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Jordan IK, Sharma S, Mariño-Ramírez L. Population Pharmacogenomics for Health Equity. Genes (Basel) 2023; 14:1840. [PMID: 37895188 PMCID: PMC10606908 DOI: 10.3390/genes14101840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Health equity means the opportunity for all people and populations to attain optimal health, and it requires intentional efforts to promote fairness in patient treatments and outcomes. Pharmacogenomic variants are genetic differences associated with how patients respond to medications, and their presence can inform treatment decisions. In this perspective, we contend that the study of pharmacogenomic variation within and between human populations-population pharmacogenomics-can and should be leveraged in support of health equity. The key observation in support of this contention is that racial and ethnic groups exhibit pronounced differences in the frequencies of numerous pharmacogenomic variants, with direct implications for clinical practice. The use of race and ethnicity to stratify pharmacogenomic risk provides a means to avoid potential harm caused by biases introduced when treatment regimens do not consider genetic differences between population groups, particularly when majority group genetic profiles are assumed to hold for minority groups. We focus on the mitigation of adverse drug reactions as an area where population pharmacogenomics can have a direct and immediate impact on public health.
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Affiliation(s)
- I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Shivam Sharma
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA;
| | - Leonardo Mariño-Ramírez
- National Institute on Minority Health and Health Disparities, National Institutes of Health, Bethesda, MD 20892, USA;
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2
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Park A, Steel D, Maine E. Evidence-based Medicine and Mechanistic Evidence: The Case of the Failed Rollout of Efavirenz in Zimbabwe. THE JOURNAL OF MEDICINE AND PHILOSOPHY 2023:7151042. [PMID: 37137159 DOI: 10.1093/jmp/jhad019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Evidence-based medicine (EBM) has long deemphasized mechanistic reasoning and pathophysiological rationale in assessing the effectiveness of interventions. The EBM+ movement has challenged this stance, arguing that evidence of mechanisms and comparative studies should both be seen as necessary and complementary. Advocates of EBM+ provide a combination of theoretical arguments and examples of mechanistic reasoning in medical research. However, EBM+ proponents have not provided recent examples of how downplaying mechanistic reasoning resulted in worse medical results than would have occurred otherwise. Such examples are necessary to make the case that EBM+ responds to a problem in clinical practice that urgently demands a solution. In light of this, we examine the failed rollout of efavirenz as a first-line HIV treatment in Zimbabwe as evidence of the importance of mechanistic reasoning in improving clinical practice and public health policy decisions. We suggest that this case is analogous to examples commonly given to support EBM.
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Affiliation(s)
- Andrew Park
- University of Victoria, Victoria, British Columbia, Canada
| | - Daniel Steel
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Elicia Maine
- Simon Fraser University, Burnaby, British Columbia, Canada
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3
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Marima R, Mbeje M, Hull R, Demetriou D, Mtshali N, Dlamini Z. Prostate Cancer Disparities and Management in Southern Africa: Insights into Practices, Norms and Values. Cancer Manag Res 2022; 14:3567-3579. [PMID: 36597514 PMCID: PMC9805733 DOI: 10.2147/cmar.s382903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/01/2022] [Indexed: 12/29/2022] Open
Abstract
Prostate cancer (PCa) is a leading cause of mortality in men of African origin. While men of African descent in high-income countries (HICs) demonstrate poor prognosis compared to their European counterparts, African men on the African continent, particularly Southern Africa have shown even higher PCa mortality rates. Extrinsic factors such as the socioeconomic status, education level, income level, geographic location and race contribute to PCa patient outcome. These are further deepened by the African norms which are highly esteemed and may have detrimental effects on PCa patients' health. Insights into African cultures and social constructs have been identified as key elements towards improving men's health care seeking behaviour which will in turn improve PCa patients' outcome. Compared to Southern Africa, the Eastern, Western and Central African regions have lower PCa incidence rates but higher mortality rates. The availability of cancer medical equipment has also been reported to be disproportionate in Africa, with most cancer resources in Northern and Southern Africa. Even within Southern Africa, cancer management resources are unevenly available where one country must access PCa specialised care in the neighbouring countries. While PCa seems to be better managed in HICs, steps towards effective PCa management are urgently needed in Africa, as this continent represents a significant portion of low-middle-income countries (LMICs). Replacing African men in Africa with African American men may not optimally resolve PCa challenges in Africa. Adopting western PCa management practices can be optimised by integrating improved core-African norms. The aim of this review is to discuss PCa disparities in Africa, deliberate on the significance of integrating African norms around masculinity and discuss challenges and opportunities towards effective PCa care in Africa, particularly in Southern Africa.
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Affiliation(s)
- Rahaba Marima
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa
| | - Mandisa Mbeje
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa,Department of Medical Oncology, Faculty of Health Sciences, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Rodney Hull
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa
| | - Demetra Demetriou
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa
| | - Nompumelelo Mtshali
- Department of Anatomical Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zodwa Dlamini
- SAMRC Precision Oncology Research Unit (PORU), DSI/NRF SARChI Chair in Precision Oncology and Cancer Prevention (POCP), Pan African Cancer Research Institute (PACRI), University of Pretoria, Pretoria, South Africa,Correspondence: Zodwa Dlamini, Tel +27 12 319 2614, Email
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Omotoso OE, Teibo JO, Atiba FA, Oladimeji T, Adebesin AO, Babalghith AO. Bridging the genomic data gap in Africa: implications for global disease burdens. Global Health 2022; 18:103. [PMID: 36494695 PMCID: PMC9733397 DOI: 10.1186/s12992-022-00898-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
This paper highlights the gap in the use of genomic data of Africans for global research efforts for disease cures. Genomic data represents an important tool used in disease research for understanding how diseases affect several populations and how these differences can be harnessed for the development of effective cures especially vaccines that have an impact at the genetic level e.g., RNA vaccines.This paper then provides a review of global genomic data status where three continents are reported to be the major contributor of genomic data to repositories used for disease research and the development of vaccines and medicines around the world.We reviewed the most recently published information about genetic data inclusiveness of populations, explaining how genomic data of Africans is lacking in global research efforts that cater towards the eradication of pandemics via the development of vaccines and other cures. We also discuss the implication of this non-inclusiveness for global disease burdens and indicate where changes need to be made in the last part of the paper.Lastly, the entire centers on some general policy recommendations to fully include African genomic data in such global genetic repositories. These recommendations can be implemented in African countries to improve genetic data collection, storage, and usage policies.
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Affiliation(s)
- Olabode Ebenezer Omotoso
- grid.9582.60000 0004 1794 5983Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - John Oluwafemi Teibo
- grid.9582.60000 0004 1794 5983Department of Biochemistry, College of Medicine, University of Ibadan, Ibadan, Nigeria ,grid.11899.380000 0004 1937 0722Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Festus Adebayo Atiba
- grid.11899.380000 0004 1937 0722Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Tolulope Oladimeji
- grid.9582.60000 0004 1794 5983Department of Zoology, University of Ibadan, Ibadan, Nigeria
| | | | - Ahmad O. Babalghith
- grid.412832.e0000 0000 9137 6644Medical Genetics Department, College of Medicine, Umm al-qura University, Makkah, Saudi Arabia
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Hoang DT, Hiep TV, Thi Phuong Nguyen T, Nhung HTM, Tran KT, Vinh LS. Exploring the Kinh Vietnamese genomic database for the polymorphisms of the P450 genes toward precision public health. Ann Hum Biol 2022; 49:152-155. [PMID: 35289678 DOI: 10.1080/03014460.2022.2052961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Human cytochrome P450 (CYPs) genes are essential in metabolizing drugs. Due to their high polymorphism, population-specific studies are of great interest. AIM This research examined the six CYP genes, including CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, and CYP4F2 in the Kinh Vietnamese (KHV) for population-scale precision medicine. SUBJECTS AND METHODS We processed data from a genomics database of 206 healthy and unrelated KHV individuals to calculate CYP allele frequencies. First, we compared the CYP genes of the KHV to six other populations retrieved from the 1000 Genomes Project. Second, we searched the PharmGBK database for drug-CYP interaction data to compile a drug dosage recommendation for KHV. RESULTS We observed diverging trends in the genetic variations of CYP2B6, CYP2D6, and CYP3A5 in KHV. In terms of the phenotypic drug responses in KHV, CYP2C19 exhibited all of the metabolic phenotypes at a non-trivial frequency. CYP3A5 metabolized drugs at a lower rate than the other five CYPs. CONCLUSION This is the first large-scale study to investigate multiple CYP genes in the KHV for precision medicine from a public health perspective. Differences found in the distributions of metabolizers for the KHV suggest careful prescriptions for CYP2C19 and CYP3A5-metabolized drugs.
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Affiliation(s)
- Diep Thi Hoang
- VNU University of Engineering and Technology, Vietnam National University Hanoi, Ha Noi, Vietnam
| | - Tran Van Hiep
- VNU University of Science, Vietnam National University Hanoi, 334 Nguyen Trai, Hanoi, Vietnam
| | - Thao Thi Phuong Nguyen
- Institute of Information Technology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Hoang Thi My Nhung
- VNU University of Science, Vietnam National University Hanoi, 334 Nguyen Trai, Hanoi, Vietnam.,Vinmec Research Institute of Stem Cell and Gene Technology, Ha Noi, Vietnam
| | - Kien Trung Tran
- Vinmec Research Institute of Stem Cell and Gene Technology, Ha Noi, Vietnam
| | - Le Sy Vinh
- VNU University of Engineering and Technology, Vietnam National University Hanoi, Ha Noi, Vietnam
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Role of Precision Oncology in Type II Endometrial and Prostate Cancers in the African Population: Global Cancer Genomics Disparities. Int J Mol Sci 2022; 23:ijms23020628. [PMID: 35054814 PMCID: PMC8776204 DOI: 10.3390/ijms23020628] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/05/2023] Open
Abstract
Precision oncology can be defined as molecular profiling of tumors to identify targetable alterations. Emerging research reports the high mortality rates associated with type II endometrial cancer in black women and with prostate cancer in men of African ancestry. The lack of adequate genetic reference information from the African genome is one of the major obstacles in exploring the benefits of precision oncology in the African context. Whilst external factors such as the geography, environment, health-care access and socio-economic status may contribute greatly towards the disparities observed in type II endometrial and prostate cancers in black populations compared to Caucasians, the contribution of African ancestry to the contribution of genetics to the etiology of these cancers cannot be ignored. Non-coding RNAs (ncRNAs) continue to emerge as important regulators of gene expression and the key molecular pathways involved in tumorigenesis. Particular attention is focused on activated/repressed genes and associated pathways, while the redundant pathways (pathways that have the same outcome or activate the same downstream effectors) are often ignored. However, comprehensive evidence to understand the relationship between type II endometrial cancer, prostate cancer and African ancestry remains poorly understood. The sub-Saharan African (SSA) region has both the highest incidence and mortality of both type II endometrial and prostate cancers. Understanding how the entire transcriptomic landscape of these two reproductive cancers is regulated by ncRNAs in an African cohort may help elucidate the relationship between race and pathological disparities of these two diseases. This review focuses on global disparities in medicine, PCa and ECa. The role of precision oncology in PCa and ECa in the African population will also be discussed.
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Zhong A, Xia K, Hadjis Z, Lifman G, Njambi L, Dimaras H. Opportunities and barriers for genetic service delivery in Kenya from a health personnel perspective. J Community Genet 2021; 12:525-538. [PMID: 34228349 PMCID: PMC8257851 DOI: 10.1007/s12687-021-00532-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 05/04/2021] [Indexed: 11/25/2022] Open
Abstract
Genetic counselling and testing are essential health services for the management of heritable diseases. However, in low-and-middle income countries like Kenya, genetic counsellors are not yet a licenced profession, and there is limited availability of and access to genetic testing. This study aimed to uncover opportunities and barriers for genetic service delivery in the Kenyan healthcare system from the perspectives of those who provide genetic testing and/or genetic counselling. Participants included Kenyan health personnel who deliver genetic services. This was a qualitative study that collected data via semi-structured one-on-one interviews and analyzed it using inductive thematic analysis. Participant demographics and characteristics of clinical genetic service provision were collected using a survey and results summarized using descriptive statistics. Themes revealed during analysis were compared to the clinical characteristics of genetic service provision to inform the opportunities and barriers. Fifteen interviews were conducted in total. Thematic analysis indicated that participants believed that the barriers facing genetic service delivery were linked to three themes: (1) education and training, (2) costs, and (3) counselling challenges. The opportunities for genetic service delivery were linked to four themes: (1) demand, (2) education and training, (3) encouraging a multidisciplinary approach to care, and (4) enhancing laboratory infrastructure. These findings are crucial for the development of a national evidence-informed and culturally appropriate model for genetic service delivery.
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Affiliation(s)
- Adrina Zhong
- Department of Social and Behavioural Health Sciences, Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada
- Schulich School of Medicine & Dentistry, Western University, London, ON, Canada
| | - Kaiwen Xia
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Zissis Hadjis
- The Munk School of Global Affairs and Public Policy, University of Toronto, Toronto, ON, Canada
| | - Gavin Lifman
- Centre for Global Child Health, SickKids Research Institute, Toronto, ON, Canada
| | - Lucy Njambi
- Department of Ophthalmology, Kenyatta National Hospital, University of Nairobi, Nairobi, Kenya
| | - Helen Dimaras
- Centre for Global Child Health, SickKids Research Institute, Toronto, ON, Canada.
- Division Clinical Public Health, Dalla Lana School of Public Health, The University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada.
- Child Health Evaluative Sciences Program, SickKids Research Institute, Toronto, ON, Canada.
- Department of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
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8
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Pharmacogene Sequencing of a Gabonese Population with Severe Plasmodium falciparum Malaria Reveals Multiple Novel Variants with Putative Relevance for Antimalarial Treatment. Antimicrob Agents Chemother 2021; 65:e0027521. [PMID: 33875422 DOI: 10.1128/aac.00275-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Malaria remains one of the deadliest diseases in Africa, particularly for children. While successful in reducing morbidity and mortality, antimalarial treatments are also a major cause of adverse drug reactions (ADRs). Host genetic variation in genes involved in drug disposition or toxicity constitutes an important determinant of ADR risk and can prime for parasite drug resistance. Importantly, however, the genetic diversity in Africa is substantial, and thus, genetic profiles in one population cannot be reliably extrapolated to other ethnogeographic groups. Gabon is considered a high-transmission country, with more than 460,000 malaria cases per year. Yet the pharmacogenetic landscape of the Gabonese population or its neighboring countries has not been analyzed. Using targeted sequencing, here, we profiled 21 pharmacogenes with importance for antimalarial treatment in 48 Gabonese pediatric patients with severe Plasmodium falciparum malaria. Overall, we identified 347 genetic variants, of which 18 were novel, and each individual was found to carry 87.3 ± 9.2 (standard deviation [SD]) variants across all analyzed genes. Importantly, 16.7% of these variants were population specific, highlighting the need for high-resolution pharmacogenomic profiling. Between one in three and one in six individuals harbored reduced-activity alleles of CYP2A6, CYP2B6, CYP2D6, and CYP2C8 with important implications for artemisinin, chloroquine, and amodiaquine therapy. Furthermore, one in three patients harbored at least one G6PD-deficient allele, suggesting a considerably increased risk of hemolytic anemia upon exposure to aminoquinolines. Combined, our results reveal the unique genetic landscape of the Gabonese population and pinpoint the genetic basis for interindividual differences in antimalarial drug responses and toxicity.
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9
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African genetic diversity and adaptation inform a precision medicine agenda. Nat Rev Genet 2021; 22:284-306. [PMID: 33432191 DOI: 10.1038/s41576-020-00306-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 01/29/2023]
Abstract
The deep evolutionary history of African populations, since the emergence of modern humans more than 300,000 years ago, has resulted in high genetic diversity and considerable population structure. Selected genetic variants have increased in frequency due to environmental adaptation, but recent exposures to novel pathogens and changes in lifestyle render some of them with properties leading to present health liabilities. The unique discoverability potential from African genomic studies promises invaluable contributions to understanding the genomic and molecular basis of health and disease. Globally, African populations are understudied, and precision medicine approaches are largely based on data from European and Asian-ancestry populations, which limits the transferability of findings to the continent of Africa. Africa needs innovative precision medicine solutions based on African data that use knowledge and implementation strategies aligned to its climatic, cultural, economic and genomic diversity.
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Mboowa G, Sserwadda I, Aruhomukama D. Genomics and bioinformatics capacity in Africa: no continent is left behind. Genome 2021; 64:503-513. [PMID: 33433259 DOI: 10.1139/gen-2020-0013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Despite the poor genomics research capacity in Africa, efforts have been made to empower African scientists to get involved in genomics research, particularly that involving African populations. As part of the Human Heredity and Health in Africa (H3Africa) Consortium, an initiative was set to make genomics research in Africa an African endeavor and was developed through funding from the United States' National Institutes of Health Common Fund and the Wellcome Trust. H3Africa is intended to encourage a contemporary research approach by African investigators and to stimulate the study of genomic and environmental determinants of common diseases. The goal of these endeavors is to improve the health of African populations. To build capacity for bioinformatics and genomics research, organizations such as the African Society for Bioinformatics and Computational Biology have been established. In this article, we discuss the current status of the bioinformatics infrastructure in Africa as well as the training challenges and opportunities.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda.,Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda.,The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, Infectious Disease Institute, Makerere University, P.O. Box 22418, Kampala, Uganda
| | - Ivan Sserwadda
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Uganda, P.O. Box 7072, Kampala, Uganda
| | - Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, P.O. Box 7072, Kampala, Uganda
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Abstract
Over the past four decades, research on the natural history of HIV infection has described how HIV wreaks havoc on human immunity and causes AIDS. HIV host genomic research, which aims to understand how human genetic variation affects our response to HIV infection, has progressed from early candidate gene studies to recent multi-omic efforts, benefiting from spectacular advances in sequencing technology and data science. In addition to invading cells and co-opting the host machinery for replication, HIV also stably integrates into our own genome. The study of the complex interactions between the human and retroviral genomes has improved our understanding of pathogenic mechanisms and suggested novel preventive and therapeutic approaches against HIV infection.
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Affiliation(s)
- Paul J. McLaren
- grid.415368.d0000 0001 0805 4386National HIV and Retrovirology Laboratory at the JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB Canada ,grid.21613.370000 0004 1936 9609Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB Canada
| | - Jacques Fellay
- grid.5333.60000000121839049School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.8515.90000 0001 0423 4662Precision Medicine Unit, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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12
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Gingras SN, Tang D, Tuff J, McLaren PJ. Minding the gap in HIV host genetics: opportunities and challenges. Hum Genet 2020; 139:865-875. [PMID: 32409920 PMCID: PMC7272494 DOI: 10.1007/s00439-020-02177-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/12/2020] [Indexed: 12/15/2022]
Abstract
Genome-wide association studies (GWAS) have been successful in identifying and confirming novel genetic variants that are associated with diverse HIV phenotypes. However, these studies have predominantly focused on European cohorts. HLA molecules have been consistently associated with HIV outcomes, some of which have been found to be population specific, underscoring the need for diversity in GWAS. Recently, there has been a concerted effort to address this gap that leads to health care (disease prevention, diagnosis, treatment) disparities with marginal improvement. As precision medicine becomes more utilized, non-European individuals will be more and more disadvantaged, as the genetic variants identified in genomic research based on European populations may not accurately reflect that of non-European individuals. Leveraging pre-existing, large, multiethnic cohorts, such as the UK Biobank, 23andMe, and the National Institute of Health's All of Us Research Program, can contribute in raising genomic research in non-European populations and ultimately lead to better health outcomes.
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Affiliation(s)
- Shanelle N. Gingras
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - David Tang
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Jeffrey Tuff
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Paul J. McLaren
- JC Wilt Infectious Diseases Research Centre, National HIV and Retrovirology Lab, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
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13
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Matimba A, Chimatira A, Kuguyo O, January J, Mupambireyi Z, Marimbe-Dube B, Chikwasha V, Nyati-Jokomo Z, Muteti S, Mangezvo P, Kangwende A, Chingono A, Chidzonga M, Gandari J, Hakim J, Nathoo K, Samkange C, Mangezi W, Lee S, Gwanzura L, Cho M, Ndebele P. Understanding Ethical, Legal and Societal Issues (ELSIs) in Human Biobanking and Genomics for Research and Healthcare in Zimbabwe: The Genomics Inheritance Law Ethics and Society (GILES) initiative. AAS Open Res 2020; 2:1. [PMID: 32382699 PMCID: PMC7194152 DOI: 10.12688/aasopenres.12917.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2019] [Indexed: 11/20/2022] Open
Abstract
Biobanks and human genomics applications are key for understanding health, disease and heredity in Africa and globally. Growing interest in these technologies calls for strengthening relevant legal, ethical and policy systems to address knowledge disparities and ensure protection of society, while supporting advancement of science. In Zimbabwe there is limited understanding of ethical, legal, and societal issues (ELSI) for biobanking and genomics. The Genomics Inheritance Law Ethics and Society (GILES) initiative was established in 2015 to explore the current status and gaps in the ethical and legal frameworks, knowledge among various stakeholders, and to establish capacity for addressing ELSI of biobanking and genomics as applied in biomedical and population research, and healthcare. The project was conducted over a countrywide geographical region and established one of the most comprehensive studies for ELSI of human biobanking and genomics in Africa. This paper outlines the strategy undertaken during the implementation of the GILES initiative and discusses the importance of such an initiative for characterisation of ELSI of human biobanking and genomics in Zimbabwe and Africa.
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Affiliation(s)
- Alice Matimba
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Andrew Chimatira
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Oppah Kuguyo
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - James January
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Zivayi Mupambireyi
- Centre for Sexual Health and HIV Research Zimbabwe (CeSHHAR Zimbabwe), Harare, Zimbabwe
| | | | - Vasco Chikwasha
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - Shamiso Muteti
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | | | - Alfred Chingono
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Midion Chidzonga
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Jonathan Gandari
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - James Hakim
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Kusum Nathoo
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | | | - Walter Mangezi
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Sandra Lee
- Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Lovemore Gwanzura
- College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Mildred Cho
- Biomedical Ethics, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul Ndebele
- Medical Research Council of Zimbabwe, Harare, Zimbabwe.,Milken Institute School of Public Health, George Washington University, Washington, DC, USA
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14
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Radouani F, Zass L, Hamdi Y, Rocha JD, Sallam R, Abdelhak S, Ahmed S, Azzouzi M, Benamri I, Benkahla A, Bouhaouala-Zahar B, Chaouch M, Jmel H, Kefi R, Ksouri A, Kumuthini J, Masilela P, Masimirembwa C, Othman H, Panji S, Romdhane L, Samtal C, Sibira R, Ghedira K, Fadlelmola F, Kassim SK, Mulder N. A review of clinical pharmacogenetics Studies in African populations. Per Med 2020; 17:155-170. [PMID: 32125935 PMCID: PMC8093600 DOI: 10.2217/pme-2019-0110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Effective interventions and treatments for complex diseases have been implemented globally, however, coverage in Africa has been comparatively lower due to lack of capacity, clinical applicability and knowledge on the genetic contribution to disease and treatment. Currently, there is a scarcity of genetic data on African populations, which have enormous genetic diversity. Pharmacogenomics studies have the potential to revolutionise treatment of diseases, therefore, African populations are likely to benefit from these approaches to identify likely responders, reduce adverse side effects and optimise drug dosing. This review discusses clinical pharmacogenetics studies conducted in African populations, focusing on studies that examined drug response in complex diseases relevant to healthcare. Several pharmacogenetics associations have emerged from African studies, as have gaps in knowledge.
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Affiliation(s)
- Fouzia Radouani
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Lyndon Zass
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Yosr Hamdi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Jorge da Rocha
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Reem Sallam
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Samah Ahmed
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Faculty of Clinical & Industrial Pharmacy, National University, Khartoum, Sudan
| | - Maryame Azzouzi
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco
| | - Ichrak Benamri
- Research Department, Chlamydiae & Mycoplasmas Laboratory, Institut Pasteur du Maroc, Casablanca 20360, Morocco.,Systems & Data Engineering Team, National School of Applied Sciences of Tangier, Morocco
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Balkiss Bouhaouala-Zahar
- Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Haifa Jmel
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Rym Kefi
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie
| | - Ayoub Ksouri
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia.,Laboratory of Venoms & Therapeutic Molecules, Pasteur Institute of Tunis, 13 Place Pasteur, BP74, Tunis Belvedere- University of Tunis El Manar, Tunisia
| | - Judit Kumuthini
- H3ABioNet, Bioinformatics Department, Centre for Proteomic & Genomic Research, Cape Town, South Africa
| | - Phumlani Masilela
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Collen Masimirembwa
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa.,DMPK Department, African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Houcemeddine Othman
- Sydney Brenner Institute for Molecular Bioscience, University of The Witwatersrand, Johannesburg, South Africa
| | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
| | - Lilia Romdhane
- Laboratory of Biomedical Genomics & Oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002 Tunis, Belvédère, Tunisie.,Département des Sciences de la Vie, Faculté des Sciences de Bizerte, Université Carthage, 7021 Jarzouna, BP 21, Tunisie
| | - Chaimae Samtal
- Biotechnology Laboratory, Faculty of Sciences Dhar El Mahraz, Sidi Mohammed Ben Abdellah University, Fez 30000, Morocco.,Department of Biology, University of Mohammed Premier, Oujda, Morocco.,Department of Biology Faculty of Sciences, University of Sidi Mohamed Ben Abdellah, Fez, Morocco
| | - Rania Sibira
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan.,Department of Neurosurgery, National Center For Neurological Sciences, Khartoum, Sudan
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics & Biostatistics LR 16 IPT 09, Institute Pasteur de Tunis, Tunisia
| | - Faisal Fadlelmola
- Centre for Bioinformatics & Systems Biology, Faculty of Science, University of Khartoum, 321 Khartoum, Sudan
| | - Samar Kamal Kassim
- Medical Biochemistry & Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo 11381, Egypt
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, South Africa
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15
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16
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Rajman I, Pasqua OD. Introducing Project Africa GRADIENT. Drug Discov Today 2019; 24:2229-2230. [PMID: 31693869 DOI: 10.1016/j.drudis.2019.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/23/2019] [Accepted: 10/23/2019] [Indexed: 11/25/2022]
Affiliation(s)
- Iris Rajman
- Translational Medicine Asia, Novartis Institutes for Biomedical Research, Novartis NKK, Tokyo, Japan.
| | - Oscar Della Pasqua
- Clinical Pharmacology Modelling & Simulation, GlaxoSmithKline, Uxbridge London UK
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- Clinical Pharmacology Modelling & Simulation, GlaxoSmithKline, Uxbridge London UK
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17
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Secolin R, Mas-Sandoval A, Arauna LR, Torres FR, de Araujo TK, Santos ML, Rocha CS, Carvalho BS, Cendes F, Lopes-Cendes I, Comas D. Distribution of local ancestry and evidence of adaptation in admixed populations. Sci Rep 2019; 9:13900. [PMID: 31554886 PMCID: PMC6761108 DOI: 10.1038/s41598-019-50362-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/11/2019] [Indexed: 12/14/2022] Open
Abstract
Admixed American populations have different global proportions of European, Sub-Saharan African, and Native-American ancestry. However, individuals who display the same global ancestry could exhibit remarkable differences in the distribution of local ancestry blocks. We studied for the first time the distribution of local ancestry across the genome of 264 Brazilian admixed individuals, ascertained within the scope of the Brazilian Initiative on Precision Medicine. We found a decreased proportion of European ancestry together with an excess of Native-American ancestry on chromosome 8p23.1 and showed that this is due to haplotypes created by chromosomal inversion events. Furthermore, Brazilian non-inverted haplotypes were more similar to Native-American haplotypes than to European haplotypes, in contrast to what was found in other American admixed populations. We also identified signals of recent positive selection on chromosome 8p23.1, and one gene within this locus, PPP1R3B, is related to glycogenesis and has been associated with an increased risk of type 2 diabetes and obesity. These findings point to a selection event after admixture, which is still not entirely understood in recent admixture events.
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Affiliation(s)
- Rodrigo Secolin
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alex Mas-Sandoval
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lara R Arauna
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
| | - Fábio R Torres
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Tânia K de Araujo
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Marilza L Santos
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Cristiane S Rocha
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Benilton S Carvalho
- Department of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Fernando Cendes
- Department of Neurology, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil
| | - Iscia Lopes-Cendes
- Department of Medical Genetics and Genomic Medicine, University of Campinas-UNICAMP, and the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), Campinas, SP, Brazil.
| | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, Barcelona, Spain
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18
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Nagar SD, Moreno AM, Norris ET, Rishishwar L, Conley AB, O'Neal KL, Vélez-Gómez S, Montes-Rodríguez C, Jaraba-Álvarez WV, Torres I, Medina-Rivas MA, Valderrama-Aguirre A, Jordan IK, Gallo JE. Population Pharmacogenomics for Precision Public Health in Colombia. Front Genet 2019; 10:241. [PMID: 30967898 PMCID: PMC6439339 DOI: 10.3389/fgene.2019.00241] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
While genomic approaches to precision medicine hold great promise, they remain prohibitively expensive for developing countries. The precision public health paradigm, whereby healthcare decisions are made at the level of populations as opposed to individuals, provides one way for the genomics revolution to directly impact health outcomes in the developing world. Genomic approaches to precision public health require a deep understanding of local population genomics, which is still missing for many developing countries. We are investigating the population genomics of genetic variants that mediate drug response in an effort to inform healthcare decisions in Colombia. Our work focuses on two neighboring populations with distinct ancestry profiles: Antioquia and Chocó. Antioquia has primarily European genetic ancestry followed by Native American and African components, whereas Chocó shows mainly African ancestry with lower levels of Native American and European admixture. We performed a survey of the global distribution of pharmacogenomic variants followed by a more focused study of pharmacogenomic allele frequency differences between the two Colombian populations. Worldwide, we found pharmacogenomic variants to have both unusually high minor allele frequencies and high levels of population differentiation. A number of these pharmacogenomic variants also show anomalous effect allele frequencies within and between the two Colombian populations, and these differences were found to be associated with their distinct genetic ancestry profiles. For example, the C allele of the single nucleotide polymorphism (SNP) rs4149056 [Solute Carrier Organic Anion Transporter Family Member 1B1 (SLCO1B1)∗5], which is associated with an increased risk of toxicity to a commonly prescribed statin, is found at relatively high frequency in Antioquia and is associated with European ancestry. In addition to pharmacogenomic alleles related to increased toxicity risk, we also have evidence that alleles related to dosage and metabolism have large frequency differences between the two populations, which are associated with their specific ancestries. Using these findings, we have developed and validated an inexpensive allele-specific PCR assay to test for the presence of such population-enriched pharmacogenomic SNPs in Colombia. These results serve as an example of how population-centered approaches to pharmacogenomics can help to realize the promise of precision medicine in resource-limited settings.
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Affiliation(s)
- Shashwat Deepali Nagar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | | | - Emily T Norris
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Lavanya Rishishwar
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Andrew B Conley
- IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Kelly L O'Neal
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | | | | | | | | | - Miguel A Medina-Rivas
- PanAmerican Bioinformatics Institute, Cali, Colombia.,Centro de Investigación en Biodiversidad y Hábitat, Universidad Tecnológica del Chocó, Quibdó, Colombia
| | - Augusto Valderrama-Aguirre
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia.,Biomedical Research Institute, Cali, Colombia
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States.,IHRC-Georgia Tech Applied Bioinformatics Laboratory, Atlanta, GA, United States.,PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Juan Esteban Gallo
- PanAmerican Bioinformatics Institute, Cali, Colombia.,GenomaCES, Universidad CES, Medellín, Colombia
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19
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Pfeiffer S, Harrington L, Lombard M. The people behind the samples: Biographical features of Past Hunter-Gatherers from KwaZulu-Natal who yielded aDNA. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 24:158-164. [PMID: 30399480 DOI: 10.1016/j.ijpp.2018.10.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/18/2018] [Accepted: 10/25/2018] [Indexed: 05/25/2023]
Abstract
PURPOSE Skeletons sampled for ancient human DNA analysis are sometimes complete enough to provide information about the lives of the people they represent. We focus on three Later Stone Age skeletons, ca. 2000 B.P., from coastal KwaZulu-Natal, South Africa, whose ancient genomes have been sequenced (Schlebusch et al., 2017). METHODS Bioarchaeological approaches are integrated with aDNA information. RESULTS All skeletons are male. Dental development shows that the boy, with prominent cribra orbitalia, died at age 6-7 years. Two men show cranial and spinal trauma, extensive tooth wear, plus mild cribra orbitalia in one. CONCLUSIONS Dental wear and trauma of the adults are consistent with hunter-gatherer lives. Even partial aDNA evidence contributes to sex determination. Parasitic infection such as schistosomiasis is the best-fit cause for the child's anemia in this case. CONTRIBUTION TO KNOWLEDGE The convergence of genomic and bioarchaeological approaches expands our knowledge of the past lives of a boy and two men whose lives as hunter-gatherers included episodes of trauma and disease. LIMITATIONS The skeletons are incomplete, in variable condition, and from poorly characterized local cultural contexts. SUGGESTIONS FOR FURTHER RESEARCH Thorough osteobiographic analysis should accompany paleogenomic investigations. Such disciplinary collaboration enriches our understanding of the human past.
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Affiliation(s)
- Susan Pfeiffer
- Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, M5S 2S2, Canada; Department of Archaeology, University of Cape Town, Rondebosch 7701, South Africa; Department of Anthropology, George Washington University, D.C., USA.
| | - Lesley Harrington
- Department of Anthropology, University of Alberta, 13-15 H.M. Tory Building, Edmonton, T6G 2H4, Canada
| | - Marlize Lombard
- Centre for Anthropological Research, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa
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20
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Matimba A, Chimatira A, Kuguyo O, January J, Mupambireyi Z, Marimbe-Dube B, Chikwasha V, Nyati-Jokomo Z, Muteti S, Mangezvo P, Kangwende A, Chingono A, Chidzonga M, Gandari J, Hakim J, Nathoo K, Samkange C, Mangezi W, Lee S, Gwanzura L, Cho M, Ndebele P. Understanding Ethical, Legal and Societal Issues (ELSIs) in Human Biobanking and Genomics for Research and Healthcare in Zimbabwe: The Genomics Inheritance Law Ethics and Society GILES initiative. AAS Open Res 2019; 2:1. [DOI: 10.12688/aasopenres.12917.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2018] [Indexed: 11/20/2022] Open
Abstract
Biobanks and human genomics applications are key for understanding health, disease and heredity in Africa and globally. Growing interest in these technologies calls for strengthening relevant legal, ethical and policy systems to address knowledge disparities and ensure protection of society, while supporting advancement of science. In Zimbabwe there is limited understanding of ethical, legal, and societal issues (ELSI) for biobanking and genomics. The Genomics Inheritance Law Ethics and Society (GILES) initiative was established in 2015 to explore the current status and gaps in the ethical and legal frameworks, knowledge among various stakeholders, and to establish capacity for addressing ELSI of biobanking and genomics as applied in biomedical and population research, and healthcare. A multi-methods approach was applied including document reviews, focus group discussions and in-depth interviews among health and research professionals, and community members in six provinces comprising urban, peri-urban and rural areas. Emerging findings indicates a need for updating guidelines and policies for addressing ELSI in biobanking and genomics research in Zimbabwe. Emerging terminologies such as biobanking and genomics lack clarity suggesting a need for increased awareness and educational tools for health professionals, research scientists and community members. Common concerns relating to consent processes, sample and data use and sharing, particularly where there is trans-national flow of biospecimens and data, call for nationally tailored ELSI frameworks aligned to regional and international initiatives. This paper describes the strategy undertaken for the development and implementation of the GILES project and discusses the importance of such an initiative for characterisation of ELSI of human biobanking and genomics in Zimbabwe and Africa. Conducting this explorative study among a wide range of stakeholders over a countrywide geographical regions, established one of the most comprehensive studies for ELSI of human biobanking and genomics in Africa.
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21
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Drake TM, Knight SR, Harrison EM, Søreide K. Global Inequities in Precision Medicine and Molecular Cancer Research. Front Oncol 2018; 8:346. [PMID: 30234014 PMCID: PMC6131579 DOI: 10.3389/fonc.2018.00346] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/07/2018] [Indexed: 12/12/2022] Open
Abstract
Precision medicine based upon molecular testing is heralded as a revolution in how cancer is prevented, diagnosed, and treated. Large efforts across the world aim to conduct comprehensive molecular profiling of disease to inform preclinical models, translational research studies and clinical trials. However, most studies have only been performed in patients from high-income countries. As the burden on non-communicable diseases increases, cancer will become a pressing burden across the world, disproportionately affecting low-middle income settings. There is emerging evidence that the molecular landscape of disease differs geographically and by genetic ancestry, which cannot be explained by environmental factors alone. There is a lack of good quality evidence that characterises the molecular landscape of cancers found in low-middle income countries. As cancer medicine becomes increasingly driven by molecular alterations in high-income settings, low-income settings may become left behind. Further efforts on an international scale must be made by researchers, funders, and policymakers to ensure cancer research addresses disease across the world, so models are not limited to subtypes of disease found in high-income countries. In this review, we discuss differences found in the molecular profiles of tumours worldwide and the implication this has for the future of global cancer care. Finally, we identify several barriers currently limiting progress in this field and innovative solutions, which may address these shortcomings.
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Affiliation(s)
- Thomas M. Drake
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen R. Knight
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Ewen M. Harrison
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
| | - Kjetil Søreide
- Department of Clinical Surgery, University of Edinburgh, Edinburgh, United Kingdom
- Department of Gastrointestinal Surgery, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
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22
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Lee S, Gedleh A, Hill JA, Qaiser S, Umukunda Y, Odiyo P, Kitonyi G, Dimaras H. In Their Own Words: A Qualitative Study of Kenyan Breast Cancer Survivors' Knowledge, Experiences, and Attitudes Regarding Breast Cancer Genetics. J Glob Oncol 2018; 4:1-9. [PMID: 30241137 PMCID: PMC6180770 DOI: 10.1200/jgo.17.00061] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
INTRODUCTION Breast cancer ranks among the most common adult cancers in Kenya. Individuals with a family history of the disease are at increased risk. Mutations most commonly associated with breast cancer affect BRCA1 and BRCA2; mutations in several other genes may also confer breast cancer risk. Genetic testing and counseling can help patients understand their risk and assist clinicians in choosing therapies. We aimed to uncover what patients know, experience, and think with regard to breast cancer genetics in Kenya. METHODS Participants included breast cancer survivors age > 18 years. Participants completed a demographic questionnaire before participating in focus group discussions to uncover knowledge of, experiences with, and attitudes toward the genetics of breast cancer. Data were analyzed by inductive thematic analysis. RESULTS Four focus groups were conducted. Participants had rudimentary knowledge about genetics and cancer development, and although they understood breast cancer could be familial, many suspected environmental factors causing spontaneous disease. They reported limited experience with counseling about genetic risk, perceiving that their physicians were too busy to provide comprehensive information. Many indicated they promoted cancer screening among family to promote early diagnosis. Participants expressed a need for more comprehensive counseling and access to genetic testing, recognizing the added clarity it would bring to their families' risk of cancer. CONCLUSION Improved communication from health care teams could clarify the risk of cancer for affected families. The introduction of affordable genetic testing and counseling for breast cancer in Kenya is welcomed by survivors.
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Affiliation(s)
- Siwon Lee
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Amal Gedleh
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Jessica A. Hill
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Seemi Qaiser
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Yvonne Umukunda
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Philip Odiyo
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Grace Kitonyi
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
| | - Helen Dimaras
- Siwon Lee, Amal Gedleh, Seemi
Qaiser, Yvonne Umukunda, and Helen Dimaras,
University of Toronto; Jessica A. Hill and Helen
Dimaras, The Hospital for Sick Children; Helen Dimaras,
SickKids Research Institute, Toronto, Ontario, Canada; Grace
Kitonyi, and Helen Dimaras, University of Nairobi; and
Philip Odiyo, Faraja Cancer Support Trust, Nairobi,
Kenya
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23
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Zhong A, Darren B, Loiseau B, He LQB, Chang T, Hill J, Dimaras H. Ethical, social, and cultural issues related to clinical genetic testing and counseling in low- and middle-income countries: a systematic review. Genet Med 2018; 23:2270-2280. [PMID: 30072741 DOI: 10.1038/s41436-018-0090-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 06/04/2018] [Indexed: 12/17/2022] Open
Abstract
PURPOSE We performed a systematic review of the ethical, social, and cultural issues associated with delivery of genetic services in low- and middle-income countries (LMICs). METHODS We searched 11 databases for studies addressing ethical, social, and/or cultural issues associated with clinical genetic testing and/or counselling performed in LMICs. Narrative synthesis was employed to analyze findings, and resultant themes were mapped onto the social ecological model (PROSPERO #CRD42016042894). RESULTS After reviewing 13,308 articles, 192 met inclusion criteria. Nine themes emerged: (1) genetic counseling has a tendency of being directive, (2) genetic services have psychosocial consequences that require improved support, (3) medical genetics training is inadequate, (4) genetic services are difficult to access, (5) social determinants affect uptake and understanding of genetic services, (6) social stigma is often associated with genetic disease, (7) family values are at risk of disruption by genetic services, (8) religious principles pose barriers to acceptability and utilization of genetic services, and (9) cultural beliefs and practices influence uptake of information and understanding of genetic disease. CONCLUSION We identified a number of complex and interrelated ethical, cultural, and social issues with implications implications for further development of genetic services in LMICs.
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Affiliation(s)
- Adrina Zhong
- Division of Social and Behavioural Health Sciences, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.,Schulich School of Medicine & Dentistry, Western University, Canada
| | - Benedict Darren
- Human Biology Program, Faculty of Arts & Science, University of Toronto, Toronto, ON, Canada.,Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bethina Loiseau
- Human Biology Program, Faculty of Arts & Science, University of Toronto, Toronto, ON, Canada
| | - Li Qun Betty He
- Human Biology Program, Faculty of Arts & Science, University of Toronto, Toronto, ON, Canada.,Michael G. DeGroote Medical School, McMaster University, Hamilton, ON, Canada
| | - Trillium Chang
- Human Biology Program, Faculty of Arts & Science, University of Toronto, Toronto, ON, Canada
| | - Jessica Hill
- Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Helen Dimaras
- Division of Clinical Public Health, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada. .,Department of Ophthalmology & Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. .,Department of Ophthalmology & Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada. .,Child Health Evaluative Sciences Program & The Centre for Global Child Health, SickKids Research Institute, Toronto, ON, Canada. .,Department of Human Pathology, College of Health Sciences, University of Nairobi, Nairobi, Kenya.
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24
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [PMID: 30714022 PMCID: PMC6358002 DOI: 10.12688/aasopenres.12832.2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 01/25/2023] Open
Abstract
Background: Here, we describe how the Collaborative African Genomics Network ( CAfGEN) of the Human Heredity and Health in Africa (H3Africa) consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. The H3Africa was conceived to facilitate the application of genomics technologies to improve health across Africa.. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children's Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs' electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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Affiliation(s)
- Gerald Mboowa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Savannah Mwesigwa
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eric Katagirya
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gaone Retshabile
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Busisiwe C Mlotshwa
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Lesedi Williams
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - David Kateete
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Eddie Wampande
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Bio-molecular Resources, College of Veterinary Medicine, Makerere University, Kampala, Uganda
| | - Misaki Wayengera
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Betty Nsangi Kintu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation-Uganda, Kampala, Uganda
| | - Samuel Kyobe
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Chester W Brown
- Genetics Division, Department of Pediatrics , University of Tennessee Health Science Center, Memphis, Memphis, TN, USA.,Le Bonheur Children's Hospital, Memphis, Memphis, TN, USA.,St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA.,ARS/USDA/Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine , Houston, TX, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Moses Joloba
- Department of Immunology and Molecular Biology, College of Health Sciences, Makerere University, Kampala, Uganda.,Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Baylor College of Medicine Children's Foundation-Swaziland, Mbabane, Swaziland
| | - Ed Pettitt
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Masego Tsimako-Johnstone
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Ishmael Kasvosve
- Department of Medical Laboratory Sciences, University of Botswana, Gaborone, Botswana
| | - Koketso Maplanka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | - Sununguko W Mpoloka
- Department of Biological Sciences, Faculty of Sciences, University of Botswana, Gaborone, Botswana
| | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana.,Pediatric Retrovirology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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25
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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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26
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Mboowa G, Mwesigwa S, Katagirya E, Retshabile G, Mlotshwa BC, Williams L, Kekitiinwa A, Kateete D, Wampande E, Wayengera M, Kintu BN, Kisitu GP, Kyobe S, Brown CW, Hanchard NA, Mardon G, Joloba M, Anabwani G, Pettitt E, Tsimako-Johnstone M, Kasvosve I, Maplanka K, Mpoloka SW, Hlatshwayo M, Matshaba M. The Collaborative African Genomics Network (CAfGEN): Applying Genomic technologies to probe host factors important to the progression of HIV and HIV-tuberculosis infection in sub-Saharan Africa. AAS Open Res 2018; 1:3. [DOI: 10.12688/aasopenres.12832.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: The Human Heredity and Health in Africa consortium (H3Africa) was conceived to facilitate the application of genomics technologies to improve health across Africa. Here, we describe how the Collaborative African Genomics Network (CAfGEN) of the H3Africa consortium is using genomics to probe host genetic factors important to the progression of HIV and HIV-tuberculosis (TB) coinfection in sub-Saharan Africa. Methods: CAfGEN is an H3Africa collaborative centre comprising expertise from the University of Botswana; Makerere University; Baylor College of Medicine Children’s Clinical Centers of Excellence (COEs) in Botswana, Uganda, and Swaziland; as well as Baylor College of Medicine, Texas. The COEs provide clinical expertise for community engagement, participant recruitment and sample collection while the three University settings facilitate processing and management of genomic samples and provide infrastructure and training opportunities to sustain genomics research. Results: The project has focused on utilizing whole-exome sequencing to identify genetic variants contributing to extreme HIV disease progression phenotypes in children, as well as RNA sequencing and integrated genomics to identify host genetic factors associated with TB disease progression among HIV-positive children. These cohorts, developed using the COEs’ electronic medical records, are exceptionally well-phenotyped and present an unprecedented opportunity to assess genetic factors in individuals whose HIV was acquired by a different route than their adult counterparts in the context of a unique clinical course and disease pathophysiology. Conclusions: Our approach offers the prospect of developing a critical mass of well-trained, highly-skilled, continent-based African genomic scientists. To ensure long term genomics research sustainability in Africa, CAfGEN contributes to a wide range of genomics capacity and infrastructure development on the continent, has laid a foundation for genomics graduate programs at its institutions, and continues to actively promote genomics research through innovative forms of community engagement brokered by partnerships with governments and academia to support genomics policy formulation.
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27
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Abstract
Sleeping sickness is a neglected tropical disease caused by Trypanosoma brucei parasites, affecting the poorest communities in sub-Saharan Africa. The great efforts done by the scientific community, local governments, and non-governmental organizations (NGOs) via active patients' screening, vector control, and introduction of improved treatment regimens have significantly contributed to the reduction of human African trypanosomiasis (HAT) incidence during the last 15 years. Consequently, the WHO has announced the objective of HAT elimination as a public health problem by 2020. Studies at both parasite and host levels have improved our understanding of the parasite biology and the mechanisms of parasite interaction with its mammalian host. In this review, the impact that 'omics studies have had on sleeping sickness by revealing novel properties of parasite's subcellular organelles are summarized, by highlighting changes induced in the host during the infection and by proposing potential disease markers and therapeutic targets.
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Affiliation(s)
- Natalia Tiberti
- Translational Biomarker Group, University of Geneva, Geneva, Switzerland
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28
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Rotimi CN, Bentley AR, Doumatey AP, Chen G, Shriner D, Adeyemo A. The genomic landscape of African populations in health and disease. Hum Mol Genet 2017; 26:R225-R236. [PMID: 28977439 PMCID: PMC6075021 DOI: 10.1093/hmg/ddx253] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 12/12/2022] Open
Abstract
A deeper appreciation of the complex architecture of African genomes is critical to the global effort to understand human history, biology and differential distribution of disease by geography and ancestry. Here, we report on how the growing engagement of African populations in genome science is providing new insights into the forces that shaped human genomes before and after the Out-of-Africa migrations. As a result of this human evolutionary history, African ancestry populations have the greatest genomic diversity in the world, and this diversity has important ramifications for genomic research. In the case of pharmacogenomics, for instance, variants of consequence are not limited to those identified in other populations, and diversity within African ancestry populations precludes summarizing risk across different African ethnic groups. Exposure of Africans to fatal pathogens, such as Plasmodium falciparum, Lassa Virus and Trypanosoma brucei rhodesiense, has resulted in elevated frequencies of alleles conferring survival advantages for infectious diseases, but that are maladaptive in modern-day environments. Illustrating with cardiometabolic traits, we show that while genomic research in African ancestry populations is still in early stages, there are already many examples of novel and African ancestry-specific disease loci that have been discovered. Furthermore, the shorter haplotypes in African genomes have facilitated fine-mapping of loci discovered in other human ancestry populations. Given the insights already gained from the interrogation of African genomes, it is imperative to continue and increase our efforts to describe genomic risk in and across African ancestry populations.
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Affiliation(s)
- Charles N. Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Ayo P. Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Guanjie Chen
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | - Adebowale Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, Bethesda, MD 20892, USA
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