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Akintola AA, Aborode AT, Hamza MT, Amakiri A, Moore B, Abdulai S, Iyiola OA, Sulaimon LA, Effiong E, Ogunyemi A, Dosunmu B, Maigoro AY, Lawal O, Raheem K, Hwang UW. Bioinformatics proficiency among African students. FRONTIERS IN BIOINFORMATICS 2024; 4:1328714. [PMID: 38966162 PMCID: PMC11222312 DOI: 10.3389/fbinf.2024.1328714] [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: 10/27/2023] [Accepted: 01/25/2024] [Indexed: 07/06/2024] Open
Abstract
Bioinformatics, the interdisciplinary field that combines biology, computer science, and data analysis, plays a pivotal role in advancing our understanding of life sciences. In the African context, where the diversity of biological resources and healthcare challenges is substantial, fostering bioinformatics literacy and proficiency among students is important. This perspective provides an overview of the state of bioinformatics literacy among African students, highlighting the significance, challenges, and potential solutions in addressing this critical educational gap. It proposes various strategies to enhance bioinformatics literacy among African students. These include expanding educational resources, fostering collaboration between institutions, and engaging students in research projects. By addressing the current challenges and implementing comprehensive strategies, African students can harness the power of bioinformatics to contribute to innovative solutions in healthcare, agriculture, and biodiversity conservation, ultimately advancing the continent's scientific capabilities and improving the quality of life for her people. In conclusion, promoting bioinformatics literacy among African students is imperative for the continent's scientific development and advancing frontiers of biological research.
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Affiliation(s)
- Ashraf Akintayo Akintola
- School of Industrial Technology Advances, Kyungpook National University, Daegu, Republic of Korea
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
| | - Abdullahi Tunde Aborode
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Department of Chemistry, Mississippi State University, Starkville, MS, United States
| | - Muhammed Taofiq Hamza
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Green Climate Fund, Incheon, Republic of Korea
| | - Augustine Amakiri
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- ProCogia, Vancouver, BC, Canada
| | - Benjamin Moore
- European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Genome Campus, Cambridgeshire, United Kingdom
| | - Suliat Abdulai
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Department of Biochemistry, Fountain University, Osogbo, Nigeria
| | | | - Lateef Adegboyega Sulaimon
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Department of Biochemistry, Crescent University, Abeokuta, Nigeria
| | - Effiong Effiong
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Department of Medical Laboratory Sciences, Babcock University, Ilishan-Remo, Nigeria
| | - Adedeji Ogunyemi
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, United States
| | | | - Abdulkadir Yusif Maigoro
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Department of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon, Republic of Korea
| | - Opeyemi Lawal
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| | - Kayode Raheem
- NOBLEKINMAT Ltd. Bioinformatics Research Group, Ibadan, Nigeria
- Cancer Research Artificial Intelligence (CARESAI), Hobart, Australia
| | - Ui Wook Hwang
- School of Industrial Technology Advances, Kyungpook National University, Daegu, Republic of Korea
- Department of Biology, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, Republic of Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, Republic of Korea
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Kigen C, Muraya A, Kyanya C, Kingwara L, Mmboyi O, Hamm T, Musila L. Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya. Microb Genom 2023; 9:mgen001098. [PMID: 37646415 PMCID: PMC10483422 DOI: 10.1099/mgen.0.001098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023] Open
Abstract
Genomic surveillance is vital for detecting outbreaks and understanding the epidemiology and transmission of bacterial strains, yet it is not integrated into many national antimicrobial resistance (AMR) surveillance programmes. Key factors are that few scientists in the public health sector are trained in bacterial genomics, and the diverse sequencing platforms and bioinformatic tools make it challenging to generate reproducible outputs. In Kenya, these gaps were addressed by training public health scientists to conduct genomic surveillance on isolates from the national AMR surveillance repository and produce harmonized reports. The 2-week training combined theory and laboratory and bioinformatic experiences with Klebsiella pneumoniae isolates from the surveillance repository. Whole-genome sequences generated on Illumina and Nanopore sequencers were analysed using publicly available bioinformatic tools, and a harmonized report was generated using the HAMRonization tool. Pre- and post-training tests and self-assessments were used to assess the effectiveness of the training. Thirteen scientists were trained and generated data on the K. pneumoniae isolates, summarizing the AMR genes present consistently with the reported phenotypes and identifying the plasmid replicons that could transmit antibiotic resistance. Ninety per cent of the participants demonstrated an overall improvement in their post-training test scores, with an average increase of 14 %. Critical challenges were experienced in delayed delivery of equipment and supplies, power fluctuations and internet connections that were inadequate for bioinformatic analysis. Despite this, the training built the knowledge and skills to implement bacterial genomic surveillance. More advanced and immersive training experiences and building supporting infrastructure would solidify these gains to produce tangible public health outcomes.
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Affiliation(s)
- Collins Kigen
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Angela Muraya
- Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Cecilia Kyanya
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leonard Kingwara
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Onesmus Mmboyi
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Tiffany Hamm
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland, USA
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
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Infrastructure for bioinformatics applications in Tanzania: Lessons from the Sickle Cell Programme. PLoS Comput Biol 2023; 19:e1010848. [PMID: 36821534 PMCID: PMC9949651 DOI: 10.1371/journal.pcbi.1010848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Sickle cell disease (SCD) is a common genetic disorder in Africa. Some ongoing work in SCD research includes the analysis and comparisons of variation in phenotypic presentations and disease outcomes with the genotypic signatures. This has contributed to the observed growth of molecular and genetic data in SCD. However, while the "omics" data continues to pile, the capacity to interpret and turn the genetic findings into clinical practice is still underdeveloped, especially in the developing region. Building bioinformatics infrastructure and capacity in the region is key to bridging the gap. This paper seeks to illustrate how the Sickle Cell Programme (SCP) at the Muhimbili University of Health and Allied Sciences (MUHAS) in Tanzania, modeled the integration of infrastructure for bioinformatics and clinical research while running day-to-day clinical care for SCD in Tanzania.
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Mostajo-Radji MA. A Latin American perspective on neurodiplomacy. FRONTIERS IN MEDICAL TECHNOLOGY 2023; 4:1005043. [PMID: 36712171 PMCID: PMC9880232 DOI: 10.3389/fmedt.2022.1005043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/08/2022] [Indexed: 01/15/2023] Open
Affiliation(s)
- Mohammed A. Mostajo-Radji
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States,Live Cell Biotechnology Discovery Lab, University of California Santa Cruz, Santa Cruz, CA, United States,Correspondence: Mohammed A. Mostajo-Radji
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Lyimo BM, Popkin-Hall ZR, Giesbrecht DJ, Mandara CI, Madebe RA, Bakari C, Pereus D, Seth MD, Ngamba RM, Mbwambo RB, MacInnis B, Mbwambo D, Garimo I, Chacky F, Aaron S, Lusasi A, Molteni F, Njau R, Cunningham JA, Lazaro S, Mohamed A, Juliano JJ, Bailey J, Ishengoma DS. Potential Opportunities and Challenges of Deploying Next Generation Sequencing and CRISPR-Cas Systems to Support Diagnostics and Surveillance Towards Malaria Control and Elimination in Africa. Front Cell Infect Microbiol 2022; 12:757844. [PMID: 35909968 PMCID: PMC9326448 DOI: 10.3389/fcimb.2022.757844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 03/17/2022] [Indexed: 12/02/2022] Open
Abstract
Recent developments in molecular biology and genomics have revolutionized biology and medicine mainly in the developed world. The application of next generation sequencing (NGS) and CRISPR-Cas tools is now poised to support endemic countries in the detection, monitoring and control of endemic diseases and future epidemics, as well as with emerging and re-emerging pathogens. Most low and middle income countries (LMICs) with the highest burden of infectious diseases still largely lack the capacity to generate and perform bioinformatic analysis of genomic data. These countries have also not deployed tools based on CRISPR-Cas technologies. For LMICs including Tanzania, it is critical to focus not only on the process of generation and analysis of data generated using such tools, but also on the utilization of the findings for policy and decision making. Here we discuss the promise and challenges of NGS and CRISPR-Cas in the context of malaria as Africa moves towards malaria elimination. These innovative tools are urgently needed to strengthen the current diagnostic and surveillance systems. We discuss ongoing efforts to deploy these tools for malaria detection and molecular surveillance highlighting potential opportunities presented by these innovative technologies as well as challenges in adopting them. Their deployment will also offer an opportunity to broadly build in-country capacity in pathogen genomics and bioinformatics, and to effectively engage with multiple stakeholders as well as policy makers, overcoming current workforce and infrastructure challenges. Overall, these ongoing initiatives will build the malaria molecular surveillance capacity of African researchers and their institutions, and allow them to generate genomics data and perform bioinformatics analysis in-country in order to provide critical information that will be used for real-time policy and decision-making to support malaria elimination on the continent.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- School of Life Sciences and Bio-Engineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | | | - David J. Giesbrecht
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | | | - Rashid A. Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | - Ruth B. Mbwambo
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Bronwyn MacInnis
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Infectious Disease and Microbiome Program, Broad Institute, Boston, MA, United States
| | | | - Issa Garimo
- National Malaria Control Programme, Dodoma, Tanzania
| | - Frank Chacky
- National Malaria Control Programme, Dodoma, Tanzania
| | | | | | | | - Ritha Njau
- World Health Organization, Country Office, Dar es Salaam, Tanzania
| | - Jane A. Cunningham
- Global Malaria Programme, World Health Organization, Headquarters, Geneva, Switzerland
| | - Samwel Lazaro
- National Malaria Control Programme, Dodoma, Tanzania
| | - Ally Mohamed
- National Malaria Control Programme, Dodoma, Tanzania
| | - Jonathan J. Juliano
- School of Medicine, University of North Carolina, Chapel Hill, NC, United States
| | - Jeffrey A. Bailey
- Pathology and Laboratory Medicine, Center for International Health Research, Brown University, Providence, RI, United States
| | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia
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Aron S, Jongeneel CV, Chauke PA, Chaouch M, Kumuthini J, Zass L, Radouani F, Kassim SK, Fadlelmola FM, Mulder N. Ten simple rules for developing bioinformatics capacity at an academic institution. PLoS Comput Biol 2021; 17:e1009592. [PMID: 34882684 PMCID: PMC8659687 DOI: 10.1371/journal.pcbi.1009592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | | | - Paballo Abel Chauke
- 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
| | - Melek Chaouch
- Laboratory of bioinformatics, biomathematics and biostatistics, Institut Pasteur de Tunis, Université Tunis El Manar, Belvédère, Tunisia
| | - Judit Kumuthini
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - 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
| | - Fouzia Radouani
- Chlamydiae & Mycoplasmas Laboratory Research Department, Institut Pasteur du Maroc, Casablanca, Morocco
| | - Samar Kamal Kassim
- Medical Biochemistry & Molecular Biology Department, and MASRI Research Institute, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Faisal M. 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
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Mohamed SB, Kambal S, Ibrahim SAE, Abdalwhab E, Munir A, Ibrahim A, Ali QM. Bioinformatics in Sudan: Status and challenges case study: The National University-Sudan. PLoS Comput Biol 2021; 17:e1009462. [PMID: 34673773 PMCID: PMC8530284 DOI: 10.1371/journal.pcbi.1009462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The ever increasing applications of bioinformatics in providing effective interpretation of large and complex biological data require expertise in the use of sophisticated computational tools and advanced statistical tests, skills that are mostly lacking in the Sudanese research community. This can be attributed to paucity in the development and promotion of bioinformatics, lack of senior bioinformaticians, and the general status quo of inadequate research funding in Sudan. In this paper, we describe the challenges that have encountered the development of bioinformatics as a discipline in Sudan. Additionally, we highlight on specific actions that may help develop and promote its education and training. The paper takes the National University Biomedical Research Institute (NUBRI) as an example of an institute that has tackled many of these challenges and strives to drive powerful efforts in the development of bioinformatics in the country. Bioinformatics is gaining recognition globally and in Sudan as an important subdiscipline of biological sciences, one that enables researchers to efficiently interpret complex biological data. A limited number of Sudanese academic institutions have acknowledged this field despite its increasingly recognized importance. The development of bioinformatics in the country requires interdisciplinary collaborations involving experts in life sciences, research methodology, healthcare, computer, and data sciences. This can be achieved through designing educational programs and workshops alongside proposing and establishing effective collaborative research projects. In this context, we comprehensively discussed the present state of bioinformatics in Sudan, the challenges faced, as well as the efforts exerted by academic institutions including NUBRI, to upgrade infrastructure and establish local and international collaborations.
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Affiliation(s)
- Sofia B. Mohamed
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
- * E-mail:
| | - Sumaya Kambal
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
| | - Sabah A. E. Ibrahim
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
| | - Esra Abdalwhab
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
| | - Abdalla Munir
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
| | - Arwa Ibrahim
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
| | - Qurashi Mohamed Ali
- Bioinformatics and Biostatistics Department, National University Biomedical Research Institute, National University-Sudan, Khartoum, Sudan
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Imaging Africa: a strategic approach to optical microscopy training in Africa. Nat Methods 2021; 18:847-855. [PMID: 34354292 DOI: 10.1038/s41592-021-01227-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Status of Bioinformatics Education in South Asia: Past and Present. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5568262. [PMID: 33997009 PMCID: PMC8096557 DOI: 10.1155/2021/5568262] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/10/2021] [Accepted: 03/26/2021] [Indexed: 11/18/2022]
Abstract
Bioinformatics education has been a hot topic in South Asia, and the interest in this education peaks with the start of the 21st century. The governments of South Asian countries had a systematic effort for bioinformatics. They developed the infrastructures to provide maximum facility to the scientific community to gain maximum output in this field. This article renders bioinformatics, measures, and its importance of implementation in South Asia with proper ways of improving bioinformatics education flaws. It also addresses the problems faced in South Asia and proposes some recommendations regarding bioinformatics education. The information regarding bioinformatics education and institutes was collected from different existing research papers, databases, and surveys. The information was then confirmed by visiting each institution's website, while problems and solutions displayed in the article are mostly in line with South Asian bioinformatics conferences and institutions' objectives. Among South Asian countries, India and Pakistan have developed infrastructure and education regarding bioinformatics rapidly as compared to other countries, whereas Bangladesh, Sri Lanka, and Nepal are still in a progressing phase in this field. To advance in a different sector, the bioinformatics industry has to be revolutionized, and it will contribute to strengthening the pharmaceutical, agricultural, and molecular sectors in South Asia. To advance in bioinformatics, universities' infrastructure needs to be on a par with the current international standards, which will produce well-trained professionals with skills in multiple fields like biotechnology, mathematics, statistics, and computer science. The bioinformatics industry has revolutionized and strengthened the pharmaceutical, agricultural, and molecular sectors in South Asia, and it will serve as the standard of education increases in the South Asian countries. A framework for developing a centralized database is suggested after the literature review to collect and store the information on the current status of South Asian bioinformatics education. This will be named as the South Asian Bioinformatics Education Database (SABE). This will provide comprehensive information regarding the bioinformatics in South Asian countries by the country name, the experts of this field, and the university name to explore the top-ranked outputs relevant to queries.
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Using a multiple-delivery-mode training approach to develop local capacity and infrastructure for advanced bioinformatics in Africa. PLoS Comput Biol 2021; 17:e1008640. [PMID: 33630830 PMCID: PMC7906323 DOI: 10.1371/journal.pcbi.1008640] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
With more microbiome studies being conducted by African-based research groups, there is an increasing demand for knowledge and skills in the design and analysis of microbiome studies and data. However, high-quality bioinformatics courses are often impeded by differences in computational environments, complicated software stacks, numerous dependencies, and versions of bioinformatics tools along with a lack of local computational infrastructure and expertise. To address this, H3ABioNet developed a 16S rRNA Microbiome Intermediate Bioinformatics Training course, extending its remote classroom model. The course was developed alongside experienced microbiome researchers, bioinformaticians, and systems administrators, who identified key topics to address. Development of containerised workflows has previously been undertaken by H3ABioNet, and Singularity containers were used here to enable the deployment of a standard replicable software stack across different hosting sites. The pilot ran successfully in 2019 across 23 sites registered in 11 African countries, with more than 200 participants formally enrolled and 106 volunteer staff for onsite support. The pulling, running, and testing of the containers, software, and analyses on various clusters were performed prior to the start of the course by hosting classrooms. The containers allowed the replication of analyses and results across all participating classrooms running a cluster and remained available posttraining ensuring analyses could be repeated on real data. Participants thus received the opportunity to analyse their own data, while local staff were trained and supported by experienced experts, increasing local capacity for ongoing research support. This provides a model for delivering topic-specific bioinformatics courses across Africa and other remote/low-resourced regions which overcomes barriers such as inadequate infrastructures, geographical distance, and access to expertise and educational materials.
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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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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Ibaba JD, Gubba A. High-Throughput Sequencing Application in the Diagnosis and Discovery of Plant-Infecting Viruses in Africa, A Decade Later. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1376. [PMID: 33081084 PMCID: PMC7602839 DOI: 10.3390/plants9101376] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/25/2020] [Accepted: 09/29/2020] [Indexed: 12/18/2022]
Abstract
High-throughput sequencing (HTS) application in the field of plant virology started in 2009 and has proven very successful for virus discovery and detection of viruses already known. Plant virology is still a developing science in most of Africa; the number of HTS-related studies published in the scientific literature has been increasing over the years as a result of successful collaborations. Studies using HTS to identify plant-infecting viruses have been conducted in 20 African countries, of which Kenya, South Africa and Tanzania share the most published papers. At least 29 host plants, including various agricultural economically important crops, ornamentals and medicinal plants, have been used in viromics analyses and have resulted in the detection of previously known viruses and novel ones from almost any host. Knowing that the effectiveness of any management program requires knowledge on the types, distribution, incidence, and genetic of the virus-causing disease, integrating HTS and efficient bioinformatics tools in plant virology research projects conducted in Africa is a matter of the utmost importance towards achieving and maintaining sustainable food security.
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Affiliation(s)
- Jacques Davy Ibaba
- Discipline of Plant Pathology, School of Agricultural, Earth and Environmental Sciences, Agriculture Campus, University of KwaZulu-Natal, Scottsville, Pietermaritzburg 3209, South Africa;
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Kumuthini J, Zass L, Panji S, Salifu SP, Kayondo JK, Nembaware V, Mbiyavanga M, Olabode A, Kishk A, Wells G, Mulder NJ. The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa's capacity for genomics research. BMC Bioinformatics 2019; 20:741. [PMID: 31888443 PMCID: PMC6937968 DOI: 10.1186/s12859-019-3322-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/16/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)'s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. RESULTS The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. CONCLUSION To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond.
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Affiliation(s)
- Judit Kumuthini
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa.
| | - Lyndon Zass
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Sumir Panji
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Samson P Salifu
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Victoria Nembaware
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Mamana Mbiyavanga
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Ajayi Olabode
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Ali Kishk
- Center for Informatics Science, Nile University, 6th October City, Egypt
| | - Gordon Wells
- Centre for Proteomic and Genomic Research, Cape Town, Western Cape, South Africa
| | - Nicola J Mulder
- Computational Biology Division, IDM, Faculty of Health Sciences, University of Cape Town, Cape Town, Western Cape, South Africa
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15
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Chasapi A, Aivaliotis M, Angelis L, Chanalaris A, Iliopoulos I, Kappas I, Karapiperis C, Kyrpides NC, Pafilis E, Panteris E, Topalis P, Tsiamis G, Vizirianakis IS, Vlassi M, Promponas VJ, Ouzounis CA. Establishment of computational biology in Greece and Cyprus: Past, present, and future. PLoS Comput Biol 2019; 15:e1007532. [PMID: 31856214 PMCID: PMC6922331 DOI: 10.1371/journal.pcbi.1007532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Anastasia Chasapi
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
| | - Michalis Aivaliotis
- School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessalonica, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Lefteris Angelis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Anastasios Chanalaris
- Botnar Research Centre, NDORMS, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ioannis Iliopoulos
- Division of Basic Sciences, School of Medicine, University of Crete, Heraklion, Greece
| | - Ilias Kappas
- School of Biology, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Christos Karapiperis
- School of Informatics, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, California, United States of America
| | - Evangelos Pafilis
- Institute of Marine Biology Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Eleftherios Panteris
- First Psychiatric Clinic, Papageorgiou General Hospital, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Pantelis Topalis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - George Tsiamis
- Department of Environmental Engineering, School of Engineering, University of Patras, Patras, Greece
| | - Ioannis S. Vizirianakis
- Department of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, Thessalonica, Greece
| | - Metaxia Vlassi
- Institute of Biosciences & Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Vasilis J. Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
- * E-mail: (VJP); (CAO)
| | - Christos A. Ouzounis
- Biological Computation & Process Lab, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, Thessalonica, Greece
- * E-mail: (VJP); (CAO)
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16
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Osei-Amponsah R, Chauhan SS, Leury BJ, Cheng L, Cullen B, Clarke IJ, Dunshea FR. Genetic Selection for Thermotolerance in Ruminants. Animals (Basel) 2019; 9:E948. [PMID: 31717903 PMCID: PMC6912363 DOI: 10.3390/ani9110948] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
Variations in climatic variables (temperature, humidity and solar radiation) negatively impact livestock growth, reproduction, and production. Heat stress, for instance, is a source of huge financial loss to livestock production globally. There have been significant advances in physical modifications of animal environment and nutritional interventions as tools of heat stress mitigation. Unfortunately, these are short-term solutions and may be unsustainable, costly, and not applicable to all production systems. Accordingly, there is a need for innovative, practical, and sustainable approaches to overcome the challenges posed by global warming and climate change-induced heat stress. This review highlights attempts to genetically select and breed ruminants for thermotolerance and thereby sustain production in the face of changing climates. One effective way is to incorporate sustainable heat abatement strategies in ruminant production. Improved knowledge of the physiology of ruminant acclimation to harsh environments, the opportunities and tools available for selecting and breeding thermotolerant ruminants, and the matching of animals to appropriate environments should help to minimise the effect of heat stress on sustainable animal genetic resource growth, production, and reproduction to ensure protein food security.
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Affiliation(s)
- Richard Osei-Amponsah
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
- Department of Animal Science, University of Ghana, Legon, Accra, Ghana
| | - Surinder S. Chauhan
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
| | - Brian J. Leury
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
| | - Long Cheng
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
| | - Brendan Cullen
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
| | - Iain J. Clarke
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
| | - Frank R. Dunshea
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC 3010, Australia; (R.O.-A.); (B.J.L.); (L.C.); (B.C.); (I.J.C.); (F.R.D.)
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17
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Ghansah A, Kamau E, Amambua-Ngwa A, Ishengoma DS, Maiga-Ascofare O, Amenga-Etego L, Deme A, Yavo W, Randrianarivelojosia M, Ochola-Oyier LI, Helegbe GK, Bailey J, Alifrangis M, Djimde A. Targeted Next Generation Sequencing for malaria research in Africa: current status and outlook. Malar J 2019; 18:324. [PMID: 31547818 PMCID: PMC6757370 DOI: 10.1186/s12936-019-2944-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 08/29/2019] [Indexed: 11/10/2022] Open
Abstract
Targeted Next Generation Sequencing (TNGS) is an efficient and economical Next Generation Sequencing (NGS) platform and the preferred choice when specific genomic regions are of interest. So far, only institutions located in middle and high-income countries have developed and implemented the technology, however, the efficiency and cost savings, as opposed to more traditional sequencing methodologies (e.g. Sanger sequencing) make the approach potentially well suited for resource-constrained regions as well. In April 2018, scientists from the Plasmodium Diversity Network Africa (PDNA) and collaborators met during the 7th Pan African Multilateral Initiative of Malaria (MIM) conference held in Dakar, Senegal to explore the feasibility of applying TNGS to genetic studies and malaria surveillance in Africa. The group of scientists reviewed the current experience with TNGS platforms in sub-Saharan Africa (SSA) and identified potential roles the technology might play to accelerate malaria research, scientific discoveries and improved public health in SSA. Research funding, infrastructure and human resources were highlighted as challenges that will have to be mitigated to enable African scientists to drive the implementation of TNGS in SSA. Current roles of important stakeholders and strategies to strengthen existing networks to effectively harness this powerful technology for malaria research of public health importance were discussed.
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Affiliation(s)
- Anita Ghansah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, P. O. Box LG 581, Legon, Ghana
| | - Edwin Kamau
- Department of Emerging and Infectious Diseases (DEID), United States Army Medical Research Directorate -Africa (USAMR D-A), Kenya Medical Research Institute (KEMRI), Kisumu, Kenya.,U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Alfred Amambua-Ngwa
- Parasite Molecular Biology, Disease Control and Elimination, Medical Research Council Unit The Gambia at LSHTM, Atlantic Road Fajara, Banjul, The Gambia
| | | | | | - Lucas Amenga-Etego
- West Africa Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Awa Deme
- Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - William Yavo
- Faculty of Pharmacy, Department of Parasitology and Mycology, Fe ́lix Houphoue ̈t-Boigny University, BPV 34, Abidjan, Côte d'Ivoire.,Malaria Research and Control Centre, National Institute of Public Health, BPV 47, Abidjan, Côte d'Ivoire
| | | | | | | | - Gideon Kofi Helegbe
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, University for Development Studies, P. O. Box TL1883, Tamale, Northern Region, Ghana
| | - Jeffery Bailey
- Warren Alpert Medical School, Brown University, 55 Claverick St, Rm 314B, Providence, RI, 02903, USA
| | - Michael Alifrangis
- Centre for Medical Parasitology, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali. .,Wellcome Trust Sanger Institute, Hinxton, UK.
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18
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Abstract
Bioinformatics plays a key role in supporting the life sciences. In this work, we examine bioinformatics in Jordan, beginning with the current status of bioinformatics education and research, then exploring the challenges of advancing bioinformatics, and finally looking to the future for how Jordanian bioinformatics research may develop.
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Affiliation(s)
- Qanita Bani Baker
- Department of Computer Science, Jordan University of Science and Technology, Irbid, Jordan
| | - Maryam S. Nuser
- Department of Computer Science, Jordan University of Science and Technology, Irbid, Jordan
- Department of Information Systems, Yarmouk University, Irbid, Jordan
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19
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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20
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Shaffer JG, Mather FJ, Wele M, Li J, Tangara CO, Kassogue Y, Srivastav SK, Thiero O, Diakite M, Sangare M, Dabitao D, Toure M, Djimde AA, Traore S, Diakite B, Coulibaly MB, Liu Y, Lacey M, Lefante JJ, Koita O, Schieffelin JS, Krogstad DJ, Doumbia SO. Expanding Research Capacity in Sub-Saharan Africa Through Informatics, Bioinformatics, and Data Science Training Programs in Mali. Front Genet 2019; 10:331. [PMID: 31031807 PMCID: PMC6473184 DOI: 10.3389/fgene.2019.00331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/28/2019] [Indexed: 12/04/2022] Open
Abstract
Bioinformatics and data science research have boundless potential across Africa due to its high levels of genetic diversity and disproportionate burden of infectious diseases, including malaria, tuberculosis, HIV and AIDS, Ebola virus disease, and Lassa fever. This work lays out an incremental approach for reaching underserved countries in bioinformatics and data science research through a progression of capacity building, training, and research efforts. Two global health informatics training programs sponsored by the Fogarty International Center (FIC) were carried out at the University of Sciences, Techniques and Technologies of Bamako, Mali (USTTB) between 1999 and 2011. Together with capacity building efforts through the West Africa International Centers of Excellence in Malaria Research (ICEMR), this progress laid the groundwork for a bioinformatics and data science training program launched at USTTB as part of the Human Heredity and Health in Africa (H3Africa) initiative. Prior to the global health informatics training, its trainees published first or second authorship and third or higher authorship manuscripts at rates of 0.40 and 0.10 per year, respectively. Following the training, these rates increased to 0.70 and 1.23 per year, respectively, which was a statistically significant increase (p < 0.001). The bioinformatics and data science training program at USTTB commenced in 2017 focusing on student, faculty, and curriculum tiers of enhancement. The program's sustainable measures included institutional support for core elements, university tuition and fees, resource sharing and coordination with local research projects and companion training programs, increased student and faculty publication rates, and increased research proposal submissions. Challenges reliance of high-speed bandwidth availability on short-term funding, lack of a discounted software portal for basic software applications, protracted application processes for United States visas, lack of industry job positions, and low publication rates in the areas of bioinformatics and data science. Long-term, incremental processes are necessary for engaging historically underserved countries in bioinformatics and data science research. The multi-tiered enhancement approach laid out here provides a platform for generating bioinformatics and data science technicians, teachers, researchers, and program managers. Increased literature on bioinformatics and data science training approaches and progress is needed to provide a framework for establishing benchmarks on the topics.
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Affiliation(s)
- Jeffrey G. Shaffer
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Frances J. Mather
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Mamadou Wele
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Jian Li
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Cheick Oumar Tangara
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Yaya Kassogue
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sudesh K. Srivastav
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Oumar Thiero
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamadou Diakite
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Modibo Sangare
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Djeneba Dabitao
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mahamoudou Toure
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Abdoulaye A. Djimde
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Sekou Traore
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Brehima Diakite
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Mamadou B. Coulibaly
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - Yaozhong Liu
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Michelle Lacey
- Department of Mathematics, Tulane University, New Orleans, LA, United States
| | - John J. Lefante
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Ousmane Koita
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | - John S. Schieffelin
- Sections of Pediatric & Adult Infectious Diseases, School of Medicine, Tulane University, New Orleans, LA, United States
| | - Donald J. Krogstad
- Department of Global Biostatistics and Data Science, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, United States
| | - Seydou O. Doumbia
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
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Guerfali FZ, Laouini D, Boudabous A, Tekaia F. Designing and running an advanced Bioinformatics and genome analyses course in Tunisia. PLoS Comput Biol 2019; 15:e1006373. [PMID: 30689625 PMCID: PMC6349305 DOI: 10.1371/journal.pcbi.1006373] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Genome data, with underlying new knowledge, are accumulating at exponential rate thanks to ever-improving sequencing technologies and the parallel development of dedicated efficient Bioinformatics methods and tools. Advanced Education in Bioinformatics and Genome Analyses is to a large extent not accessible to students in developing countries where endeavors to set up Bioinformatics courses concern most often only basic levels. Here, we report a pioneering pilot experience concerning the design and implementation, from scratch, of a three-months advanced and extensive course in Bioinformatics and Genome Analyses in the Institut Pasteur de Tunis. Most significantly the outcome of the course was upgrading the participants’ skills in Bioinformatics and Genome Analyses to recognized international standards. Here we detail the different steps involved in the implementation of this course as well as the topics covered in the program. The description of this pilot experience might be helpful for the implementation of other similar educational projects, notably in developing countries, aiming to go beyond basics and providing young researchers with high-level skills.
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Affiliation(s)
- Fatma Z. Guerfali
- Université Tunis El Manar, Tunis, Tunisia
- Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia
| | - Dhafer Laouini
- Université Tunis El Manar, Tunis, Tunisia
- Institut Pasteur de Tunis, LR11IPT02, Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), Tunis-Belvédère, Tunisia
| | - Abdellatif Boudabous
- Université Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire Microorganisme et Biomolécules Actives, Campus Universitaire Farhat Heched, El Manar, Tunis, Tunisia
| | - Fredj Tekaia
- Institut Pasteur Paris, 28 rue du Dr Roux, 75724 Paris cedex 15, France
- * E-mail:
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22
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Shoko R, Manasa J, Maphosa M, Mbanga J, Mudziwapasi R, Nembaware V, Sanyika WT, Tinago T, Chikwambi Z, Mawere C, Matimba A, Mugumbate G, Mufandaedza J, Mulder N, Patterton H. Strategies and opportunities for promoting bioinformatics in Zimbabwe. PLoS Comput Biol 2018; 14:e1006480. [PMID: 30496170 PMCID: PMC6264469 DOI: 10.1371/journal.pcbi.1006480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Ryman Shoko
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- * E-mail:
| | - Justen Manasa
- African Institute of Biomedical Science & Technology, Harare, Zimbabwe
| | - Mcebisi Maphosa
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, Faculty of Applied Sciences, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Crop and Soil Science, School of Agricultural Sciences, Lupane State University, Lupane, Zimbabwe
| | - Victoria Nembaware
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Walter T. Sanyika
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Tawanda Tinago
- Department of Biology, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Zedias Chikwambi
- Department of Biotechnology, School of Agricultural Sciences and Technology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Cephas Mawere
- Department of Biotechnology, School of Industrial Science and Technology, Harare Institute of Technology, Harare, Zimbabwe
| | - Alice Matimba
- Department of Clinical Pharmacology, College of Health Sciences, University of Zimbabwe, Harare, Zimbabwe
| | - Grace Mugumbate
- Department of Chemistry, School of Natural Science and Mathematics, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | | | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Hugh Patterton
- Centre for Bioinformatics and Computational Biology, Stellenbosch University, Stellenbosch, South Africa
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23
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Bah SY, Morang'a CM, Kengne-Ouafo JA, Amenga-Etego L, Awandare GA. Highlights on the Application of Genomics and Bioinformatics in the Fight Against Infectious Diseases: Challenges and Opportunities in Africa. Front Genet 2018; 9:575. [PMID: 30538723 PMCID: PMC6277583 DOI: 10.3389/fgene.2018.00575] [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] [Received: 06/18/2018] [Accepted: 11/08/2018] [Indexed: 01/18/2023] Open
Abstract
Genomics and bioinformatics are increasingly contributing to our understanding of infectious diseases caused by bacterial pathogens such as Mycobacterium tuberculosis and parasites such as Plasmodium falciparum. This ranges from investigations of disease outbreaks and pathogenesis, host and pathogen genomic variation, and host immune evasion mechanisms to identification of potential diagnostic markers and vaccine targets. High throughput genomics data generated from pathogens and animal models can be combined with host genomics and patients’ health records to give advice on treatment options as well as potential drug and vaccine interactions. However, despite accounting for the highest burden of infectious diseases, Africa has the lowest research output on infectious disease genomics. Here we review the contributions of genomics and bioinformatics to the management of infectious diseases of serious public health concern in Africa including tuberculosis (TB), dengue fever, malaria and filariasis. Furthermore, we discuss how genomics and bioinformatics can be applied to identify drug and vaccine targets. We conclude by identifying challenges to genomics research in Africa and highlighting how these can be overcome where possible.
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Affiliation(s)
- Saikou Y Bah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Vaccine and Immunity Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, Gambia
| | - Collins Misita Morang'a
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Jonas A Kengne-Ouafo
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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24
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Ducrocq V, Laloe D, Swaminathan M, Rognon X, Tixier-Boichard M, Zerjal T. Genomics for Ruminants in Developing Countries: From Principles to Practice. Front Genet 2018; 9:251. [PMID: 30057590 PMCID: PMC6053532 DOI: 10.3389/fgene.2018.00251] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 12/03/2022] Open
Abstract
Using genomic information, local ruminant populations can be better characterized and compared to selected ones. Genetic relationships between animals can be established even without systematic pedigree recording, provided a budget is available for genotyping. Genomic selection (GS) can rely on a subset of the total population and does not require a costly national infrastructure, e.g., based on progeny testing. Yet, the use of genomic tools for animal breeding in developing countries is still limited. We identify three main reasons for this: (i) the instruments for cheap recording of phenotypes and data management are still limiting. (ii) many developing countries are recurrently exposed to unfavorable conditions (heat, diseases, poor nutrition) requiring special attention to fitness traits, (iii) a high level of expertise in quantitative genetics, modeling, and data manipulation is needed to perform genomic analyses. Yet, the potential outcomes go much beyond genetic improvements and can improve the resilience of the whole farming system. They include a better management of genetic diversity of local populations, a more balanced genetic progress and the possibility to unravel the genetic basis of adaptation of local breeds through whole genome approaches. A GS program being developed by BAIF, a large Indian NGO, is analyzed as a pilot case. It relies on the creation of a female reference population of Bos indicus and crossbreds, recorded with modern technology (e.g., smartphones) to collect performances at low cost in tiny herds on production and fertility. Finally, recommendations for the implementation of GS in developing countries are proposed.
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Affiliation(s)
- Vincent Ducrocq
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Denis Laloe
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | | | - Xavier Rognon
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Michèle Tixier-Boichard
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Tatiana Zerjal
- Génétique Animale et Biologie Intégrative, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Pollett S, Melendrez MC, Maljkovic Berry I, Duchêne S, Salje H, Cummings DAT, Jarman RG. Understanding dengue virus evolution to support epidemic surveillance and counter-measure development. INFECTION GENETICS AND EVOLUTION 2018; 62:279-295. [PMID: 29704626 DOI: 10.1016/j.meegid.2018.04.032] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 04/20/2018] [Accepted: 04/24/2018] [Indexed: 11/30/2022]
Abstract
Dengue virus (DENV) causes a profound burden of morbidity and mortality, and its global burden is rising due to the co-circulation of four divergent DENV serotypes in the ecological context of globalization, travel, climate change, urbanization, and expansion of the geographic range of the Ae.aegypti and Ae.albopictus vectors. Understanding DENV evolution offers valuable opportunities to enhance surveillance and response to DENV epidemics via advances in RNA virus sequencing, bioinformatics, phylogenetic and other computational biology methods. Here we provide a scoping overview of the evolution and molecular epidemiology of DENV and the range of ways that evolutionary analyses can be applied as a public health tool against this arboviral pathogen.
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Affiliation(s)
- S Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA; Marie Bashir Institute, University of Sydney, NSW, Australia; Institute for Global Health Sciences, University of California at San Francisco, CA, USA.
| | - M C Melendrez
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - I Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - S Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Australia
| | - H Salje
- Institut Pasteur, Paris, France; Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - D A T Cummings
- Johns Hopkins School of Public Health, Baltimore, MD, USA; University of Florida, FL, USA
| | - R G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
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Fang L, Wang Y, Chen X. Gene expression profiling and bioinformatics analysis of hereditary gingival fibromatosis. Biomed Rep 2018; 8:133-137. [PMID: 29435271 DOI: 10.3892/br.2017.1031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/11/2017] [Indexed: 01/01/2023] Open
Abstract
Hereditary gingival fibromatosis (HGF) is a benign, non-hemorrhagic and fibrous gingival overgrowth that may cover all or part of the teeth. It typically interferes with speech, lip closure and chewing, and can also be a psychological burden that affects the self-esteem of patients. Owing to high genetic heterogeneity, genetic testing to confirm diagnosis is not justified. It is therefore important to identify key signature genes and to understand the molecular mechanisms underlying HGF. The aim of the present study was to determine HGF-related genes and to analyze these genes through bioinformatics methods. A total of 249 differentially expressed genes (DEGs), consisting of 65 upregulated and 184 downregulated genes, were identified in the GSE4250 dataset of Gene Expression Omnibus (GEO) when comparing with the gums of HGF patients with those of healthy controls using the affy and limma packages in R. Subsequently, 28 enriched gene ontology terms were obtained from the Database for Annotation, Visualization and Integrated Discovery, and a protein-protein interaction (PPI) network was constructed and analyzed using STRING and Cytoscape. There were 99 nodes and 118 edges in the PPI network of these DEGs obtained through STRING. Among these nodes, 12 core genes were identified, of which the highest degree node was the gene for POTE ankyrin domain family member I. Collectively the results indicate that bioinformatics methods may provide effective strategies for predicting HGF-related genes and for understanding the molecular mechanisms of HGF.
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Affiliation(s)
- Lei Fang
- Department of Pathology and Pathophysiology, Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
| | - Yu Wang
- Department of Ultrasound in Medicine, Shanghai Jiaotong University Affiliated Sixth People's Hospital, Shanghai Institute of Ultrasound in Medicine, Shanghai 200233, P.R. China
| | - Xuejun Chen
- Department of Pathology and Pathophysiology, Jinzhou Medical University, Jinzhou, Liaoning 121001, P.R. China
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Quansah E, McGregor NW. Towards diversity in genomics: The emergence of neurogenomics in Africa? Genomics 2018; 110:1-9. [PMID: 28774809 DOI: 10.1016/j.ygeno.2017.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 07/24/2017] [Accepted: 07/30/2017] [Indexed: 12/11/2022]
Abstract
There is a high burden of mental and neurological disorders in Africa. Nevertheless, there appears to be an under-representation of African ancestry populations in large-scale genomic studies. Here, we evaluated the extent of under-representation of Africans in neurogenomic studies in the GWAS Catalog. We found 569 neurogenomic studies, of which 88.9% were exclusively focused on people with European ancestry and the remaining 11.1% having African ancestry cases included. In terms of population, only 1.2% of the total populations involved in these 569 GWAS studies were of African descent. Further, most of the individuals in the African ancestry category were identified to be African-Americans/Afro-Caribbeans, highlighting the huge under-representation of homogenous African populations in large-scale neurogenomic studies. Efforts geared at establishing strong collaborative ties with European/American researchers, maintaining freely accessible biobanks and establishing comprehensive African genome data repositories to track African genome variations are critical for propelling neurogenomics/precision medicine in Africa.
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Affiliation(s)
- Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK.
| | - Nathaniel W McGregor
- Department of Genetics, Stellenbosch University, Stellenbosch, South Africa; Department of Psychiatry, Stellenbosch University, Tygerberg Medical Campus, Tygerberg, South Africa.
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Hernández-de-Diego R, de Villiers EP, Klingström T, Gourlé H, Conesa A, Bongcam-Rudloff E. The eBioKit, a stand-alone educational platform for bioinformatics. PLoS Comput Biol 2017; 13:e1005616. [PMID: 28910280 PMCID: PMC5598936 DOI: 10.1371/journal.pcbi.1005616] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.
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Affiliation(s)
- Rafael Hernández-de-Diego
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Etienne P. de Villiers
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Tomas Klingström
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hadrien Gourlé
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ana Conesa
- Genomics of Gene Expression Lab, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, United States of America
| | - Erik Bongcam-Rudloff
- SLU-Global Bioinformatics Centre, Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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Karikari TK, Yawson NA. A Model Approach to Public Engagement Training for Students in Developing Countries. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2017; 18:jmbe-18-21. [PMID: 28912933 PMCID: PMC5524467 DOI: 10.1128/jmbe.v18i1.1244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/09/2016] [Indexed: 06/07/2023]
Abstract
Early involvement in public engagement activities may enhance undergraduate and graduate students’ long-term interest in science careers and their ability to dialogue with the public about topics of importance to science and society. While several public engagement training programs have been created and implemented in universities in the developed world, such opportunities are limited in developing countries. In their pursuit to develop appropriate public engagement training programs for their students, outreach providers and educators in developing countries will benefit from tried-and-tested training schemes from specific developing country contexts. In this paper, we describe the development, implementation, outcomes and possible extensions to an initiative to train budding scientists in a Ghanaian university to enable them to more effectively interact with the non-scientist public about the relevance of their research and the contribution of scientific endeavors to improving our daily lives. In order to address specific public engagement challenges identified in the target society, the program focuses on training students to become initiators of outreach activities who proactively seek engagement opportunities and can independently develop innovative events particularly for communities with poor public inclination to participate in scientific outreach.
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Affiliation(s)
- Thomas K. Karikari
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, UK
| | - Nat Ato Yawson
- Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
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Karikari TK, Yawson NA, Quansah E. Build the Future of Science Communication in Developing Countries through Systematic Training of Young Scientists. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2016; 17:327-328. [PMID: 28101256 PMCID: PMC5134933 DOI: 10.1128/jmbe.v17i3.1150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
While we are excited about the efforts of this journal to support scientific citizenship, we are concerned that science communication training efforts for budding scientists are lacking in many developing countries, casting doubts on measures to develop public engagement interest among the future scientific workforce in these environments. We discuss the need to address this challenge.
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Affiliation(s)
- Thomas K Karikari
- School of Life Sciences and Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, UK, E-mail:
| | - Nat Ato Yawson
- Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Quansah
- Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
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Helmy M, Awad M, Mosa KA. Limited resources of genome sequencing in developing countries: Challenges and solutions. Appl Transl Genom 2016; 9:15-9. [PMID: 27354935 PMCID: PMC4911431 DOI: 10.1016/j.atg.2016.03.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The differences between countries in national income, growth, human development and many other factors are used to classify countries into developed and developing countries. There are several classification systems that use different sets of measures and criteria. The most common classifications are the United Nations (UN) and the World Bank (WB) systems. The UN classification system uses the UN Human Development Index (HDI), an indicator that uses statistic of life expectancy, education, and income per capita for countries' classification. While the WB system uses gross national income (GNI) per capita that is calculated using the World Bank Atlas method. According to the UN and WB classification systems, there are 151 and 134 developing countries, respectively, with 89% overlap between the two systems. Developing countries have limited human development, and limited expenditure in education and research, among several other limitations. The biggest challenge facing genomic researchers and clinicians is limited resources. As a result, genomic tools, specifically genome sequencing technologies, which are rapidly becoming indispensable, are not widely available. In this report, we explore the current status of sequencing technologies in developing countries, describe the associated challenges and emphasize potential solutions.
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Affiliation(s)
- Mohamed Helmy
- Donnelly Centre for Cellular and Biomedical Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Mohamed Awad
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
| | - Kareem A. Mosa
- Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt
- Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Corresponding author at: Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt; Department of Applied Biology, College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.Department of Biotechnology, Faculty of Agriculture, Al-Azhar University, Cairo 11651, Egypt; Department of Applied Biology, College of Sciences, University of SharjahP.O. Box 27272SharjahUnited Arab Emirates
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Karikari TK, Yawson NA, Quansah E. Developing Science Communication in Africa: Undergraduate and Graduate Students should be Trained and Actively Involved in Outreach Activity Development and Implementation. JOURNAL OF UNDERGRADUATE NEUROSCIENCE EDUCATION : JUNE : A PUBLICATION OF FUN, FACULTY FOR UNDERGRADUATE NEUROSCIENCE 2016; 14:E5-8. [PMID: 27385932 PMCID: PMC4917354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 06/06/2023]
Abstract
Despite recent improvements in scientific research output from Africa, public understanding of science in many parts of the continent remains low. Science communication there is faced with challenges such as (i) lack of interest among some scientists, (ii) low availability of training programs for scientists, (iii) low literacy rates among the public, and (iv) multiplicity of languages. To address these challenges, new ways of training and motivating scientists to dialogue with non-scientists are essential. Developing communication skills early in researchers' scientific career would be a good way to enhance their public engagement abilities. Therefore, a potentially effective means to develop science communication in Africa would be to actively involve trainee scientists (i.e., undergraduate and graduate students) in outreach activity development and delivery. These students are often enthusiastic about science, eager to develop their teaching and communication skills, and can be good mentors to younger students. Involving them in all aspects of outreach activity is, therefore, likely to be a productive implementation strategy. However, science communication training specifically for students and the involvement of these students in outreach activity design and delivery are lacking in Africa. Here, we argue that improving the training and involvement of budding scientists in science communication activities would be a good way to bridge the wide gap between scientists and the African public.
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Affiliation(s)
- Thomas K Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK;; Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, UK
| | - Nat Ato Yawson
- Department of Biochemistry and Biotechnology, College of Science, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuel Quansah
- Department of Molecular Biology and Biotechnology, School of Biological Science, University of Cape Coast, Cape Coast, Ghana;; Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
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Karikari TK, Cobham AE, Ndams IS. Building sustainable neuroscience capacity in Africa: the role of non-profit organisations. Metab Brain Dis 2016; 31:3-9. [PMID: 26055077 PMCID: PMC4718937 DOI: 10.1007/s11011-015-9687-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2015] [Accepted: 05/18/2015] [Indexed: 10/26/2022]
Abstract
While advances in neuroscience are helping to improve many aspects of human life, inequalities exist in this field between Africa and more scientifically-advanced continents. Many African countries lack the infrastructure and appropriately-trained scientists for neuroscience education and research. Addressing these challenges would require the development of innovative approaches to help improve scientific competence for neuroscience across the continent. In recent years, science-based non-profit organisations (NPOs) have been supporting the African neuroscience community to build state-of-the-art scientific capacity for sustainable education and research. Some of these contributions have included: the establishment of training courses and workshops to introduce African scientists to powerful-yet-cost-effective experimental model systems; research infrastructural support and assistance to establish research institutes. Other contributions have come in the form of the promotion of scientific networking, public engagement and advocacy for improved neuroscience funding. Here, we discuss the contributions of NPOs to the development of neuroscience in Africa.
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Affiliation(s)
- Thomas K Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Midlands Integrative Biosciences Training Partnership (MIBTP), University of Warwick, Coventry, CV4 7AL, UK.
| | - Ansa E Cobham
- Department of Anatomy, Faculty of Basic Medical Sciences, University of Calabar, Calabar, Nigeria.
| | - Iliya S Ndams
- Department of Biological Sciences, Ahmadu Bello University, Zaria, Nigeria.
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Quansah E, Karikari TK. Neuroscience-related research in Ghana: a systematic evaluation of direction and capacity. Metab Brain Dis 2016; 31:11-24. [PMID: 26344503 PMCID: PMC4718959 DOI: 10.1007/s11011-015-9724-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/24/2015] [Indexed: 12/01/2022]
Abstract
Neurological and neuropsychiatric diseases account for considerable healthcare, economic and social burdens in Ghana. In order to effectively address these burdens, appropriately-trained scientists who conduct high-impact neuroscience research will be needed. Additionally, research directions should be aligned with national research priorities. However, to provide information about current neuroscience research productivity and direction, the existing capacity and focus need to be identified. This would allow opportunities for collaborative research and training to be properly explored and developmental interventions to be better targeted. In this study, we sought to evaluate the existing capacity and direction of neuroscience-related research in Ghana. To do this, we examined publications reporting research investigations authored by scientists affiliated with Ghanaian institutions in specific areas of neuroscience over the last two decades (1995-2015). 127 articles that met our inclusion criteria were systematically evaluated in terms of research foci, annual publication trends and author affiliations. The most actively-researched areas identified include neurocognitive impairments in non-nervous system disorders, depression and suicide, epilepsy and seizures, neurological impact of substance misuse, and neurological disorders. These studies were mostly hospital and community-based surveys. About 60% of these articles were published in the last seven years, suggesting a recent increase in research productivity. However, data on experimental and clinical research outcomes were particularly lacking. We suggest that future investigations should focus on the following specific areas where information was lacking: large-scale disease epidemiology, effectiveness of diagnostic platforms and therapeutic treatments, and the genetic, genomic and molecular bases of diseases.
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Affiliation(s)
- Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester, LE1 9BH, UK.
- Department of Molecular Biology and Biotechnology, School of Biological Science, University of Cape Coast, Cape Coast, Ghana.
| | - Thomas K Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.
- Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.
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Karikari TK, Quansah E, Mohamed WM. Developing expertise in bioinformatics for biomedical research in Africa. Appl Transl Genom 2015; 6:31-34. [PMID: 26767162 PMCID: PMC4699396 DOI: 10.1016/j.atg.2015.10.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Research in bioinformatics has a central role in helping to advance biomedical research. However, its introduction to Africa has been met with some challenges (such as inadequate infrastructure, training opportunities, research funding, human resources, biorepositories and databases) that have contributed to the slow pace of development in this field across the continent. Fortunately, recent improvements in areas such as research funding, infrastructural support and capacity building are helping to develop bioinformatics into an important discipline in Africa. These contributions are leading to the establishment of world-class research facilities, biorepositories, training programmes, scientific networks and funding schemes to improve studies into disease and health in Africa. With increased contribution from all stakeholders, these developments could be further enhanced. Here, we discuss how the recent developments are contributing to the advancement of bioinformatics in Africa.
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Affiliation(s)
- Thomas K. Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, UK
| | - Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK
- Department of Molecular Biology and Biotechnology, School of Biological Science, University of Cape Coast, Cape Coast, Ghana
| | - Wael M.Y. Mohamed
- Clinical Pharmacology Department, Menoufia Medical School, Menoufia University, Egypt
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Karikari TK, Quansah E, Mohamed WMY. Widening participation would be key in enhancing bioinformatics and genomics research in Africa. Appl Transl Genom 2015; 6:35-41. [PMID: 26767163 PMCID: PMC4699381 DOI: 10.1016/j.atg.2015.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Bioinformatics and genome science (BGS) are gradually gaining roots in Africa, contributing to studies that are leading to improved understanding of health, disease, agriculture and food security. While a few African countries have established foundations for research and training in these areas, BGS appear to be limited to only a few institutions in specific African countries. However, improving the disciplines in Africa will require pragmatic efforts to expand training and research partnerships to scientists in yet-unreached institutions. Here, we discuss the need to expand BGS programmes in Africa, and propose mechanisms to do so.
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Affiliation(s)
- Thomas K Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, UK
| | - Emmanuel Quansah
- Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, UK; Department of Molecular Biology and Biotechnology, School of Biological Science, University of Cape Coast, Cape Coast, Ghana
| | - Wael M Y Mohamed
- Clinical Pharmacology Department, Menoufia Medical School, Menoufia University, Egypt
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Motor Neuron Diseases in Sub-Saharan Africa: The Need for More Population-Based Studies. BIOMED RESEARCH INTERNATIONAL 2015; 2015:298409. [PMID: 26347879 PMCID: PMC4549542 DOI: 10.1155/2015/298409] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/01/2015] [Indexed: 11/25/2022]
Abstract
Motor neuron diseases (MNDs) are devastating neurological diseases that are characterised by gradual degeneration and death of motor neurons. Major types of MNDs include amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). These diseases are incurable, with limited disease-modifying treatment options. In order to improve MND-based biomedical research, drug development, and clinical care, population-based studies will be important. These studies, especially among less-studied populations, might identify novel factors controlling disease susceptibility and resistance. To evaluate progress in MND research in Africa, we examined the published literature on MNDs in Sub-Saharan Africa to identify disease prevalence, genetic factors, and other risk factors. Our findings indicate that the amount of research evidence on MNDs in Sub-Saharan Africa is scanty; molecular and genetics-based studies are particularly lacking. While only a few genetic studies were identified, these studies strongly suggest that there appear to be population-specific causes of MNDs among Africans. MND genetic underpinnings vary among different African populations and also between African and non-African populations. Further studies, especially molecular, genetic and genomic studies, will be required to advance our understanding of MND biology among African populations. Insights from these studies would help to improve the timeliness and accuracy of clinical diagnosis and treatment.
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Karikari TK, Quansah E. Neurogenomics: Challenges and opportunities for Ghana. Appl Transl Genom 2015; 5:11-14. [PMID: 26751686 PMCID: PMC4691957 DOI: 10.1016/j.atg.2015.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Accepted: 06/12/2015] [Indexed: 12/05/2022]
Abstract
The application of genomic tools and technologies has shown the potential to help improve healthcare and our understanding of disease mechanisms. While genomic tools are increasingly being applied to research on infectious diseases, malaria and neglected tropical diseases in Africa, an area that has seen little application of genomic approaches on this continent is neuroscience. In this article, we examined the prospects of developing neurogenomics research and its clinical use in Ghana, one of the African countries actively involved in genomics research. We noted that established international research funding sources and foundations in genomic research such as H3ABioNet nodes established at a couple of research centres in Ghana provide excellent platforms for extending the usage of genomic tools and techniques to neuroscience-related research areas. However, existing challenges such as the (i) lack of degree programmes in neuroscience, genomics and bioinformatics; (ii) low availability of infrastructure and appropriately-trained scientists; and (iii) lack of local research funding opportunities, need to be addressed. To promote and safeguard the long-term sustainability of neurogenomics research in the country, the impact of the existing challenges and possible ways of addressing them have been discussed.
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Affiliation(s)
- Thomas K Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom; Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Emmanuel Quansah
- Department of Molecular Biology and Biotechnology, School of Biological Science, University of Cape Coast, Cape Coast, Ghana; Pharmacology, Faculty of Health and Life Sciences, De Montfort University, Leicester LE1 9BH, United Kingdom
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Karikari TK, Aleksic J. Neurogenomics: An opportunity to integrate neuroscience, genomics and bioinformatics research in Africa. Appl Transl Genom 2015; 5:3-10. [PMID: 26937352 PMCID: PMC4745356 DOI: 10.1016/j.atg.2015.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/22/2015] [Accepted: 06/23/2015] [Indexed: 02/02/2023]
Abstract
Modern genomic approaches have made enormous contributions to improving our understanding of the function, development and evolution of the nervous system, and the diversity within and between species. However, most of these research advances have been recorded in countries with advanced scientific resources and funding support systems. On the contrary, little is known about, for example, the possible interplay between different genes, non-coding elements and environmental factors in modulating neurological diseases among populations in low-income countries, including many African countries. The unique ancestry of African populations suggests that improved inclusion of these populations in neuroscience-related genomic studies would significantly help to identify novel factors that might shape the future of neuroscience research and neurological healthcare. This perspective is strongly supported by the recent identification that diseased individuals and their kindred from specific sub-Saharan African populations lack common neurological disease-associated genetic mutations. This indicates that there may be population-specific causes of neurological diseases, necessitating further investigations into the contribution of additional, presently-unknown genomic factors. Here, we discuss how the development of neurogenomics research in Africa would help to elucidate disease-related genomic variants, and also provide a good basis to develop more effective therapies. Furthermore, neurogenomics would harness African scientists' expertise in neuroscience, genomics and bioinformatics to extend our understanding of the neural basis of behaviour, development and evolution.
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Affiliation(s)
- Thomas K. Karikari
- Neuroscience, School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
- Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Jelena Aleksic
- Wellcome Trust — Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 1QR, United Kingdom
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