1079-1089. [PMID: 32440765 PMCID: PMC7240165 DOI: 10.1007/s00438-020-01684-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/06/2020] [Indexed: 12/22/2022]
Abstract
Population substructure within human populations is globally evident and a well-known confounding factor in many genetic studies. In contrast, admixture mapping exploits population stratification to detect genotype-phenotype correlations in admixed populations. Southern Africa has untapped potential for disease mapping of ancestry-specific disease risk alleles due to the distinct genetic diversity in its populations compared to other populations worldwide. This diversity contributes to a number of phenotypes, including ancestry-specific disease risk and response to pathogens. Although the 1000 Genomes Project significantly improved our understanding of genetic variation globally, southern African populations are still severely underrepresented in biomedical and human genetic studies due to insufficient large-scale publicly available data. In addition to a lack of genetic data in public repositories, existing software, algorithms and resources used for imputation and phasing of genotypic data (amongst others) are largely ineffective for populations with a complex genetic architecture such as that seen in southern Africa. This review article, therefore, aims to summarise the current limitations of conducting genetic studies on populations with a complex genetic architecture to identify potential areas for further research and development.
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Grogan KE, Perry GH. Studying human and nonhuman primate evolutionary biology with powerful in vitro and in vivo functional genomics tools. Evol Anthropol 2020; 29:143-158. [PMID: 32142200 PMCID: PMC10574139 DOI: 10.1002/evan.21825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 02/06/2020] [Indexed: 12/19/2022]
Abstract
In recent years, tools for functional genomic studies have become increasingly feasible for use by evolutionary anthropologists. In this review, we provide brief overviews of several exciting in vitro techniques that can be paired with "-omics" approaches (e.g., genomics, epigenomics, transcriptomics, proteomics, and metabolomics) for potentially powerful evolutionary insights. These in vitro techniques include ancestral protein resurrection, cell line experiments using primary, immortalized, and induced pluripotent stem cells, and CRISPR-Cas9 genetic manipulation. We also discuss how several of these methods can be used in vivo, for transgenic organism studies of human and nonhuman primate evolution. Throughout this review, we highlight example studies in which these approaches have already been used to inform our understanding of the evolutionary biology of modern and archaic humans and other primates while simultaneously identifying future opportunities for anthropologists to use this toolkit to help answer additional outstanding questions in evolutionary anthropology.
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Affiliation(s)
- Kathleen E. Grogan
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
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Reid KM, Heathfield LJ. Allele frequency data for 23 Y-chromosome short tandem repeats (STRs) for the South African population. Forensic Sci Int Genet 2020; 46:102270. [PMID: 32163904 DOI: 10.1016/j.fsigen.2020.102270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 02/13/2020] [Accepted: 03/01/2020] [Indexed: 01/31/2023]
Affiliation(s)
- Kate Megan Reid
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa.
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa.
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22
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Boua PR, Brandenburg JT, Choudhury A, Hazelhurst S, Sengupta D, Agongo G, Nonterah EA, Oduro AR, Tinto H, Mathew CG, Sorgho H, Ramsay M. Novel and Known Gene-Smoking Interactions With cIMT Identified as Potential Drivers for Atherosclerosis Risk in West-African Populations of the AWI-Gen Study. Front Genet 2020; 10:1354. [PMID: 32117412 PMCID: PMC7025492 DOI: 10.3389/fgene.2019.01354] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 12/10/2019] [Indexed: 12/22/2022] Open
Abstract
Introduction Atherosclerosis is a key contributor to the burden of cardiovascular diseases (CVDs) and many epidemiological studies have reported on the effect of smoking on carotid intima-media thickness (cIMT) and its subsequent effect on CVD risk. Gene-environment interaction studies have contributed towards understanding some of the missing heritability of genome-wide association studies. Gene-smoking interactions on cIMT have been studied in non-African populations (European, Latino-American, and African American) but no comparable African research has been reported. Our aim was to investigate smoking-SNP interactions on cIMT in two West African populations by genome-wide analysis. Materials and methods Only male participants from Burkina Faso (Nanoro = 993) and Ghana (Navrongo = 783) were included, as smoking was extremely rare among women. Phenotype and genotype data underwent stringent QC and genotype imputation was performed using the Sanger African Imputation Panel. Smoking prevalence among men was 13.3% in Nanoro and 42.5% in Navrongo. We analyzed gene-smoking interactions with PLINK after adjusting for covariates: age and 6 PCs (Model 1); age, BMI, blood pressure, fasting glucose, cholesterol levels, MVPA, and 6 PCs (Model 2). All analyses were performed at site level and for the combined data set. Results In Nanoro, we identified new gene-smoking interaction variants for cIMT within the previously described RCBTB1 region (rs112017404, rs144170770, and rs4941649) (Model 1: p = 1.35E-07; Model 2: p = 3.08E-08). In the combined sample, two novel intergenic interacting variants were identified, rs1192824 in the regulatory region of TBC1D8 (p = 5.90E-09) and rs77461169 (p = 4.48E-06) located in an upstream region of open chromatin. In silico functional analysis suggests the involvement of genes implicated in biological processes related to cell or biological adhesion and regulatory processes in gene-smoking interactions with cIMT (as evidenced by chromatin interactions and eQTLs). Discussion This is the first gene-smoking interaction study for cIMT, as a risk factor for atherosclerosis, in sub-Saharan African populations. In addition to replicating previously known signals for RCBTB1, we identified two novel genomic regions (TBC1D8, near BCHE) involved in this gene-environment interaction.
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Affiliation(s)
- Palwende Romuald Boua
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso.,Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jean-Tristan Brandenburg
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Ananyo Choudhury
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Dhriti Sengupta
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa
| | - Godfred Agongo
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Engelbert A Nonterah
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana.,Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Christopher G Mathew
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Department of Medical and Molecular Genetics, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
| | - Hermann Sorgho
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Nanoro, Burkina Faso
| | - Michèle Ramsay
- Faculty of Health Sciences, Sydney Brenner Institute for Molecular Bioscience (SBIMB), University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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23
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Differential admixture, human leukocyte antigen diversity, and hematopoietic cell transplantation in Latin America: challenges and opportunities. Bone Marrow Transplant 2019; 55:496-504. [DOI: 10.1038/s41409-019-0737-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]
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Abstract
PURPOSE OF REVIEW The goal of the review is to provide a comprehensive overview of the current understanding of the mechanisms underlying variation in human stature. RECENT FINDINGS Human height is an anthropometric trait that varies considerably within human populations as well as across the globe. Historically, much research focus was placed on understanding the biology of growth plate chondrocytes and how modifications to core chondrocyte proliferation and differentiation pathways potentially shaped height attainment in normal as well as pathological contexts. Recently, much progress has been made to improve our understanding regarding the mechanisms underlying the normal and pathological range of height variation within as well as between human populations, and today, it is understood to reflect complex interactions among a myriad of genetic, environmental, and evolutionary factors. Indeed, recent improvements in genetics (e.g., GWAS) and breakthroughs in functional genomics (e.g., whole exome sequencing, DNA methylation analysis, ATAC-sequencing, and CRISPR) have shed light on previously unknown pathways/mechanisms governing pathological and common height variation. Additionally, the use of an evolutionary perspective has also revealed important mechanisms that have shaped height variation across the planet. This review provides an overview of the current knowledge of the biological mechanisms underlying height variation by highlighting new research findings on skeletal growth control with an emphasis on previously unknown pathways/mechanisms influencing pathological and common height variation. In this context, this review also discusses how evolutionary forces likely shaped the genomic architecture of height across the globe.
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Affiliation(s)
| | - Terence D Capellini
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Thami PK, Chimusa ER. Population Structure and Implications on the Genetic Architecture of HIV-1 Phenotypes Within Southern Africa. Front Genet 2019; 10:905. [PMID: 31611910 PMCID: PMC6777512 DOI: 10.3389/fgene.2019.00905] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/26/2019] [Indexed: 12/12/2022] Open
Abstract
The interesting history of Southern Africa has put the region in the spotlight for population medical genetics. Major events including the Bantu expansion and European colonialism have imprinted unique genetic signatures within autochthonous populations of Southern Africa, this resulting in differential allele frequencies across the region. This genetic structure has potential implications on susceptibility and resistance to infectious diseases such as human immunodeficiency virus (HIV) infection. Southern Africa is the region affected worst by HIV. Here, we discuss advances made in genome-wide association studies (GWAS) of HIV-1 in the past 12 years and dissect population diversity within Southern Africa. Our findings accentuate that a plethora of factors such as migration, language and culture, admixture, and natural selection have profiled the genetics of the people of Southern Africa. Genetic structure has been observed among the Khoe-San, among Bantu speakers, and between the Khoe-San, Coloureds, and Bantu speakers. Moreover, Southern African populations have complex admixture scenarios. Few GWAS of HIV-1 have been conducted in Southern Africa, with only one of these identifying two novel variants (HCG22rs2535307 and CCNG1kgp22385164) significantly associated with HIV-1 acquisition and progression. High genetic diversity, multi-wave genetic mixture and low linkage disequilibrium of Southern African populations constitute a challenge in identifying genetic variants with modest risk or protective effect against HIV-1. We therefore posit that it is compelling to assess genome-wide contribution of ancestry to HIV-1 infection. We further suggest robust methods that can pin-point population-specific variants that may contribute to the control of HIV-1 in Southern Africa.
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Affiliation(s)
- Prisca K Thami
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa.,Research Laboratory, Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
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Bolaji OO, Adehin A, Adeagbo BA. Pharmacogenomics in the Nigerian population: the past, the present and the future. Pharmacogenomics 2019; 20:915-926. [DOI: 10.2217/pgs-2019-0046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The Nigerian population exhibits huge ethnic and genetic diversity, typical of African populations, which can be harnessed for improved drug-response and disease management. Existing data on genes relevant to drug response, so far generated for the population, indeed confirm the prevalence of some clinically significant pharmacogenes. These reports detail prevailing genetic alleles and metabolic phenotypes of vital drug metabolizing monooxygenases, transferases and drug transporters. While the utilization of existing pharmacogenomic data for healthcare delivery remains unpopular, several past and on-going studies suggest that a future shift toward genotype-stratified dosing of drugs and disease management in the population is imminent. This review discusses the present state of pharmacogenomics in Nigeria and the potential benefits of sustained research in this field for the population.
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Affiliation(s)
- Oluseye O Bolaji
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Ayorinde Adehin
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
- Institute of Biomedical & Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, PR China
| | - Babatunde A Adeagbo
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
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