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Zhou Y, Lauschke VM. Next-generation sequencing in pharmacogenomics - fit for clinical decision support? Expert Rev Clin Pharmacol 2024; 17:213-223. [PMID: 38247431 DOI: 10.1080/17512433.2024.2307418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
INTRODUCTION The technological advances of sequencing methods during the past 20 years have fuelled the generation of large amounts of sequencing data that comprise common variations, as well as millions of rare and personal variants that would not be identified by conventional genotyping. While comprehensive sequencing is technically feasible, its clinical utility for guiding personalized treatment decisions remains controversial. AREAS COVERED We discuss the opportunities and challenges of comprehensive sequencing compared to targeted genotyping for pharmacogenomic applications. Current pharmacogenomic sequencing panels are heterogeneous and clinical actionability of the included genes is not a major focus. We provide a current overview and critical discussion of how current studies utilize sequencing data either retrospectively from biobanks, databases or repurposed diagnostic sequencing, or prospectively using pharmacogenomic sequencing. EXPERT OPINION While sequencing-based pharmacogenomics has provided important insights into genetic variations underlying the safety and efficacy of a multitude pharmacological treatments, important hurdles for the clinical implementation of pharmacogenomic sequencing remain. We identify gaps in the interpretation of pharmacogenetic variants, technical challenges pertaining to complex loci and variant phasing, as well as unclear cost-effectiveness and incomplete reimbursement. It is critical to address these challenges in order to realize the promising prospects of pharmacogenomic sequencing.
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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
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
- University of Tübingen, Tübingen, Germany
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2
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Pisanu C, Squassina A. RNA Biomarkers in Bipolar Disorder and Response to Mood Stabilizers. Int J Mol Sci 2023; 24:10067. [PMID: 37373213 DOI: 10.3390/ijms241210067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
Bipolar disorder (BD) is a severe chronic disorder that represents one of the main causes of disability among young people. To date, no reliable biomarkers are available to inform the diagnosis of BD or clinical response to pharmacological treatment. Studies focused on coding and noncoding transcripts may provide information complementary to genome-wide association studies, allowing to correlate the dynamic evolution of different types of RNAs based on specific cell types and developmental stage with disease development or clinical course. In this narrative review, we summarize findings from human studies that evaluated the potential utility of messenger RNAs and noncoding transcripts, such as microRNAs, circular RNAs and long noncoding RNAs, as peripheral markers of BD and/or response to lithium and other mood stabilizers. The majority of available studies investigated specific targets or pathways, with large heterogeneity in the included type of cells or biofluids. However, a growing number of studies are using hypothesis-free designs, with some studies also integrating data on coding and noncoding RNAs measured in the same participants. Finally, studies conducted in neurons derived from induced-pluripotent stem cells or in brain organoids provide promising preliminary findings supporting the power and utility of these cellular models to investigate the molecular determinants of BD and clinical response.
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Affiliation(s)
- Claudia Pisanu
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, 09042 Monserrato, Italy
| | - Alessio Squassina
- Department of Biomedical Sciences, Section of Neuroscience and Clinical Pharmacology, University of Cagliari, 09042 Monserrato, Italy
- Department of Psychiatry, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 2E2, Canada
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3
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Kabbani D, Akika R, Wahid A, Daly AK, Cascorbi I, Zgheib NK. Pharmacogenomics in practice: a review and implementation guide. Front Pharmacol 2023; 14:1189976. [PMID: 37274118 PMCID: PMC10233068 DOI: 10.3389/fphar.2023.1189976] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
Considerable efforts have been exerted to implement Pharmacogenomics (PGx), the study of interindividual variations in DNA sequence related to drug response, into routine clinical practice. In this article, we first briefly describe PGx and its role in improving treatment outcomes. We then propose an approach to initiate clinical PGx in the hospital setting. One should first evaluate the available PGx evidence, review the most relevant drugs, and narrow down to the most actionable drug-gene pairs and related variant alleles. This is done based on data curated and evaluated by experts such as the pharmacogenomics knowledge implementation (PharmGKB) and the Clinical Pharmacogenetics Implementation Consortium (CPIC), as well as drug regulatory authorities such as the US Food and Drug Administration (FDA) and European Medicinal Agency (EMA). The next step is to differentiate reactive point of care from preemptive testing and decide on the genotyping strategy being a candidate or panel testing, each of which has its pros and cons, then work out the best way to interpret and report PGx test results with the option of integration into electronic health records and clinical decision support systems. After test authorization or testing requirements by the government or drug regulators, putting the plan into action involves several stakeholders, with the hospital leadership supporting the process and communicating with payers, the pharmacy and therapeutics committee leading the process in collaboration with the hospital laboratory and information technology department, and healthcare providers (HCPs) ordering the test, understanding the results, making the appropriate therapeutic decisions, and explaining them to the patient. We conclude by recommending some strategies to further advance the implementation of PGx in practice, such as the need to educate HCPs and patients, and to push for more tests' reimbursement. We also guide the reader to available PGx resources and examples of PGx implementation programs and initiatives.
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Affiliation(s)
- Danya Kabbani
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Reem Akika
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ahmed Wahid
- Department of Pharmaceutical Biochemistry, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Ann K. Daly
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Ingolf Cascorbi
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Nathalie Khoueiry Zgheib
- Department of Pharmacology and Toxicology, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
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Grant P, Cook CB, Langlois S, Nuk J, Mung S, Zhang Q, Lynd LD, Austin J, Elliott AM. Evaluation of out-of-pocket pay genetic testing in a publicly funded healthcare system. Clin Genet 2023; 103:424-433. [PMID: 36504324 DOI: 10.1111/cge.14276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/23/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022]
Abstract
When genetic tests are not funded publicly, out-of-pocket (OOP) pay options may be discussed with patients. We evaluated trends in genetic testing and OOP pay for two publicly funded British Columbia clinical programs serving >12 000 patients/year (The Hereditary Cancer Program [HCP] and Provincial Medical Genetics Program [PMGP]) between 2015-2019. Linear and regression models were used to explore the association of OOP pay with patient demographic variables at HCP. An interrupted time series and linear and logistic regression models were used on PMGP data to examine the effect of a change in the funding body. The total number of tests completed through PMGP, and HCP increased by 260% and 320%, respectively. OOP pay increased at HCP by 730%. The mean annual income of patients who paid OOP at HCP was ≥$3500 higher than in the group with funded testing (p < 0.0001). The likelihood of OOP pay increased at PMGP before the funding body change (OR per month: 1.07; 95% CI: 1.04, 1.10); while this likelihood had an immediate 87% drop when the change occurred (OR: 0.13; 95% CI: 0.06, 0.32). Patients with higher incomes are more likely to pay OOP. Financial barriers can create disparities in clinical outcomes. Funding decisions have a significant impact on rate of OOP pay.
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Affiliation(s)
- Peter Grant
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Courtney B Cook
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia, Canada
| | - Sylvie Langlois
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Jennifer Nuk
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia, Canada
| | - SzeWing Mung
- Hereditary Cancer Program, BC Cancer, Vancouver, British Columbia, Canada
| | - Qian Zhang
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
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- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Larry D Lynd
- Collaboration for Outcomes Research and Evaluation (CORE), Department of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Health Evaluation and Outcomes Sciences (CHEOS), Providence Health Research Institute, Vancouver, British Columbia, Canada
| | - Jehannine Austin
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Psychiatry, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alison M Elliott
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- BC Children's Hospital Research Institute, Vancouver, British Columbia, Canada
- Women's Health Research Institute, Vancouver, British Columbia, Canada
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Oluwole OG, Henry M. Genomic medicine in Africa: a need for molecular genetics and pharmacogenomics experts. Curr Med Res Opin 2023; 39:141-147. [PMID: 36094413 DOI: 10.1080/03007995.2022.2124072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The large-scale implementation of genomic medicine in Africa has not been actualized. This overview describes how routine molecular genetics and advanced protein engineering/structural biotechnology could accelerate the implementation of genomic medicine. By using data-mining and analysis approaches, we analyzed relevant information obtained from public genomic databases on pharmacogenomics biomarkers and reviewed published studies to discuss the ideas. The results showed that only 68 very important pharmacogenes currently exist, while 867 drug label annotations, 201 curated functional pathways, and 746 annotated drugs have been catalogued on the largest pharmacogenomics database (PharmGKB). Only about 5009 variants of the reported ∼25,000 have been clinically annotated. Predominantly, the genetic variants were derived from 43 genes that contribute to 2318 clinically relevant variations in 57 diseases. Majority (∼60%) of the clinically relevant genetic variations in the pharmacogenes are missense variants (1390). The enrichment analysis showed that 15 pharmacogenes are connected biologically and are involved in the metabolism of cardiovascular and cancer drugs. The review of studies showed that cardiovascular diseases are the most frequent non-communicable diseases responsible for approximately 13% of all deaths in Africa. Also, warfarin pharmacogenomics is the most studied drug on the continent, while CYP2D6, CYP2C9, DPD, and TPMT are the most investigated pharmacogenes with allele activities indicated in African and considered to be intermediate metaboliser for DPD and TPMT (8.4% and 11%). In summary, we highlighted a framework for implementing genomic medicine starting from the available resources on ground.
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Affiliation(s)
- Oluwafemi G Oluwole
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Marc Henry
- Medical Biotechnology and Immunotherapy Unit, Department of Integrative Biomedical Sciences Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Koleva-Kolarova R, Buchanan J, Vellekoop H, Huygens S, Versteegh M, Mölken MRV, Szilberhorn L, Zelei T, Nagy B, Wordsworth S, Tsiachristas A. Financing and Reimbursement Models for Personalised Medicine: A Systematic Review to Identify Current Models and Future Options. Appl Health Econ Health Policy 2022; 20:501-524. [PMID: 35368231 PMCID: PMC9206925 DOI: 10.1007/s40258-021-00714-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND The number of healthcare interventions described as 'personalised medicine' (PM) is increasing rapidly. As healthcare systems struggle to decide whether to fund PM innovations, it is unclear what models for financing and reimbursement are appropriate to apply in this context. OBJECTIVE To review financing and reimbursement models for PM, summarise their key characteristics, and describe whether they can influence the development and uptake of PM. METHODS A literature review was conducted in Medline, Embase, Web of Science, and Econlit to identify studies published in English between 2009 and 2021, and reviews published before 2009. Grey literature was identified through Google Scholar, Google and subject-specific webpages. Articles that described financing and reimbursement of PM, and financing of non-PM were included. Data were extracted and synthesised narratively to report on the models, as well as facilitators, incentives, barriers and disincentives that could influence PM development and uptake. RESULTS One hundred and fifty-three papers were included. Research and development of PM was financed through both public and private sources and reimbursed largely through traditional models such as single fees, Diagnosis-Related Groups, and bundled payments. Financial-based reimbursement, including rebates and price-volume agreements, was mainly applied to targeted therapies. Performance-based reimbursement was identified mainly for gene and targeted therapies, and some companion diagnostics. Gene therapy manufacturers offered outcome-based rebates for treatment failure for interventions including Luxturna®, Kymriah®, Yescarta®, Zynteglo®, Zolgensma® and Strimvelis®, and coverage with evidence development for Kymriah® and Yescarta®. Targeted testing with OncotypeDX® was granted value-based reimbursement through initial coverage with evidence development. The main barriers and disincentives to PM financing and reimbursement were the lack of strong links between stakeholders and the lack of demonstrable benefit and value of PM. CONCLUSIONS Public-private financing agreements and performance-based reimbursement models could help facilitate the development and uptake of PM interventions with proven clinical benefit.
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Affiliation(s)
| | - James Buchanan
- Health Economics Research Centre, University of Oxford, Oxford, UK
| | - Heleen Vellekoop
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Simone Huygens
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Matthijs Versteegh
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Maureen Rutten-van Mölken
- Institute for Medical Technology Assessment, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands
- Erasmus School of Health Policy and Management, Erasmus University Rotterdam, Rotterdam, The Netherlands
| | - László Szilberhorn
- Syreon Research Institute, Budapest, Hungary
- Faculty of Social Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Tamás Zelei
- Syreon Research Institute, Budapest, Hungary
| | - Balázs Nagy
- Syreon Research Institute, Budapest, Hungary
| | - Sarah Wordsworth
- Health Economics Research Centre, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
| | - Apostolos Tsiachristas
- Health Economics Research Centre, University of Oxford, Oxford, UK
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, UK
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7
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Leo CG, Tumolo MR, Sabina S, Colella R, Recchia V, Ponzini G, Fotiadis DI, Bodini A, Mincarone P. Health Technology Assessment for In Silico Medicine: Social, Ethical and Legal Aspects. Int J Environ Res Public Health 2022; 19:ijerph19031510. [PMID: 35162529 PMCID: PMC8835251 DOI: 10.3390/ijerph19031510] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 12/28/2022]
Abstract
The application of in silico medicine is constantly growing in the prevention, diagnosis, and treatment of diseases. These technologies allow us to support medical decisions and self-management and reduce, refine, and partially replace real studies of medical technologies. In silico medicine may challenge some key principles: transparency and fairness of data usage; data privacy and protection across platforms and systems; data availability and quality; data integration and interoperability; intellectual property; data sharing; equal accessibility for persons and populations. Several social, ethical, and legal issues may consequently arise from its adoption. In this work, we provide an overview of these issues along with some practical suggestions for their assessment from a health technology assessment perspective. We performed a narrative review with a search on MEDLINE/Pubmed, ISI Web of Knowledge, Scopus, and Google Scholar. The following key aspects emerge as general reflections with an impact on the operational level: cultural resistance, level of expertise of users, degree of patient involvement, infrastructural requirements, risks for health, respect of several patients’ rights, potential discriminations for access and use of the technology, and intellectual property of innovations. Our analysis shows that several challenges still need to be debated to allow in silico medicine to express all its potential in healthcare processes.
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Affiliation(s)
- Carlo Giacomo Leo
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy; (C.G.L.); (M.R.T.); (V.R.)
| | - Maria Rosaria Tumolo
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy; (C.G.L.); (M.R.T.); (V.R.)
- Department of Biological and Environmental Sciences and Technology, University of Salento, 73100 Lecce, Italy;
| | - Saverio Sabina
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy; (C.G.L.); (M.R.T.); (V.R.)
- Correspondence:
| | - Riccardo Colella
- Department of Biological and Environmental Sciences and Technology, University of Salento, 73100 Lecce, Italy;
| | - Virginia Recchia
- Institute of Clinical Physiology, National Research Council, 73100 Lecce, Italy; (C.G.L.); (M.R.T.); (V.R.)
| | - Giuseppe Ponzini
- Institute for Research on Population and Social Policies, National Research Council, 72100 Brindisi, Italy; (G.P.); (P.M.)
| | - Dimitrios Ioannis Fotiadis
- Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, 45110 Ioannina, Greece;
- Department of Biomedical Research, Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas (IMBB-FORTH), 45115 Ioannina, Greece
| | - Antonella Bodini
- Institute for Applied Mathematics and Information Technologies “E. Magenes”, National Research Council, 20133 Milan, Italy;
| | - Pierpaolo Mincarone
- Institute for Research on Population and Social Policies, National Research Council, 72100 Brindisi, Italy; (G.P.); (P.M.)
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8
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Lam BL, Leroy BP, Black G, Ong T, Yoon D, Trzupek K. Genetic testing and diagnosis of inherited retinal diseases. Orphanet J Rare Dis 2021; 16:514. [PMID: 34906171 PMCID: PMC8670140 DOI: 10.1186/s13023-021-02145-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 11/28/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) are a diverse group of degenerative diseases of the retina that can lead to significant reduction in vision and blindness. Because of the considerable phenotypic overlap among IRDs, genetic testing is a critical step in obtaining a definitive diagnosis for affected individuals and enabling access to emerging gene therapy–based treatments and ongoing clinical studies. While advances in molecular diagnostic technologies have significantly improved the understanding of IRDs and identification of disease-causing variants, training in genetic diagnostics among ophthalmologists is limited. In this review, we will provide ophthalmologists with an overview of genetic testing for IRDs, including the types of available testing, variant interpretation, and genetic counseling. Additionally, we will discuss the clinical applications of genetic testing in the molecular diagnosis of IRDs through case studies.
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Affiliation(s)
- Byron L Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, 900 NW 17th Street, Miami, FL, 33156, USA.
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Ophthalmic Genetics and Visual Electrophysiology, Division of Ophthalmology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Graeme Black
- UK Inherited Retinal Disease Consortium, Manchester, UK.,Genomics England Clinical Interpretation Partnership, Manchester, UK.,Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, UK
| | - Tuyen Ong
- Ring Therapeutics, Cambridge, MA, USA
| | | | - Karmen Trzupek
- Ocular and Rare Disease Genetics Services, InformedDNA, St Petersburg, FL, USA
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9
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Eric V, Yi V, Murdock D, Kalla SE, Wu TJ, Sabo A, Li S, Meng Q, Tian X, Murugan M, Cohen M, Kovar C, Wei WQ, Chung WK, Weng C, Wiesner GL, Jarvik GP, Muzny D, Gibbs RA. Neptune: an environment for the delivery of genomic medicine. Genet Med 2021; 23:1838-1846. [PMID: 34257418 PMCID: PMC8487966 DOI: 10.1038/s41436-021-01230-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 05/13/2021] [Indexed: 11/08/2022] Open
Abstract
PURPOSE Genomic medicine holds great promise for improving health care, but integrating searchable and actionable genetic data into electronic health records (EHRs) remains a challenge. Here we describe Neptune, a system for managing the interaction between a clinical laboratory and an EHR system during the clinical reporting process. METHODS We developed Neptune and applied it to two clinical sequencing projects that required report customization, variant reanalysis, and EHR integration. RESULTS Neptune has been applied for the generation and delivery of over 15,000 clinical genomic reports. This work spans two clinical tests based on targeted gene panels that contain 68 and 153 genes respectively. These projects demanded customizable clinical reports that contained a variety of genetic data types including single-nucleotide variants (SNVs), copy-number variants (CNVs), pharmacogenomics, and polygenic risk scores. Two variant reanalysis activities were also supported, highlighting this important workflow. CONCLUSION Methods are needed for delivering structured genetic data to EHRs. This need extends beyond developing data formats to providing infrastructure that manages the reporting process itself. Neptune was successfully applied on two high-throughput clinical sequencing projects to build and deliver clinical reports to EHR systems. The software is open source and available at https://gitlab.com/bcm-hgsc/neptune .
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Affiliation(s)
- Venner Eric
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Victoria Yi
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - David Murdock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sara E Kalla
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Tsung-Jung Wu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Shoudong Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xia Tian
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Mullai Murugan
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Michelle Cohen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Chunhua Weng
- Department of Biomedical Informatics, Columbia University, New York, New York, NY, USA
| | - Georgia L Wiesner
- Division of Genetic Medicine, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Gail P Jarvik
- Department of Medicine (Medical Genetics), University of Washington School of Medicine, Seattle, WA, USA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
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10
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Rogers SL, Patrinos GP, Mitropoulou C, Formea CM, Jones JS, Brown BG. Inaugural Pharmacogenomics Access and Reimbursement Symposium. Pharmacogenomics 2021; 22:515-517. [PMID: 34032472 DOI: 10.2217/pgs-2021-0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Pharmacogenomics Access & Reimbursement Symposium, a landmark event presented by the Golden Helix Foundation and the Pharmacogenomics Access & Reimbursement Coalition, was a 1-day interactive meeting comprised of plenary keynotes from thought leaders across healthcare that focused on value-based strategies to improve patient access to personalized medicine. Stakeholders including patients, healthcare providers, industry, government agencies, payer organizations, health systems and health policy organizations convened to define opportunities to improve patient access to personalized medicine through best practices, successful reimbursement models, high quality economic evaluations and strategic alignment. Session topics included health technology assessment, health economics, health policy and value-based payment models and innovation.
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Affiliation(s)
- Sara L Rogers
- American Society of Pharmacovigilance, Houston, TX 77225, USA
| | - George P Patrinos
- Department of Pharmacy, University of Patras, School of Health Sciences, Patras, 265 04, Greece.,Department of Pathology, United Arab Emirates University, College of Medicine & Health Sciences, Al-Ain, UAE.,United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
| | | | - Christine M Formea
- Department of Pharmacy Services & Intermountain Precision Genomics, Intermountain Healthcare Pharmacy Services, Taylorsville, UT 84123, USA
| | - J Shawn Jones
- Texas Tech University Health Sciences Center, Jerry H Hodge School of Pharmacy, Dallas, TX 75235, USA
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11
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Abstract
Genetic research is advancing rapidly. One important area for the application of the results from this work is personalized health. These are treatments and preventive interventions tailored to the genetic profile of specific groups or individuals. The inclusion of personalized health in existing health systems is a challenge for policymakers. In this article, we present the results of a thematic scoping review of the literature dealing with governance and policy of personalized health. Our analysis points to four governance challenges that decisionmakers face against the background of personalized health. First, researchers have highlighted the need to further extend and harmonize existing research infrastructures in order to combine different types of genetic data. Second, decisionmakers face the challenge to create trust in personalized health applications, such as genetic tests. Third, scholars have pointed to the importance of the regulation of data production and sharing to avoid discrimination of disadvantaged groups and to facilitate collaboration. Fourth, researchers have discussed the challenge to integrate personalized health into regulatory-, financing-, and service provision structures of existing health systems. Our findings summarize existing research and help to guide further policymaking and research in the field of personalized health governance.
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Affiliation(s)
- Philipp Trein
- Department of Political Science and International Relations, University of Geneva, Geneva, Switzerland
| | - Joël Wagner
- Department of Actuarial Science, Faculty of Business and Economics (HEC Lausanne), University of Lausanne, Lausanne, Switzerland.,Swiss Finance Institute, University of Lausanne, Lausanne, Switzerland
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12
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Winfree KB, Molife C, Peterson PM, Chen Y, Visseren-Grul CM, Leusch MS, Beyrer J, Dimou A. Real-world characteristics and outcomes of advanced non-small-cell lung cancer patients with EGFR exon 19 deletions or exon 21 mutations. Future Oncol 2021; 17:2867-2881. [PMID: 33866796 DOI: 10.2217/fon-2021-0218] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: To estimate real-world (rw) outcomes for first-line therapy in patients with advanced EGF receptor (EGFR)-mutated non-small-cell lung cancer (NSCLC), focusing on specific mutation types. Patients & methods: Retrospective observational study (n = 244 patients). Results: Univariate/multivariate analyses showed longer rw progression-free survival (rwPFS) and rwPFS2 in patients with ex19del versus Leu858Arg mutations. Median overall survival was 12.3 months longer with ex19del versus Leu858Arg mutations (HR: 1.47 [95% CI: 0.96-2.25]; p = 0.074). With EGFR-tyrosine kinase inhibitor monotherapy, unadjusted rwPFS for ex19del mutations was longer than for Leu858Arg mutations (HR: 1.62 [95% CI: 1.03-2.56]; p = 0.036). Conclusion: In this rw cohort of patients with advanced EGFR+ NSCLC, ex19del mutations conferred a prognostic advantage over Leu858Arg mutations, with significantly better rwPFS and rwPFS2.
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Affiliation(s)
| | - Cliff Molife
- Lilly Corporate Center, Eli Lilly & Company, Indianapolis, IN 46285, USA
| | - Patrick M Peterson
- Lilly Corporate Center, Eli Lilly & Company, Indianapolis, IN 46285, USA
| | - Yongmei Chen
- Lilly Corporate Center, Eli Lilly & Company, Indianapolis, IN 46285, USA
| | | | - Mark S Leusch
- Lilly Corporate Center, Eli Lilly & Company, Indianapolis, IN 46285, USA
| | - Julie Beyrer
- Lilly Corporate Center, Eli Lilly & Company, Indianapolis, IN 46285, USA
| | - Anastasios Dimou
- Department of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA
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13
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Vigliar E, Iaccarino A, Sciortino M, De Luca C, Malapelle U, Bellevicine C, Troncone G. Molecular predictive testing in precision oncology: The Italian experience. Cancer Cytopathol 2021; 128:622-628. [PMID: 32885914 DOI: 10.1002/cncy.22290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/24/2022]
Abstract
In this review, we describe molecular pathology testing to predict response to targeted treatment of solid tumors, focusing on Italian routine clinical practice. The combination of the universal health care system organized at national, regional, and local levels has led a decentralized model, with a large number of local laboratories performing in-house molecular testing following guidelines issued and external quality assessment organized by the Italian Society of Pathology and Cytopathology-Italian Division of the International Academy of Pathology. In this framework, in the early days of predictive testing, sponsored informatics platforms support to set up national programs that aimed to integrate the activity of oncologists and pathologists to test cancer patients for druggable alterations. More recently, reimbursement for molecular testing is being covered completely by the Italian National Health Service. In the near future, considering the development of complex technologies, we expect that outsourcing samples to next-generation sequencing referral laboratories will take place.
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Affiliation(s)
- Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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14
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Rogers SL, Patrinos GP, Mitropoulou C, Formea CM, Shawn Jones J, Brown BG. Conference report: inaugural Pharmacogenomics Access & Reimbursement Symposium. Pharmacogenomics J 2021; 21:622-624. [PMID: 34140646 PMCID: PMC8210499 DOI: 10.1038/s41397-021-00240-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/23/2021] [Accepted: 04/23/2021] [Indexed: 02/02/2023]
Abstract
The Pharmacogenomics Access & Reimbursement Symposium, a landmark event presented by the Golden Helix Foundation and the Pharmacogenomics Access & Reimbursement Coalition (PARC), was a one-day interactive meeting comprised of plenary keynotes from thought leaders across health care that focused on value-based strategies to improve patient access to personalized medicine. Stakeholders including patients, healthcare providers, industry, government agencies, payer organizations, health systems and health policy organizations convened to define opportunities to improve patient access to personalized medicine through best practices, successful reimbursement models, high-quality economic evaluations, and strategic alignment. Session topics included health technology assessment, health economics, health policy, and value-based payment models and innovation.
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Affiliation(s)
| | - George P. Patrinos
- grid.11047.330000 0004 0576 5395Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece ,grid.43519.3a0000 0001 2193 6666Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, UAE ,grid.43519.3a0000 0001 2193 6666Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, UAE
| | | | - Christine M. Formea
- grid.420884.20000 0004 0460 774XDepartment of Pharmacy Services & Intermountain Precision Genomics, Intermountain Healthcare Pharmacy Services, Taylorsville, UT USA
| | - J. Shawn Jones
- grid.416992.10000 0001 2179 3554Jerry H. Hodge School of Pharmacy, Texas Tech University Health Sciences Center, Dallas, TX USA
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15
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Mitropoulou C, Litinski V, Kabakchiev B, Rogers S, P Patrinos G. PARC report: health outcomes and value of personalized medicine interventions: impact on patient care. Pharmacogenomics 2020; 21:797-807. [PMID: 32635813 DOI: 10.2217/pgs-2019-0194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The incorporation of personalized medicine interventions into routine healthcare constitutes an opportunity to improve patients' quality of life, as it empowers implementation of innovative, individualized clinical interventions that maximize efficacy and/or minimize the risk of adverse drug reactions. In order to ensure equal access to genomic testing for all patients, the costs associated with these interventions must be reimbursed by payers and insurance bodies. As such, it is of utmost importance to thoroughly evaluate these interventions both in terms of their clinical effectiveness and their economic cost. This article discusses the impact of personalized medicine interventions in terms of both health outcomes and value, which directly impacts on their pricing and reimbursement by the various national healthcare systems.
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Affiliation(s)
| | | | | | - Sara Rogers
- American Society of Pharmacovigilance, Houston, TX 77225-0433, USA
| | - George P Patrinos
- University of Patras School of Health Sciences, Department of Pharmacy, Patras, 26504, Greece.,United Arab Emirates University, College of Medicine & Health Sciences, Department of Pathology, Al-Ain, UAE.,United Arab Emirates University, Zayed Center of Health Sciences, Al-Ain, UAE
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16
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Caspar SM, Dubacher N, Kopps AM, Meienberg J, Henggeler C, Matyas G. Clinical sequencing: From raw data to diagnosis with lifetime value. Clin Genet 2019; 93:508-519. [PMID: 29206278 DOI: 10.1111/cge.13190] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/22/2022]
Abstract
High-throughput sequencing (HTS) has revolutionized genetics by enabling the detection of sequence variants at hitherto unprecedented large scale. Despite these advances, however, there are still remaining challenges in the complete coverage of targeted regions (genes, exome or genome) as well as in HTS data analysis and interpretation. Moreover, it is easy to get overwhelmed by the plethora of available methods and tools for HTS. Here, we review the step-by-step process from the generation of sequence data to molecular diagnosis of Mendelian diseases. Highlighting advantages and limitations, this review addresses the current state of (1) HTS technologies, considering targeted, whole-exome, and whole-genome sequencing on short- and long-read platforms; (2) read alignment, variant calling and interpretation; as well as (3) regulatory issues related to genetic counseling, reimbursement, and data storage.
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Affiliation(s)
- S M Caspar
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - N Dubacher
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - A M Kopps
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - J Meienberg
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - C Henggeler
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland
| | - G Matyas
- Center for Cardiovascular Genetics and Gene Diagnostics, Foundation for People with Rare Diseases, Schlieren-Zurich, Switzerland.,Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
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17
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Peterson JF, Roden DM, Orlando LA, Ramirez AH, Mensah GA, Williams MS. Building evidence and measuring clinical outcomes for genomic medicine. Lancet 2019; 394:604-610. [PMID: 31395443 PMCID: PMC6730663 DOI: 10.1016/s0140-6736(19)31278-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/08/2019] [Accepted: 05/16/2019] [Indexed: 12/13/2022]
Abstract
Human genomic sequencing has potential diagnostic, prognostic, and therapeutic value across a wide breadth of clinical disciplines. One barrier to widespread adoption is the paucity of evidence for improved outcomes in patients who do not already have an indication for more focused testing. In this Series paper, we review clinical outcome studies in genomic medicine and discuss the important features and key challenges to building evidence for next generation sequencing in the context of routine patient care.
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Affiliation(s)
- Josh F Peterson
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Dan M Roden
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pharmacology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lori A Orlando
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Andrea H Ramirez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - George A Mensah
- Center for Translation Research and Implementation Science, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
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18
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Simeonidis S, Koutsilieri S, Vozikis A, Cooper DN, Mitropoulou C, Patrinos GP. Application of Economic Evaluation to Assess Feasibility for Reimbursement of Genomic Testing as Part of Personalized Medicine Interventions. Front Pharmacol 2019; 10:830. [PMID: 31427963 PMCID: PMC6688623 DOI: 10.3389/fphar.2019.00830] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/27/2019] [Indexed: 11/13/2022] Open
Abstract
Background: The incorporation of genomic testing into clinical practice constitutes an opportunity to improve patients' lives, as it makes possible the implementation of innovative, individualized clinical interventions that maximize efficacy and/or minimize the risk of adverse drug reactions. In order to ensure equal access to genomic testing for all patients, the costs associated with these tests should be reimbursed by their respective national healthcare systems. Given that funding for the public health sector is decreasing in real terms, it is of paramount importance that the emerging interventions are thoroughly evaluated both in terms of their clinical effectiveness and their full economic cost. Objective: The aim of this study was to identify those genome-guided interventions that could be adopted and reimbursed by national healthcare systems. Further, we recorded the underlying factors determining the broad adoption of genome-guided interventions in clinical practice, in order to identify potential reimbursement criteria. Methods: We performed a systematic review of published (PubMed-listed) scientific articles on the economic evaluation of those individualized clinical interventions that include genomic tests. Information on genomic tests reimbursed by the US Medicare program was also included. Subsequently, we correlated the regulatory guidance given for the interventions collated in our systematic review with the corresponding economic evaluation results and policies of the Medicare program. Regulatory guidance information was collected from the PharmGKB online knowledgebase and the Clinical Pharmacogenetics Implementation Consortium (CPIC). Results: Most of the included studies constitute cost-utility analyses, in which the outcome of the interventions has been measured in quality-adjusted life years (QALYs) whereas an estimate of the total cost has been based upon direct medical cost data. Favorable economic evaluation results, as well as concrete evidence demonstrating the clinical utility of pre-emptive genotyping, are considered as prerequisites for the broad adoption and reimbursement of the costs incurred during genomic testing. Indicatively, pre-emptive HLA-B*5701 and TPMT testing before administration of abacavir and azathioprine, respectively, is reimbursed by Medicare based on both economic and efficacy evidence. Likewise, the medical necessary screening for MMR and BRCA1/2 genes are reimbursed for high-risk populations. Conclusions: Our findings further underline the need for further cost-utility analyses within different national healthcare systems, in order to promote the reimbursement of the cost of innovative genome-guided therapeutic interventions.
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Affiliation(s)
- Stavros Simeonidis
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
| | - Stefania Koutsilieri
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
| | | | - David N. Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, United Kingdom
| | | | - George P. Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece
- Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
- Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
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19
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Mintzer V, Moran-Gilad J, Simon-Tuval T. Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology - A systematic literature review. Clin Microbiol Infect 2019; 25:1086-1095. [PMID: 31039443 DOI: 10.1016/j.cmi.2019.04.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges. OBJECTIVES The aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting. METHODS This was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted. RESULTS A total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures). CONCLUSIONS The decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.
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Affiliation(s)
- V Mintzer
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; Leumit Health Services, Israel
| | - J Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel; ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - T Simon-Tuval
- Department of Health Systems Management, Guilford Glazer Faculty of Business and Management and Faculty of Health Sciences, Ben-Gurion University of the Negev, Israel.
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20
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Mitropoulos K, Cooper DN, Mitropoulou C, Agathos S, Reichardt JKV, Al-Maskari F, Chantratita W, Wonkam A, Dandara C, Katsila T, Lopez-Correa C, Ali BR, Patrinos GP. Genomic Medicine Without Borders: Which Strategies Should Developing Countries Employ to Invest in Precision Medicine? A New "Fast-Second Winner" Strategy. OMICS 2018; 21:647-657. [PMID: 29140767 DOI: 10.1089/omi.2017.0141] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Genomic medicine has greatly matured in terms of its technical capabilities, but the diffusion of genomic innovations worldwide faces significant barriers beyond mere access to technology. New global development strategies are sorely needed for biotechnologies such as genomics and their applications toward precision medicine without borders. Moreover, diffusion of genomic medicine globally cannot adhere to a "one-size-fits-all-countries" development strategy, in the same way that drug treatments should be customized. This begs a timely, difficult but crucial question: How should developing countries, and the resource-limited regions of developed countries, invest in genomic medicine? Although a full-scale investment in infrastructure from discovery to the translational implementation of genomic science is ideal, this may not always be feasible in all countries at all times. A simple "transplantation of genomics" from developed to developing countries is unlikely to be feasible. Nor should developing countries be seen as simple recipients and beneficiaries of genomic medicine developed elsewhere because important advances in genomic medicine have materialized in developing countries as well. There are several noteworthy examples of genomic medicine success stories involving resource-limited settings that are contextualized and described in this global genomic medicine innovation analysis. In addition, we outline here a new long-term development strategy for global genomic medicine in a way that recognizes the individual country's pressing public health priorities and disease burdens. We term this approach the "Fast-Second Winner" model of innovation that supports innovation commencing not only "upstream" of discovery science but also "mid-stream," building on emerging highly promising biomarker and diagnostic candidates from the global science discovery pipeline, based on the unique needs of each country. A mid-stream entry into innovation can enhance collective learning from other innovators' mistakes upstream in discovery science and boost the probability of success for translation and implementation when resources are limited. This à la carte model of global innovation and development strategy offers multiple entry points into the global genomics innovation ecosystem for developing countries, whether or not extensive and expensive discovery infrastructures are already in place. Ultimately, broadening our thinking beyond the linear model of innovation will help us to enable the vision and practice of genomics without borders in both developed and resource-limited settings.
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Affiliation(s)
| | - David N Cooper
- 2 Institute of Medical Genetics, School of Medicine, Cardiff University , Cardiff, United Kingdom
| | | | - Spiros Agathos
- 4 Yachay Tech University , San Miguel de Urcuquí, Ecuador
| | | | - Fatima Al-Maskari
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
| | - Wasun Chantratita
- 7 Department of Pathology, Medical Genomic Center, Ramathibodi Hospital, Faculty of Medicine, Mahidol University , Bangkok, Thailand
| | - Ambroise Wonkam
- 8 Division of Human Genetics, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Collet Dandara
- 8 Division of Human Genetics, Department of Medicine and Institute of Infectious Disease and Molecular Medicine, University of Cape Town , Cape Town, South Africa
| | - Theodora Katsila
- 9 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | | | - Bassam R Ali
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
| | - George P Patrinos
- 5 Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,6 Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates .,9 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
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21
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Hayeems RZ, Bhawra J, Tsiplova K, Meyn MS, Monfared N, Bowdin S, Stavropoulos DJ, Marshall CR, Basran R, Shuman C, Ito S, Cohn I, Hum C, Girdea M, Brudno M, Cohn RD, Scherer SW, Ungar WJ. Care and cost consequences of pediatric whole genome sequencing compared to chromosome microarray. Eur J Hum Genet 2017; 25:1303-1312. [PMID: 29158552 PMCID: PMC5865210 DOI: 10.1038/s41431-017-0020-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/10/2017] [Accepted: 09/09/2017] [Indexed: 01/14/2023] Open
Abstract
The clinical use of whole-genome sequencing (WGS) is expected to alter pediatric medical management. The study aimed to describe the type and cost of healthcare activities following pediatric WGS compared to chromosome microarray (CMA). Healthcare activities prompted by WGS and CMA were ascertained for 101 children with developmental delay over 1 year. Activities following receipt of non-diagnostic CMA were compared to WGS diagnostic and non-diagnostic results. Activities were costed in 2016 Canadian dollars (CDN). Ongoing care accounted for 88.6% of post-test activities. The mean number of lab tests was greater following CMA than WGS (0.55 vs. 0.09; p = 0.007). The mean number of specialist visits was greater following WGS than CMA (0.41 vs. 0; p = 0.016). WGS results (diagnostic vs. non-diagnostic) modified the effect of test type on mean number of activities (p < 0.001). The cost of activities prompted by diagnostic WGS exceeded $557CDN for 10% of cases. In complex pediatric care, CMA prompted additional diagnostic investigations while WGS prompted tailored care guided by genotypic variants. Costs for prompted activities were low for the majority and constitute a small proportion of total test costs. Optimal use of WGS depends on robust evaluation of downstream care and cost consequences.
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Affiliation(s)
- Robin Z Hayeems
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada.
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada.
| | - Jasmin Bhawra
- School of Public Health and Health Systems, University of Waterloo, Waterloo, Canada
| | - Kate Tsiplova
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
| | - M Stephen Meyn
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Nasim Monfared
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Sarah Bowdin
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - D James Stavropoulos
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Christian R Marshall
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Raveen Basran
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Cheryl Shuman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Genetic Counselling, The Hospital for Sick Children, Toronto, Canada
| | - Shinya Ito
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Iris Cohn
- Division of Clinical Pharmacology and Toxicology, The Hospital for Sick Children, Toronto, Canada
| | - Courtney Hum
- Prenatal Diagnosis and Medical Genetics Program, Sinai Health System, Toronto, Canada
| | - Marta Girdea
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Michael Brudno
- Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Canada
- Department of Computer Science, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
| | - Ronald D Cohn
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- Division of Pediatric Medicine, The Hospital for Sick Children, Toronto, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
- Program in Genetics and Genomic Biology, The Hospital for Sick Children, Toronto, Canada
- McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, Canada
- Institute of Health Policy Management and Evaluation, University of Toronto, Toronto, Canada
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22
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Abstract
INTRODUCTION Pharmacogenomic testing has the potential to greatly benefit patients by enabling personalization of medication management, ensuring better efficacy and decreasing the risk of side effects. However, to fully realize the potential of pharmacogenomic testing, there are several important issues that must be addressed. Areas covered: In this expert review we discuss current challenges impacting the implementation of pharmacogenomic testing in the clinical practice. We emphasize issues related to testing methods, reporting of the results, test selection, clinical interpretation of the results, cost-effectiveness, and the long-term use of pharmacogenomic results in clinical practice. We identify opportunities and future directions to facilitate clinical implementation. Expert commentary: Several key elements are necessary to optimally integrate pharmacogenomic testing into clinical practice. Collaborative efforts among laboratories are needed to improve standardization of testing and reporting of the results. Clinicians need educational opportunities to improve understanding of which test to order and how to interpret the results. The electronic health records and other clinical systems need to improve their storage of the pharmacogenomics test results and interoperability to facilitate the use of clinically actionable results to improve patient care.
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Affiliation(s)
- Ann M Moyer
- a Department of Laboratory Medicine and Pathology , Mayo Clinic , Rochester , MN , USA
| | - Pedro J Caraballo
- b Department of Medicine , Mayo Clinic , Rochester , MN , USA.,c Center for Translational Informatics and Knowledge Management, Mayo Clinic , Rochester , MN , USA
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Patrinos GP, Mitropoulou C. Measuring the Value of Pharmacogenomics Evidence. Clin Pharmacol Ther 2017; 102:739-741. [DOI: 10.1002/cpt.743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/19/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
Affiliation(s)
- GP Patrinos
- University of Patras School of Health Sciences, Department of Pharmacy; Patras Greece
- United Arab Emirates University, College of Medicine, Department of Pathology; Al-Ain United Arab Emirates
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Hinderer M, Boeker M, Wagner SA, Binder H, Ückert F, Newe S, Hülsemann JL, Neumaier M, Schade-Brittinger C, Acker T, Prokosch HU, Sedlmayr B. The experience of physicians in pharmacogenomic clinical decision support within eight German university hospitals. Pharmacogenomics 2017; 18:773-785. [PMID: 28593816 DOI: 10.2217/pgs-2017-0027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aim: The aim of this study was to assess the physicians’ attitude, their knowledge and their experience in pharmacogenomic clinical decision support in German hospitals. Materials & methods: We conducted an online survey to address physicians of 13 different medical specialties across eight German university hospitals. In total, 564 returned questionnaires were analyzed. Results: The remaining knowledge gap, the uncertainty of test reimbursement and the physicians’ lack of awareness of existing pharmacogenomic clinical decision support systems (CDSS) are the major barriers for implementing pharmacogenomic CDSS into German hospitals. Furthermore, pharmacogenomic CDSS are most effective in the form of real-time decision support for internists. Conclusion: Physicians in German hospitals require additional education of both genetics and pharmacogenomics. They need to be provided with access to relevant pharmacogenomic CDSS.
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Affiliation(s)
- Marc Hinderer
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Martin Boeker
- Faculty of Medicine & Medical Center, Institute of Medical Biometry & Statistics, University of Freiburg, Freiburg, Germany
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University, Frankfurt, Germany
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology & Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Frank Ückert
- Department of Medical Informatics, Division of Translational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephanie Newe
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jan L Hülsemann
- Medical Directorate, University Hospital Magdeburg, Magdeburg, Germany
| | - Michael Neumaier
- Medical Faculty Mannheim, Institute for Clinical Chemistry, Ruprecht-Karls-University Heidelberg, Mannheim, Germany
| | | | - Till Acker
- Institute of Neuropathology, University of Giessen, Giessen, Germany
| | - Hans-Ulrich Prokosch
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Brita Sedlmayr
- Chair of Medical Informatics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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25
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Kolliopoulou A, Stratopoulos A, Siamoglou S, Sgourou A, Ali BR, Papachatzopoulou A, Katsila T, Patrinos GP. Key Pharmacogenomic Considerations for Sickle Cell Disease Patients. OMICS 2017; 21:314-322. [PMID: 28486096 DOI: 10.1089/omi.2017.0058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Sickle cell disease (SCD), although a monogenic disease, exhibits a complex clinical phenotype that hampers optimum patient stratification and disease management, especially on hydroxyurea treatment. Moreover, theranostics, the combination of diagnostics to individualize and optimize therapeutic interventions, has not been firmly on the forefront of SCD research and clinical management to date. We suggest that if tailor-made theranostics in SCD is envisaged, pharmacogenomics is anticipated to be the way forward. Herein, we present the current key pharmacogenomic opportunities and challenges in SCD, considering population variation, ethics, and socioeconomic aspects. We focus on pharmacogenomics and pain management, genethics, and cost-effectiveness in SCD. We searched for and synthesized data from PubMed and Google Scholar, and the references from relevant articles, using the keywords "pharmacogenomics," "sickle cell disease," "hydroxyurea," "ethics," "pain management," "morphine metabolism," "opioids," "pharmacogenomics and chronic pain," "cost-effectiveness," and "economic evaluation." Only articles published in English were included. So far, when pharmacogenomics in SCD has been considered, interindividual variability in hydroxyurea response/toxicity has been of primary interest. We underscore the need to extend pharmacogenomic considerations on other therapeutic interventions currently present using a holistic patient-centric approach, and taking disease complications into account as well. Furthermore, we raise awareness toward socioeconomic, ethical, and population differences in the way sickle cell pharmacogenomics might unfold in the future. If pharmacogenomics in SCD is to be used in the clinic in an evidence-based manner, cost-effectiveness and population-specific empirical ethics data are urgently needed.
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Affiliation(s)
- Alexandra Kolliopoulou
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - Apostolos Stratopoulos
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - Stavroula Siamoglou
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | | | - Bassam R Ali
- 3 Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
| | | | - Theodora Katsila
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece
| | - George P Patrinos
- 1 Department of Pharmacy, School of Health Sciences, University of Patras , Patras, Greece .,3 Department of Pathology, College of Medicine & Health Sciences, United Arab Emirates University , Al-Ain, United Arab Emirates
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Abstract
Whole-genome sequencing (WGS) is being applied within research settings across Europe to develop genomic WGS-based diagnostic tests. The focus of this perspective paper is to describe if, and how, current approaches of health technology assessment could be applied to WGS-based diagnostic tests. This perspective draws on the collective view from a trans-European multidisciplinary consortium of methodologists, clinicians and scientists. Specific challenges can be described by using the PICO (population, intervention, comparator, outcome) framework to inform health technology assessment. Practical solutions are suggested which require joined-up, multidisciplinary working across healthcare systems using existing expert networks so that emergent issues for the health technology assessment of WGS can be met in a timely fashion.
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Affiliation(s)
- Katherine Payne
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Martin Eden
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Niall Davison
- Manchester Centre for Health Economics, The University of Manchester, Manchester M13 9PL, UK
| | - Egbert Bakker
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
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Fragoulakis V, Mitropoulou C, Katelidou D, van Schaik RH, Maniadakis N, Patrinos GP. Performance Ratio Based Resource Allocation Decision-Making in Genomic Medicine. OMICS 2017; 21:67-73. [PMID: 28118098 DOI: 10.1089/omi.2016.0161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In modern healthcare systems, the available resources may influence the morbidity, mortality, and-consequently-the level of healthcare provided in every country. This is of particular interest in developing countries where the resources are limited and must be spent wisely to address social justice and the right for equal access in healthcare services by all the citizens in economically viable terms. In this light, the current allocation is, in practice, inefficient and rests mostly on each country's individual political and historical context and, thus, does not always incorporate decision-making enabled by economic models. In this study, we present a new economic model, specifically for resource allocation for genomic medicine, based on performance ratio, with potential applications in diverse healthcare sectors, which are particularly appealing for developing countries and low-resource environments. The model proposes a new method for resource allocation taking into account (1) the size of innovation of a new technology, (2) the relative effectiveness in comparison with social preferences, and (3) the cost of the technology, which permits the measurement of effectiveness to be determined differently in the context of a specific disease and then to be expressed in a relative form using a common performance ratio. The present work expands on previous work for innovation in economic models pertaining to genomic medicine and supports translational science.
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Affiliation(s)
- Vasilios Fragoulakis
- 1 Department of Pharmacy, University of Patras School of Health Sciences , Patras, Greece .,2 Department of Health Services Management, National School of Public Health , Athens, Greece
| | - Christina Mitropoulou
- 3 Erasmus MC , Department of Clinical Chemistry, Rotterdam, the Netherlands .,4 The Golden Helix Foundation , London, United Kingdom
| | | | - Ron H van Schaik
- 3 Erasmus MC , Department of Clinical Chemistry, Rotterdam, the Netherlands
| | - Nikolaos Maniadakis
- 2 Department of Health Services Management, National School of Public Health , Athens, Greece
| | - George P Patrinos
- 1 Department of Pharmacy, University of Patras School of Health Sciences , Patras, Greece
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