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Edsjö A, Russnes HG, Lehtiö J, Tamborero D, Hovig E, Stenzinger A, Rosenquist R. High-throughput molecular assays for inclusion in personalised oncology trials - State-of-the-art and beyond. J Intern Med 2024; 295:785-803. [PMID: 38698538 DOI: 10.1111/joim.13785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact. This includes the need to assess complex biomarkers, for example microsatellite instability, tumour mutation burden and homologous recombination deficiency, to identify patients suitable for specific therapies, including immunotherapy. Furthermore, the crucial role of biomarker analysis and multidisciplinary molecular tumour boards in selecting patients for trial inclusion is discussed in relation to various trial concepts, including drug repurposing. Recognising that today's exploratory techniques will evolve into tomorrow's routine diagnostics and clinical study inclusion assays, the importance of emerging technologies for multimodal diagnostics, such as proteomics and in vivo drug sensitivity testing, is also discussed. In addition, key regulatory aspects and the importance of patient engagement in all phases of a clinical trial are described. Finally, we propose a set of recommendations for consideration when planning a new precision cancer medicine trial.
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Affiliation(s)
- Anders Edsjö
- Department of Clinical Genetics, Pathology and Molecular Diagnostics, Office for Medical Services, Region Skåne, Lund, Sweden
- Division of Pathology, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Hege G Russnes
- Department of Pathology, Oslo University Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
- Cancer genomics and proteomics, Karolinska University Hospital, Solna, Sweden
| | - David Tamborero
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Stockholm, Sweden
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Albrecht Stenzinger
- Institute of Pathology, Division of Molecular Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Solna, Sweden
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2
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Wilson R, Reinke D, van Oortmerssen G, Gonzato O, Ott G, Raut CP, Guadagnolo BA, Haas RLM, Trent J, Jones R, Pretorius L, Felser B, Basson M, Schuster K, Kasper B. What Is a Sarcoma 'Specialist Center'? Multidisciplinary Research Finds an Answer. Cancers (Basel) 2024; 16:1857. [PMID: 38791936 PMCID: PMC11119625 DOI: 10.3390/cancers16101857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/26/2024] [Accepted: 05/07/2024] [Indexed: 05/26/2024] Open
Abstract
The management of sarcomas in specialist centers delivers significant benefits. In much of the world, specialists are not available, and the development of expertise is identified as a major need. However, the terms 'specialist' or 'expert' center are rarely defined. Our objective is to offer a definition for patient advocates and a tool for healthcare providers to underpin improving the care of people with sarcoma. SPAGN developed a discussion paper for a workshop at the SPAGN 2023 Conference, attended by 75 delegates. A presentation to the Connective Tissue Oncology Society (CTOS) and further discussion led to this paper. Core Principles were identified that underlie specialist sarcoma care. The primary Principle is the multi-disciplinary team discussing every patient, at first diagnosis and during treatment. Principles for optimal sarcoma management include accurate diagnosis followed by safe, high-quality treatment, with curative intent. These Principles are supplemented by Features describing areas of healthcare, professional involvement, and service provision and identifying further research and development needs. These allow for variations because of national or local policies and budgets. We propose the term 'Sarcoma Intelligent Specialist Network' to recognize expertise wherever it is found in the world. This provides a base for further discussion and local refinement.
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Affiliation(s)
- Roger Wilson
- Sarcoma Patient Advocacy Global Network (SPAGN), 61200 Woelfersheim, Germany
| | - Denise Reinke
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Ornella Gonzato
- Fondazione Paola Gonzato-Rete Sarcoma ETS, 33100 Udine, Italy
| | - Gabriele Ott
- Sarcoma Patient Advocacy Global Network (SPAGN), 61200 Woelfersheim, Germany
| | - Chandrajit P. Raut
- Division of Surgical Oncology, Brigham and Women’s Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Rick L. M. Haas
- Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
| | - Jonathan Trent
- Department of Hematology Oncology, Sylvester Comprehensive Cancer Center, Miami, FL 33136, USA
| | - Robin Jones
- Sarcoma Unit, Institute of Cancer Research, Royal Marsden Hospital, London SW3 6JJ, UK
| | | | - Brandi Felser
- Sarcoma Foundation of America, Washington, DC 20036, USA
| | | | - Kathrin Schuster
- Sarcoma Patient Advocacy Global Network (SPAGN), 61200 Woelfersheim, Germany
| | - Bernd Kasper
- Mannheim University Medical Center, University of Heidelberg, 68167 Mannheim, Germany
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3
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Aupperle-Lellbach H, Kehl A, de Brot S, van der Weyden L. Clinical Use of Molecular Biomarkers in Canine and Feline Oncology: Current and Future. Vet Sci 2024; 11:199. [PMID: 38787171 PMCID: PMC11126050 DOI: 10.3390/vetsci11050199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024] Open
Abstract
Molecular biomarkers are central to personalised medicine for human cancer patients. It is gaining traction as part of standard veterinary clinical practice for dogs and cats with cancer. Molecular biomarkers can be somatic or germline genomic alterations and can be ascertained from tissues or body fluids using various techniques. This review discusses how these genomic alterations can be determined and the findings used in clinical settings as diagnostic, prognostic, predictive, and screening biomarkers. We showcase the somatic and germline genomic alterations currently available to date for testing dogs and cats in a clinical setting, discussing their utility in each biomarker class. We also look at some emerging molecular biomarkers that are promising for clinical use. Finally, we discuss the hurdles that need to be overcome in going 'bench to bedside', i.e., the translation from discovery of genomic alterations to adoption by veterinary clinicians. As we understand more of the genomics underlying canine and feline tumours, molecular biomarkers will undoubtedly become a mainstay in delivering precision veterinary care to dogs and cats with cancer.
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Affiliation(s)
- Heike Aupperle-Lellbach
- Laboklin GmbH&Co.KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (H.A.-L.); (A.K.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 80333 München, Germany
| | - Alexandra Kehl
- Laboklin GmbH&Co.KG, Steubenstr. 4, 97688 Bad Kissingen, Germany; (H.A.-L.); (A.K.)
- School of Medicine, Institute of Pathology, Technical University of Munich, Trogerstr. 18, 80333 München, Germany
| | - Simone de Brot
- Institute of Animal Pathology, COMPATH, University of Bern, 3012 Bern, Switzerland;
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4
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Boon IS. The Increasing Role of Genomics Testing in Thyroid Cancers. Clin Oncol (R Coll Radiol) 2024; 36:e113. [PMID: 38395636 DOI: 10.1016/j.clon.2024.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Affiliation(s)
- I S Boon
- Department of Clinical Oncology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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5
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Franco I, Supek F. Genomics reveal unknown mutation-promoting agents at global sites. Nature 2024; 629:767-768. [PMID: 38773293 DOI: 10.1038/d41586-024-01190-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
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6
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Marshall DA, Hua N, Buchanan J, Christensen KD, Frederix GWJ, Goranitis I, Ijzerman M, Jansen JP, Lavelle TA, Regier DA, Smith HS, Ungar WJ, Weymann D, Wordsworth S, Phillips KA. Paving the path for implementation of clinical genomic sequencing globally: Are we ready? HEALTH AFFAIRS SCHOLAR 2024; 2:qxae053. [PMID: 38783891 PMCID: PMC11115369 DOI: 10.1093/haschl/qxae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Despite the emerging evidence in recent years, successful implementation of clinical genomic sequencing (CGS) remains limited and is challenged by a range of barriers. These include a lack of standardized practices, limited economic assessments for specific indications, limited meaningful patient engagement in health policy decision-making, and the associated costs and resource demand for implementation. Although CGS is gradually becoming more available and accessible worldwide, large variations and disparities remain, and reflections on the lessons learned for successful implementation are sparse. In this commentary, members of the Global Economics and Evaluation of Clinical Genomics Sequencing Working Group (GEECS) describe the global landscape of CGS in the context of health economics and policy and propose evidence-based solutions to address existing and future barriers to CGS implementation. The topics discussed are reflected as two overarching themes: (1) system readiness for CGS and (2) evidence, assessments, and approval processes. These themes highlight the need for health economics, public health, and infrastructure and operational considerations; a robust patient- and family-centered evidence base on CGS outcomes; and a comprehensive, collaborative, interdisciplinary approach.
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Affiliation(s)
- Deborah A Marshall
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Nicolle Hua
- Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - James Buchanan
- Health Economics and Policy Research Unit, Centre for Evaluation and Methods, Wolfson Institute of Population Health, Queen Mary University of London, London E1 2AB, United Kingdom
| | - Kurt D Christensen
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Geert W J Frederix
- Epidemiology and Health Economics, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CG Utrecht, The Netherlands
| | - Ilias Goranitis
- Health Economics Unit, Centre for Health Policy, Melbourne School of Population and Global Health, University of Melbourne, Parkville, Victoria 3010, Australia
- Australian Genomics, Parkville, Victoria 3052, Australia
| | - Maarten Ijzerman
- University of Melbourne Centre for Cancer Research, University of Melbourne, Melbourne, Victoria 3000, Australia
- Erasmus School of Health Policy & Management, Eramus University Rotterdam, 3062 PA Rotterdam, The Netherlands
| | - Jeroen P Jansen
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
| | - Tara A Lavelle
- Center for the Evaluation of Value and Risk in Health, Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, MA 02111, United States
| | - Dean A Regier
- Canadian Centre for Applied Research in Cancer Control, Cancer Control Research, BC Cancer Research Institute, Vancouver, British Columbia V5Z 1L3, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Hadley S Smith
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, United States
| | - Wendy J Ungar
- Program of Child Health Evaluative Sciences, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, Ontario M5T 3M6, Canada
| | - Deirdre Weymann
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Faculty of Health Sciences, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health and NIHR Biomedical Research Centre, University of Oxford, Oxford OX3 7LF, United Kingdom
| | - Kathryn A Phillips
- Center for Translational and Policy Research on Precision Medicine (TRANSPERS), Department of Clinical Pharmacy, School of Pharmacy, University of California, San Francisco, San Francisco, CA 94158, United States
- Health Affairs Scholar Emerging & Global Health Policy, Health Affairs, Washington, DC 20036, United States
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7
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Gremke N, Rodepeter FR, Teply-Szymanski J, Griewing S, Boekhoff J, Stroh A, Tarawneh TS, Riera-Knorrenschild J, Balser C, Hattesohl A, Middeke M, Ross P, Litmeyer AS, Romey M, Stiewe T, Wündisch T, Neubauer A, Denkert C, Wagner U, Mack EKM. NGS-Guided Precision Oncology in Breast Cancer and Gynecological Tumors-A Retrospective Molecular Tumor Board Analysis. Cancers (Basel) 2024; 16:1561. [PMID: 38672643 PMCID: PMC11048446 DOI: 10.3390/cancers16081561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Background: Precision oncology treatments are being applied more commonly in breast and gynecological oncology through the implementation of Molecular Tumor Boards (MTBs), but real-world clinical outcome data remain limited. Methods: A retrospective analysis was conducted in patients with breast cancer (BC) and gynecological malignancies referred to our center's MTB from 2018 to 2023. The analysis covered patient characteristics, next-generation sequencing (NGS) results, MTB recommendations, therapy received, and clinical outcomes. Results: Sixty-three patients (77.8%) had metastatic disease, and forty-four patients (54.3%) had previously undergone three or more lines of systemic treatment. Personalized treatment recommendations were provided to 50 patients (63.3%), while 29 (36.7%) had no actionable target. Ultimately, 23 patients (29.1%) underwent molecular-matched treatment (MMT). Commonly altered genes in patients with pan-gyn tumors (BC and gynecological malignancies) included TP53 (n = 42/81, 51.9%), PIK3CA (n = 18/81, 22.2%), BRCA1/2 (n = 10/81, 12.3%), and ARID1A (n = 9/81, 11.1%). Patients treated with MMT showed significantly prolonged progression-free survival (median PFS 5.5 vs. 3.5 months, p = 0.0014). Of all patients who underwent molecular profiling, 13.6% experienced a major clinical benefit (PFSr ≥ 1.3 and PR/SD ≥ 6 months) through precision oncology. Conclusions: NGS-guided precision oncology demonstrated improved clinical outcomes in a subgroup of patients with gynecological and breast cancers.
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Affiliation(s)
- Niklas Gremke
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Fiona R. Rodepeter
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Julia Teply-Szymanski
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Sebastian Griewing
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Jelena Boekhoff
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Alina Stroh
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas S. Tarawneh
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Jorge Riera-Knorrenschild
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Christina Balser
- Practice for Internal Medicine, Hematology and Internal Oncology, 35043 Marburg, Germany;
| | - Akira Hattesohl
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Martin Middeke
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Petra Ross
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Anne-Sophie Litmeyer
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Marcel Romey
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Thorsten Stiewe
- Institute of Molecular Oncology, Philipps-University, 35043 Marburg, Germany;
| | - Thomas Wündisch
- Comprehensive Cancer Center Marburg, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (M.M.); (T.W.)
| | - Andreas Neubauer
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
| | - Carsten Denkert
- Institute of Pathology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (F.R.R.); (J.T.-S.); (A.H.); (A.-S.L.); (M.R.); (C.D.)
| | - Uwe Wagner
- Department of Gynecology, Gynecological Endocrinology and Oncology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (S.G.); (J.B.); (A.S.); (U.W.)
| | - Elisabeth K. M. Mack
- Department of Hematology, Oncology and Immunology, University Hospital Gießen and Marburg Campus Marburg, Philipps-University, 35043 Marburg, Germany; (T.S.T.); (J.R.-K.); (P.R.); (A.N.); (E.K.M.M.)
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Mahdiani H, Münch N, Paul NW. A QALY is [still] a QALY is [still] a QALY? : Evaluating proportional shortfall as the answer to the problem of equity in healthcare allocations. BMC Med Ethics 2024; 25:35. [PMID: 38521941 PMCID: PMC10960401 DOI: 10.1186/s12910-024-01036-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: 09/19/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
Despite clinical evidence of drug superiority, therapeutic modalities, like combination immunotherapy, are mostly considered cost-ineffective due to their high costs per life year(s) gained. This paper, taking an ethical stand, reevaluates the standard cost-effectiveness analysis with that of the more recent justice-enhanced methods and concludes by pointing out the shortcomings of the current methodologies.
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Affiliation(s)
- Hamideh Mahdiani
- Institute for History, Philosophy and Ethics of Medicine, Johannes Gutenberg University Medical Center, Am Pulverturm 13, 55131, Mainz, Germany.
| | - Nikolai Münch
- Institute for History, Philosophy and Ethics of Medicine, Johannes Gutenberg University Medical Center, Am Pulverturm 13, 55131, Mainz, Germany
| | - Norbert W Paul
- Institute for History, Philosophy and Ethics of Medicine, Johannes Gutenberg University Medical Center, Am Pulverturm 13, 55131, Mainz, Germany
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9
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Brlek P, Bulić L, Bračić M, Projić P, Škaro V, Shah N, Shah P, Primorac D. Implementing Whole Genome Sequencing (WGS) in Clinical Practice: Advantages, Challenges, and Future Perspectives. Cells 2024; 13:504. [PMID: 38534348 DOI: 10.3390/cells13060504] [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: 02/06/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
The integration of whole genome sequencing (WGS) into all aspects of modern medicine represents the next step in the evolution of healthcare. Using this technology, scientists and physicians can observe the entire human genome comprehensively, generating a plethora of new sequencing data. Modern computational analysis entails advanced algorithms for variant detection, as well as complex models for classification. Data science and machine learning play a crucial role in the processing and interpretation of results, using enormous databases and statistics to discover new and support current genotype-phenotype correlations. In clinical practice, this technology has greatly enabled the development of personalized medicine, approaching each patient individually and in accordance with their genetic and biochemical profile. The most propulsive areas include rare disease genomics, oncogenomics, pharmacogenomics, neonatal screening, and infectious disease genomics. Another crucial application of WGS lies in the field of multi-omics, working towards the complete integration of human biomolecular data. Further technological development of sequencing technologies has led to the birth of third and fourth-generation sequencing, which include long-read sequencing, single-cell genomics, and nanopore sequencing. These technologies, alongside their continued implementation into medical research and practice, show great promise for the future of the field of medicine.
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Affiliation(s)
- Petar Brlek
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Luka Bulić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Matea Bračić
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
| | - Petar Projić
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
| | | | - Nidhi Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Parth Shah
- Dartmouth Hitchcock Medical Center, Lebannon, NH 03766, USA
| | - Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- International Center for Applied Biological Research, 10000 Zagreb, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Eberly College of Science, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- REGIOMED Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Mostar, 88000 Mostar, Bosnia and Herzegovina
- National Forensic Sciences University, Gujarat 382007, India
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10
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Fielding D, Lakis V, Dalley AJ, Chittoory H, Newell F, Koufariotis LT, Patch AM, Kazakoff S, Bashirzadeh F, Son JH, Ryan K, Steinfort D, Williamson JP, Bint M, Pahoff C, Nguyen PT, Twaddell S, Arnold D, Grainge C, Pattison A, Fairbairn D, Gune S, Christie J, Holmes O, Leonard C, Wood S, Pearson JV, Lakhani SR, Waddell N, Simpson PT, Nones K. Evaluation of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration (EBUS-TBNA) Samples from Advanced Non-Small Cell Lung Cancer for Whole Genome, Whole Exome and Comprehensive Panel Sequencing. Cancers (Basel) 2024; 16:785. [PMID: 38398180 PMCID: PMC10887389 DOI: 10.3390/cancers16040785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/04/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is often the only source of tumor tissue from patients with advanced, inoperable lung cancer. EBUS-TBNA aspirates are used for the diagnosis, staging, and genomic testing to inform therapy options. Here we extracted DNA and RNA from 220 EBUS-TBNA aspirates to evaluate their suitability for whole genome (WGS), whole exome (WES), and comprehensive panel sequencing. For a subset of 40 cases, the same nucleic acid extraction was sequenced using WGS, WES, and the TruSight Oncology 500 assay. Genomic features were compared between sequencing platforms and compared with those reported by clinical testing. A total of 204 aspirates (92.7%) had sufficient DNA (100 ng) for comprehensive panel sequencing, and 109 aspirates (49.5%) had sufficient material for WGS. Comprehensive sequencing platforms detected all seven clinically reported tier 1 actionable mutations, an additional three (7%) tier 1 mutations, six (15%) tier 2-3 mutations, and biomarkers of potential immunotherapy benefit (tumor mutation burden and microsatellite instability). As expected, WGS was more suited for the detection and discovery of emerging novel biomarkers of treatment response. WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.
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Affiliation(s)
- David Fielding
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Andrew J. Dalley
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Haarika Chittoory
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Lambros T. Koufariotis
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Ann-Marie Patch
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Farzad Bashirzadeh
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Jung Hwa Son
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Kimberley Ryan
- Department of Thoracic Medicine, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia; (F.B.); (J.H.S.); (K.R.)
| | - Daniel Steinfort
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Jonathan P. Williamson
- Department of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, NSW 2170, Australia;
| | - Michael Bint
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - Carl Pahoff
- Department of Thoracic Medicine, Gold Coast University Hospital, Southport, QLD 4215, Australia;
| | - Phan Tien Nguyen
- Department of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, SA 5000, Australia;
| | - Scott Twaddell
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - David Arnold
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Christopher Grainge
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW 2305, Australia; (S.T.); (D.A.); (C.G.)
| | - Andrew Pattison
- Department of Respiratory and Sleep Medicine, Sunshine Coast University Hospital, Birtinya, QLD 4575, Australia; (M.B.); (A.P.)
| | - David Fairbairn
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Shailendra Gune
- NSW Health Pathology South, Liverpool Hospital, Sydney, NSW 2170, Australia;
| | - Jemma Christie
- Department of Respiratory and Sleep Medicine, Royal Melbourne Hospital, Melbourne, VIC 3050, Australia; (D.S.); (J.C.)
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - John V. Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Sunil R. Lakhani
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
- Pathology Queensland, The Royal Brisbane & Women’s Hospital, Brisbane, QLD 4006, Australia;
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
| | - Peter T. Simpson
- UQ Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Brisbane, QLD 4029, Australia; (A.J.D.); (H.C.); (S.R.L.); (P.T.S.)
| | - Katia Nones
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; (V.L.); (F.N.); (L.T.K.); (A.-M.P.); (S.K.); (O.H.); (C.L.); (S.W.); (J.V.P.); (N.W.); (K.N.)
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4067, Australia
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Stafylidis C, Vlachopoulou D, Kontandreopoulou CN, Diamantopoulos PΤ. Unmet Horizons: Assessing the Challenges in the Treatment of TP53-Mutated Acute Myeloid Leukemia. J Clin Med 2024; 13:1082. [PMID: 38398394 PMCID: PMC10889132 DOI: 10.3390/jcm13041082] [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: 12/27/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Acute myeloid leukemia (AML) remains a challenging hematologic malignancy. The presence of TP53 mutations in AML poses a therapeutic challenge, considering that standard treatments face significant setbacks in achieving meaningful responses. There is a pressing need for the development of innovative treatment modalities to overcome resistance to conventional treatments attributable to the unique biology of TP53-mutated (TP53mut) AML. This review underscores the role of TP53 mutations in AML, examines the current landscape of treatment options, and highlights novel therapeutic approaches, including targeted therapies, combination regimens, and emerging immunotherapies, as well as agents being explored in preclinical studies according to their potential to address the unique hurdles posed by TP53mut AML.
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Affiliation(s)
| | | | | | - Panagiotis Τ. Diamantopoulos
- Hematology Unit, First Department of Internal Medicine, Laikon General Hospital, National and Kapodistrian University of Athens, 11527 Athens, Greece; (C.S.); (D.V.); (C.-N.K.)
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Iacobucci G. Whole genome sequencing can help guide cancer care, study reports. BMJ 2024; 384:q65. [PMID: 38212052 DOI: 10.1136/bmj.q65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
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13
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Akhoundova D, Rubin MA. The grand challenge of moving cancer whole-genome sequencing into the clinic. Nat Med 2024; 30:39-40. [PMID: 38200256 DOI: 10.1038/s41591-023-02697-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Affiliation(s)
- Dilara Akhoundova
- Department for BioMedical Research, University of Bern, Bern, Switzerland
- Department of Medical Oncology, Inselspital, University Hospital of Bern, Bern, Switzerland
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland
| | - Mark A Rubin
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- Bern Center for Precision Medicine, Inselspital, University Hospital of Bern, Bern, Switzerland.
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