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Hamdi Y, Trabelsi M, Ghedira K, Boujemaa M, Ben Ayed I, Charfeddine C, Souissi A, Rejeb I, Kammoun Rebai W, Hkimi C, Neifar F, Jandoubi N, Mkaouar R, Chaouch M, Bennour A, Kamoun S, Chaker Masmoudi H, Abid N, Mezghani Khemakhem M, Masmoudi S, Saad A, BenJemaa L, BenKahla A, Boubaker S, Mrad R, Kamoun H, Abdelhak S, Gribaa M, Belguith N, Kharrat N, Hmida D, Rebai A. Genome Tunisia Project: paving the way for precision medicine in North Africa. Genome Med 2024; 16:104. [PMID: 39187811 PMCID: PMC11348534 DOI: 10.1186/s13073-024-01365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/16/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Key discoveries and innovations in the field of human genetics have led to the foundation of molecular and personalized medicine. Here, we present the Genome Tunisia Project, a two-phased initiative (2022-2035) which aims to deliver the reference sequence of the Tunisian Genome and to support the implementation of personalized medicine in Tunisia, a North African country that represents a central hub of population admixture and human migration between African, European, and Asian populations. The main goal of this initiative is to develop a healthcare system capable of incorporating omics data for use in routine medical practice, enabling medical doctors to better prevent, diagnose, and treat patients. METHODS A multidisciplinary partnership involving Tunisian experts from different institutions has come to discern all requirements that would be of high priority to fulfill the project's goals. One of the most urgent priorities is to determine the reference sequence of the Tunisian Genome. In addition, extensive situation analysis and revision of the education programs, community awareness, appropriate infrastructure including sequencing platforms and biobanking, as well as ethical and regulatory frameworks, have been undertaken towards building sufficient capacity to integrate personalized medicine into the Tunisian healthcare system. RESULTS In the framework of this project, an ecosystem with all engaged stakeholders has been implemented including healthcare providers, clinicians, researchers, pharmacists, bioinformaticians, industry, policymakers, and advocacy groups. This initiative will also help to reinforce research and innovation capacities in the field of genomics and to strengthen discoverability in the health sector. CONCLUSIONS Genome Tunisia is the first initiative in North Africa that seeks to demonstrate the major impact that can be achieved by Human Genome Projects in low- and middle-income countries to strengthen research and to improve disease management and treatment outcomes, thereby reducing the social and economic burden on healthcare systems. Sharing this experience within the African scientific community is a chance to turn a major challenge into an opportunity for dissemination and outreach. Additional efforts are now being made to advance personalized medicine in patient care by educating consumers and providers, accelerating research and innovation, and supporting necessary changes in policy and regulation.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia.
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Ikhlas Ben Ayed
- Department of Medical Genetics, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, BiotechPole of Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Imen Rejeb
- Department of Congenital and Hereditary Diseases, Mongi Slim University Hospital, Sidi Daoud La Marsa, Tunis, Tunisia
- Santé Mère-Enfant (LR22SP01), Tunis, Tunisia
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fadoua Neifar
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nouha Jandoubi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ayda Bennour
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Selim Kamoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hend Chaker Masmoudi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Histology and Cytogenetics, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Ibn Sina Street, Monastir, 5000, Tunisia
| | - Maha Mezghani Khemakhem
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 1068, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ali Saad
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Lamia BenJemaa
- Department of Congenital and Hereditary Diseases, Mongi Slim University Hospital, Sidi Daoud La Marsa, Tunis, Tunisia
- Santé Mère-Enfant (LR22SP01), Tunis, Tunisia
| | - Alia BenKahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hassen Kamoun
- Department of Medical Genetics, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
- Laboratory of Human Molecular Genetics, LR99ES33, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Communication, Science and Society Support Unit (UniSS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Moez Gribaa
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Neila Belguith
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Molecular Genetics, LR99ES33, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Dorra Hmida
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Phanthunane C, Pongcharoen S, Pannarunothai S, Roboon J, Phanthunane P, Nontarak J. Precision medicine in Asia enhanced by next-generation sequencing: Implications for Thailand through a scoping review and interview study. Clin Transl Sci 2024; 17:e13868. [PMID: 38924657 PMCID: PMC11197108 DOI: 10.1111/cts.13868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Next-generation sequencing (NGS) significantly enhances precision medicine (PM) by offering personalized approaches to diagnosis, treatment, and prevention of unmet medical needs. Little is known about the current situation of PM in Asia. Thus, we aimed to conduct an overview of the progress and gaps in PM in Asia and enrich it with in-depth insight into the possibilities of future PM in Thailand. This scoping review focused on Asian countries starting with non-cancer studies, including rare and undiagnosed diseases (RUDs), non-communicable diseases (NCDs), infectious diseases (IDs), and pharmacogenomics, with a focus on NGS. Subsequent in-depth interviews with experts in Thailand were performed, and a thematic analysis served as the main qualitative methodology. Out of 2898 searched articles, 387 studies were included after the review. Although most of the studies focused on cancer, 89 (23.0%) studies were related to RUDs (17.1%), NCDs (2.8%), IDs (1.8%), and pharmacogenomics (1.3%). Apart from medicine and related sciences, the studies were mostly composed of PM (61.8%), followed by genetics medicine and bioinformatics. Interestingly, 28% of articles were conducted exclusively within the fields of medicine and related sciences, emphasizing interdisciplinary integration. The experts emphasized the need for sustainability-driven political will, nurturing collaboration, reinforcing computational infrastructure, and expanding the bioinformatic workforce. In Asia, developments of NGS have made remarkable progress in PM. Thailand has extended PM beyond cancer and focused on clinical implementation. We summarized the PM challenges, including equity and efficiency targeting, guided research funding, sufficient sample size, integrated collaboration, computational infrastructure, and sufficient trained human resources.
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Affiliation(s)
- Chumut Phanthunane
- Division of Medical OncologyChulabhorn Hospital, Chulabhorn Royal AcademyBangkokThailand
| | - Sutatip Pongcharoen
- Department of Medicine, Faculty of MedicineNaresuan UniversityPhitsanulokThailand
| | | | - Jureepon Roboon
- Department of Anatomy, Faculty of Medical ScienceNaresuan UniversityPhitsanulokThailand
- Centre of Excellence in Medical BiotechnologyNaresuan UniversityPhitsanulokThailand
| | - Pudtan Phanthunane
- Department of Economics, Faculty of Business, Economics and CommunicationsNaresuan UniversityPhitsanulokThailand
| | - Jiraluck Nontarak
- Department of Epidemiology, Faculty of Public HealthMahidol UniversityBangkokThailand
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Lecoquierre F, Quenez O, Fourneaux S, Coutant S, Vezain M, Rolain M, Drouot N, Boland A, Olaso R, Meyer V, Deleuze JF, Dabbagh D, Gilles I, Gayet C, Saugier-Veber P, Goldenberg A, Guerrot AM, Nicolas G. High diagnostic potential of short and long read genome sequencing with transcriptome analysis in exome-negative developmental disorders. Hum Genet 2023; 142:773-783. [PMID: 37076692 DOI: 10.1007/s00439-023-02553-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/05/2023] [Indexed: 04/21/2023]
Abstract
Exome sequencing (ES) has become the method of choice for diagnosing rare diseases, while the availability of short-read genome sequencing (SR-GS) in a medical setting is increasing. In addition, new sequencing technologies, such as long-read genome sequencing (LR-GS) and transcriptome sequencing, are being increasingly used. However, the contribution of these techniques compared to widely used ES is not well established, particularly in regards to the analysis of non-coding regions. In a pilot study of five probands affected by an undiagnosed neurodevelopmental disorder, we performed trio-based short-read GS and long-read GS as well as case-only peripheral blood transcriptome sequencing. We identified three new genetic diagnoses, none of which affected the coding regions. More specifically, LR-GS identified a balanced inversion in NSD1, highlighting a rare mechanism of Sotos syndrome. SR-GS identified a homozygous deep intronic variant of KLHL7 resulting in a neoexon inclusion, and a de novo mosaic intronic 22-bp deletion in KMT2D, leading to the diagnosis of Perching and Kabuki syndromes, respectively. All three variants had a significant effect on the transcriptome, which showed decreased gene expression, mono-allelic expression and splicing defects, respectively, further validating the effect of these variants. Overall, in undiagnosed patients, the combination of short and long read GS allowed the detection of cryptic variations not or barely detectable by ES, making it a highly sensitive method at the cost of more complex bioinformatics approaches. Transcriptome sequencing is a valuable complement for the functional validation of variations, particularly in the non-coding genome.
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Affiliation(s)
- François Lecoquierre
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
| | - Olivier Quenez
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Steeve Fourneaux
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Sophie Coutant
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Myriam Vezain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Marion Rolain
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Nathalie Drouot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), 91057, Evry, France
| | - Dana Dabbagh
- Department of Pediatrics, Elbeuf Hospital, Elbeuf, France
| | | | - Claire Gayet
- Department of Pediatrics, CHU Rouen, F-76000, Rouen, France
| | - Pascale Saugier-Veber
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Alice Goldenberg
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Anne-Marie Guerrot
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France
| | - Gaël Nicolas
- Univ Rouen Normandie, Inserm U12045 and CHU Rouen, Department of Genetics and Reference Center for Developmental Disorders, FHU-G4 Génomique, F-76000, Rouen, France.
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Aguilera-Cobos L, García-Sanz P, Rosario-Lozano MP, Claros MG, Blasco-Amaro JA. An innovative framework to determine the implementation level of personalized medicine: A systematic review. Front Public Health 2023; 11:1039688. [PMID: 36817923 PMCID: PMC9936069 DOI: 10.3389/fpubh.2023.1039688] [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: 09/08/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Background Personalized medicine (PM) is now the new frontier in patient care. The application of this new paradigm extends to various pathologies and different patient care phases, such as diagnosis and treatment. Translating biotechnological advances to clinical routine means adapting health services at all levels is necessary. Purpose This article aims to identify the elements for devising a framework that will allow the level of PM implementation in the country under study to be quantitatively and qualitatively assessed and that can be used as a guideline for future implementation plans. Methods A systematic review was conducted per the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The research question was: What are the domains for determining the level of implementation of PM at the national level? The domains for assessing the degree of PM implementation, which would form the framework, were established. Results 19 full-text studies that met the inclusion criteria were peer-selected in the systematic review. From all the studies that were included, 37 elements-encompassed in 11 domains-were extracted for determining the degree of PM implementation. These domains and their constituent elements comprise the qualitative and quantitative assessment framework presented herein. Each of the elements can be assessed individually. On the other hand, the domains were standardized to all have the same weight in an overall assessment. Conclusions A framework has been developed that takes a multi-factorial approach to determine the degree of implementation of PM at the national level. This framework could also be used to rank countries and their implementation strategies according to the score they receive in the application of the latter. It could also be used as a guide for developing future national PM implementation strategies. Systematic review registration https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022338611, Identifier: CRD42022338611.
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Affiliation(s)
- Lorena Aguilera-Cobos
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain,Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain,*Correspondence: Lorena Aguilera-Cobos ✉
| | - Patricia García-Sanz
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain,Patricia García-Sanz ✉
| | - María Piedad Rosario-Lozano
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
| | - M. Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, Málaga, Spain,Institute of Biomedical Research in Málaga (IBIMA), Málaga, Spain,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Málaga, Spain,Institute for Mediterranean and Subtropical Horticulture “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Málaga, Spain
| | - Juan Antonio Blasco-Amaro
- Health Technology Assessment Area-AETSA, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
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Husereau D, Steuten L, Muthu V, Thomas DM, Spinner DS, Ivany C, Mengel M, Sheffield B, Yip S, Jacobs P, Sullivan T. Effective and Efficient Delivery of Genome-Based Testing-What Conditions Are Necessary for Health System Readiness? Healthcare (Basel) 2022; 10:healthcare10102086. [PMID: 36292532 PMCID: PMC9602865 DOI: 10.3390/healthcare10102086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 01/09/2023] Open
Abstract
Health systems internationally must prepare for a future of genetic/genomic testing to inform healthcare decision-making while creating research opportunities. High functioning testing services will require additional considerations and health system conditions beyond traditional diagnostic testing. Based on a literature review of good practices, key informant interviews, and expert discussion, this article attempts to synthesize what conditions are necessary, and what good practice may look like. It is intended to aid policymakers and others designing future systems of genome-based care and care prevention. These conditions include creating communities of practice and healthcare system networks; resource planning; across-region informatics; having a clear entry/exit point for innovation; evaluative function(s); concentrated or coordinated service models; mechanisms for awareness and care navigation; integrating innovation and healthcare delivery functions; and revisiting approaches to financing, education and training, regulation, and data privacy and security. The list of conditions we propose was developed with an emphasis on describing conditions that would be applicable to any healthcare system, regardless of capacity, organizational structure, financing, population characteristics, standardization of care processes, or underlying culture.
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Affiliation(s)
- Don Husereau
- School of Epidemiology and Public Health, University of Ottawa, Ottawa, ON K1G 5Z3, Canada
- Correspondence: ; Tel.: +1-6132994379
| | - Lotte Steuten
- Office of Health Economics, London SE1 2HB, UK
- City Health Economics Centre (CHEC), City University of London, London EC1V 0HB, UK
| | - Vivek Muthu
- Marivek Healthcare Consulting, Epsom KT18 7PF, UK
| | - David M. Thomas
- Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
- Omico, Sydney, NSW 2010, Australia
| | - Daryl S. Spinner
- Menarini Silicon Biosystems Inc., Huntingdon Valley, PA 19006, USA
| | - Craig Ivany
- Provincial Health Services Authority, Vancouver, BC V5Z 1G1, Canada
| | - Michael Mengel
- Department of Laboratory Medicine & Pathology, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | | | - Stephen Yip
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada
| | - Philip Jacobs
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - Terrence Sullivan
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON M5T 3M6, Canada
- Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H4A 3T2, Canada
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Santos Simarro F. Advances in clinical genetics and its current challenges. An Pediatr (Barc) 2022; 97:281.e1-281.e5. [PMID: 36115780 DOI: 10.1016/j.anpede.2022.08.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/30/2022] [Indexed: 11/27/2022] Open
Abstract
The great advances in the development of genomic technologies and their incorporation into routine clinical practice is bringing about a change in which an individual's genetic information is becoming increasingly relevant to their medical care. This is known as genomic medicine. Its implementation is not without barriers, including difficulties in the assessment and interpretation of genomic data, deficient training of professionals and patients in this field, unequal access to units with expertise, and a lack of professional profiles and infrastructures necessary for the incorporation of genomic technologies into routine clinical practice. This article reviews the advances and challenges of genomic medicine.
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Affiliation(s)
- Fernando Santos Simarro
- Unidad de Diagnóstico Molecular y Genética Clínica, Hospital Universitario Son Espases, Palma de Mallorca, Spain.
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Santos Simarro F. Avances en genética clínica y sus retos actuales. An Pediatr (Barc) 2022. [DOI: 10.1016/j.anpedi.2022.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Onstwedder SM, Jansen ME, Leonardo Alves T, Cornel MC, Rigter T. Pursuing Public Health Benefit Within National Genomic Initiatives: Learning From Different Policies. Front Genet 2022; 13:865799. [PMID: 35685439 PMCID: PMC9171010 DOI: 10.3389/fgene.2022.865799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/28/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Population-based genomic research is expected to deliver substantial public health benefits. National genomics initiatives are widespread, with large-scale collection and research of human genomic data. To date, little is known about the actual public health benefit that is yielded from such initiatives. In this study, we explore how public health benefit is being pursued in a selection of national genomics initiatives.Methods: A mixed-method study was carried out, consisting of a literature-based comparison of 11 purposively sampled national genomics initiatives (Belgium, Denmark, Estonia, Finland, Germany, Iceland, Qatar, Saudi Arabia, Taiwan, United Kingdom (UK), and United States (USA)), and five semi-structured interviews with experts (Denmark, Estonia, Finland, UK, USA). It was analyzed to what extent and how public health benefit was pursued and then operationalized in each phase of an adapted public health policy cycle: agenda setting, governance, (research) strategy towards health benefit, implementation, evaluation.Results: Public health benefit within national genomics initiatives was pursued in all initiatives and also operationalized in all phases of the public health policy cycle. The inclusion of public health benefit in genomics initiatives seemed dependent on the outcomes of agenda setting, such as the aims and values, as well as design of governance, for example involved actors and funding. Some initiatives focus on a research-based strategy to contribute to public health, while others focus on research translation into healthcare, or a combination of both. Evaluation of public health benefits could be performed qualitatively, such as assessing improved public trust, and/or quantitatively, e.g. research output or number of new diagnoses. However, the created health benefit for the general public, both short- and long-term, appears to be difficult to determine.Conclusion: Genomics initiatives hold the potential to deliver health promises of population-based genomics. Yet, universal tools to measure public health benefit and clarity in roles and responsibilities of collaborating stakeholders are lacking. Advancements in both aspects will help to facilitate and achieve the expected impact of genomics initiatives and enable effective research translation, implementation, and ultimately improved public health.
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Affiliation(s)
- Suzanne M. Onstwedder
- National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, Netherlands
- Department of Human Genetics, Section Community Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Netherlands
- Personalized Medicine program, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
- *Correspondence: Suzanne M. Onstwedder,
| | - Marleen E. Jansen
- National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, Netherlands
- Department of Human Genetics, Section Community Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Netherlands
- Personalized Medicine program, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Teresa Leonardo Alves
- National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, Netherlands
| | - Martina C. Cornel
- Department of Human Genetics, Section Community Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Netherlands
- Personalized Medicine program, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Tessel Rigter
- National Institute for Public Health and the Environment (RIVM), Centre for Health Protection, Bilthoven, Netherlands
- Department of Human Genetics, Section Community Genetics, Amsterdam UMC location Vrije Universiteit Amsterdam, Netherlands
- Personalized Medicine program, Amsterdam Public Health Research Institute, Amsterdam, Netherlands
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9
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El-Attar EA, Helmy Elkaffas RM, Aglan SA, Naga IS, Nabil A, Abdallah HY. Genomics in Egypt: Current Status and Future Aspects. Front Genet 2022; 13:797465. [PMID: 35664315 PMCID: PMC9157251 DOI: 10.3389/fgene.2022.797465] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Egypt is the third most densely inhabited African country. Due to the economic burden and healthcare costs of overpopulation, genomic and genetic testing is a huge challenge. However, in the era of precision medicine, Egypt is taking a shift in approach from “one-size-fits all” to more personalized healthcare via advancing the practice of medical genetics and genomics across the country. This shift necessitates concrete knowledge of the Egyptian genome and related diseases to direct effective preventive, diagnostic and counseling services of prevalent genetic diseases in Egypt. Understanding disease molecular mechanisms will enhance the capacity for personalized interventions. From this perspective, we highlight research efforts and available services for rare genetic diseases, communicable diseases including the coronavirus 2019 disease (COVID19), and cancer. The current state of genetic services in Egypt including availability and access to genetic services is described. Drivers for applying genomics in Egypt are illustrated with a SWOT analysis of the current genetic/genomic services. Barriers to genetic service development in Egypt, whether economic, geographic, cultural or educational are discussed as well. The sensitive topic of communicating genomic results and its ethical considerations is also tackled. To understand disease pathogenesis, much can be gained through the advancement and integration of genomic technologies via clinical applications and research efforts in Egypt. Three main pillars of multidisciplinary collaboration for advancing genomics in Egypt are envisaged: resources, infrastructure and training. Finally, we highlight the recent national plan to establish a genome center that will aim to prepare a map of the Egyptian human genome to discover and accurately determine the genetic characteristics of various diseases. The Reference Genome Project for Egyptians and Ancient Egyptians will initialize a new genomics era in Egypt. We propose a multidisciplinary governance system in Egypt to support genomic medicine research efforts and integrate into the healthcare system whilst ensuring ethical conduct of data.
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Affiliation(s)
- Eman Ahmed El-Attar
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
- *Correspondence: Eman Ahmed El-Attar,
| | | | - Sarah Ahmed Aglan
- Chemical Pathology Department, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Iman S. Naga
- Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Amira Nabil
- Department of Human Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Hoda Y. Abdallah
- Medical Genetics Unit, Histology and Cell Biology Department, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Center of Excellence in Molecular and Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
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10
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Abstract
Applications of genomics to population screening are expanding in the United States and internationally. Many of these programs are being implemented in the context of healthcare systems, mostly in a clinical research setting, but there are some emerging examples of clinical models. This review examines these genomic population screening programs to identify common features and differences in screened conditions, genomic technology employed, approach to results disclosure, health outcomes, financial models, and sustainability. The diversity of approaches provides opportunities to learn and better understand the optimal approach to implementation based on the contextual setting. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marc S Williams
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania, USA;
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11
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Zimani AN, Peterlin B, Kovanda A. Increasing Genomic Literacy Through National Genomic Projects. Front Genet 2021; 12:693253. [PMID: 34456970 PMCID: PMC8387713 DOI: 10.3389/fgene.2021.693253] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/15/2021] [Indexed: 11/13/2022] Open
Abstract
Genomics is an advancing field of medicine, science, ethics, and legislation. Keeping up to date with this challenging discipline requires continuous education and exchange of knowledge between many target groups. Specific challenges in genomic education include tailoring complex topics to diverse audiences ranging from the general public and patients to highly educated professionals. National genomic projects face many of the same challenges and thus offer many opportunities to highlight common educational strategies for improving genomic literacy. We have reviewed 41 current national genomic projects and have identified 16 projects specifically describing their approach to genomic education. The following target groups were included in the educational efforts: the general public (nine projects), patients (six projects), and genomic professionals (16 projects), reflecting the general overall aims of the projects such as determining normal and pathological genomic variation, improving infrastructure, and facilitating personalized medicine. The national genomic projects aim to increase genomic literacy through supplementing existing national education in genomics as well as independent measures specifically tailored to each target group, such as training events, research collaboration, and online resources for healthcare professionals, patients, and patient organizations. This review provides the current state of educational activities within national genomic projects for different target groups and identifies good practices that could contribute to patient empowerment, public engagement, proficient healthcare professionals, and lend support to personalized medicine.
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Affiliation(s)
- Ana Nyasha Zimani
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Anja Kovanda
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
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12
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Zhou Y, Lauschke VM. Computational Tools to Assess the Functional Consequences of Rare and Noncoding Pharmacogenetic Variability. Clin Pharmacol Ther 2021; 110:626-636. [PMID: 33998671 DOI: 10.1002/cpt.2289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Interindividual differences in drug response are a common concern in both drug development and across layers of care. While genetics clearly influences drug response and toxicity of many drugs, a substantial fraction of the heritable pharmacological and toxicological variability remains unexplained by known genetic polymorphisms. In recent years, population-scale sequencing projects have unveiled tens of thousands of coding and noncoding pharmacogenetic variants with unclear functional effects that might explain at least part of this missing heritability. However, translating these personalized variant signatures into drug response predictions and actionable advice remains challenging and constitutes one of the most important frontiers of contemporary pharmacogenomics. Conventional prediction methods are primarily based on evolutionary conservation, which drastically reduces their predictive accuracy when applied to poorly conserved pharmacogenes. Here, we review the current state-of-the-art of computational variant effect predictors across variant classes and critically discuss their utility for pharmacogenomics. Besides missense variants, we discuss recent progress in the evaluation of synonymous, splice, and noncoding variations. Furthermore, we discuss emerging possibilities to assess haplotypes and structural variations. We advocate for the development of algorithms trained on pharmacogenomic instead of pathogenic data sets to improve the predictive accuracy in order to facilitate the utilization of next-generation sequencing data for personalized clinical decision support and precision pharmacogenomics.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
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