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Hamdi Y, Trabelsi M, Ghedira K, Boujemaa M, Ben Ayed I, Charfeddine C, Souissi A, Rejeb I, Kammoun Rebai W, Hkimi C, Neifar F, Jandoubi N, Mkaouar R, Chaouch M, Bennour A, Kamoun S, Chaker Masmoudi H, Abid N, Mezghani Khemakhem M, Masmoudi S, Saad A, BenJemaa L, BenKahla A, Boubaker S, Mrad R, Kamoun H, Abdelhak S, Gribaa M, Belguith N, Kharrat N, Hmida D, Rebai A. Genome Tunisia Project: paving the way for precision medicine in North Africa. Genome Med 2024; 16:104. [PMID: 39187811 PMCID: PMC11348534 DOI: 10.1186/s13073-024-01365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 07/16/2024] [Indexed: 08/28/2024] Open
Abstract
BACKGROUND Key discoveries and innovations in the field of human genetics have led to the foundation of molecular and personalized medicine. Here, we present the Genome Tunisia Project, a two-phased initiative (2022-2035) which aims to deliver the reference sequence of the Tunisian Genome and to support the implementation of personalized medicine in Tunisia, a North African country that represents a central hub of population admixture and human migration between African, European, and Asian populations. The main goal of this initiative is to develop a healthcare system capable of incorporating omics data for use in routine medical practice, enabling medical doctors to better prevent, diagnose, and treat patients. METHODS A multidisciplinary partnership involving Tunisian experts from different institutions has come to discern all requirements that would be of high priority to fulfill the project's goals. One of the most urgent priorities is to determine the reference sequence of the Tunisian Genome. In addition, extensive situation analysis and revision of the education programs, community awareness, appropriate infrastructure including sequencing platforms and biobanking, as well as ethical and regulatory frameworks, have been undertaken towards building sufficient capacity to integrate personalized medicine into the Tunisian healthcare system. RESULTS In the framework of this project, an ecosystem with all engaged stakeholders has been implemented including healthcare providers, clinicians, researchers, pharmacists, bioinformaticians, industry, policymakers, and advocacy groups. This initiative will also help to reinforce research and innovation capacities in the field of genomics and to strengthen discoverability in the health sector. CONCLUSIONS Genome Tunisia is the first initiative in North Africa that seeks to demonstrate the major impact that can be achieved by Human Genome Projects in low- and middle-income countries to strengthen research and to improve disease management and treatment outcomes, thereby reducing the social and economic burden on healthcare systems. Sharing this experience within the African scientific community is a chance to turn a major challenge into an opportunity for dissemination and outreach. Additional efforts are now being made to advance personalized medicine in patient care by educating consumers and providers, accelerating research and innovation, and supporting necessary changes in policy and regulation.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia.
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia.
| | - Mediha Trabelsi
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Kais Ghedira
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Maroua Boujemaa
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Ikhlas Ben Ayed
- Department of Medical Genetics, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Cherine Charfeddine
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, BiotechPole of Sidi Thabet, University of Manouba, Ariana, Tunisia
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Imen Rejeb
- Department of Congenital and Hereditary Diseases, Mongi Slim University Hospital, Sidi Daoud La Marsa, Tunis, Tunisia
- Santé Mère-Enfant (LR22SP01), Tunis, Tunisia
| | - Wafa Kammoun Rebai
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Chaima Hkimi
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fadoua Neifar
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nouha Jandoubi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Rahma Mkaouar
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
| | - Melek Chaouch
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ayda Bennour
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Selim Kamoun
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hend Chaker Masmoudi
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Histology and Cytogenetics, Institute Pasteur of Tunis, Tunis, Tunisia
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances LR99ES27, Faculty of Pharmacy, University of Monastir, Ibn Sina Street, Monastir, 5000, Tunisia
| | - Maha Mezghani Khemakhem
- Laboratory of Biochemistry and Biotechnology (LR01ES05), Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, 1068, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ali Saad
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Lamia BenJemaa
- Department of Congenital and Hereditary Diseases, Mongi Slim University Hospital, Sidi Daoud La Marsa, Tunis, Tunisia
- Santé Mère-Enfant (LR22SP01), Tunis, Tunisia
| | - Alia BenKahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics, Institut Pasteur de Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Samir Boubaker
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Laboratory of Human and Experimental Pathology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ridha Mrad
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Genetics, Faculty of Medicine of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Hassen Kamoun
- Department of Medical Genetics, Hedi Chaker University Hospital, University of Sfax, Sfax, Tunisia
- Laboratory of Human Molecular Genetics, LR99ES33, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Sonia Abdelhak
- Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Institut Pasteur de Tunis, University of Tunis El Manar, 13, place Pasteur, B.P. 74, Tunis, Belvédère, 1002, Tunisia
- Communication, Science and Society Support Unit (UniSS), Institut Pasteur de Tunis, Tunis, Tunisia
| | - Moez Gribaa
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Neila Belguith
- Department of Congenital and Hereditary Diseases, Charles Nicolle Hospital, Tunis, University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Human Molecular Genetics, LR99ES33, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Dorra Hmida
- Faculty of Medicine, University of Sousse, Sousse, Tunisia
- Department of Genetics, Farhat HACHED University Hospital, Sousse, Tunisia
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
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Opoku KB, Santiago T, Kumar P, Roush SM, Fedoriw Y, Tomoka T, Leventaki V, Furtado LV, Bhakta N, Alexander TB, Wang JR. Transcriptome profiling of pediatric extracranial solid tumors and lymphomas enables rapid low-cost diagnostic classification. Sci Rep 2024; 14:19456. [PMID: 39169157 PMCID: PMC11339337 DOI: 10.1038/s41598-024-70541-0] [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: 02/09/2024] [Accepted: 08/18/2024] [Indexed: 08/23/2024] Open
Abstract
Approximately 80% of pediatric tumors occur in low- and middle-income countries (LMIC), where diagnostic tools essential for treatment decisions are often unavailable or incomplete. Development of cost-effective molecular diagnostics will help bridge the cancer diagnostic gap and ultimately improve pediatric cancer outcomes in LMIC settings. We investigated the feasibility of using nanopore whole transcriptome sequencing on formalin-fixed paraffin embedded (FFPE)-derived RNA and a composite machine learning model for pediatric solid tumor diagnosis. Transcriptome cDNA sequencing was performed on a heterogenous set of 221 FFPE and 32 fresh frozen pediatric solid tumor and lymphoma specimens on Oxford Nanopore Technologies' sequencing platforms. A composite machine learning model was then used to classify transcriptional profiles into clinically actionable tumor types and subtypes. In total, 95.6% and 89.7% of pediatric solid tumors and lymphoma specimens were correctly classified, respectively. 71.5% of pediatric solid tumors had prediction probabilities > 0.8 and were classified with 100% accuracy. Similarly, for lymphomas, 72.4% of samples that had prediction probabilities > 0.6 were classified with 97.6% accuracy. Additionally, FOXO1 fusion status was predicted accurately for 97.4% of rhabdomyosarcomas and MYCN amplification was predicted with 88% accuracy in neuroblastoma. Whole transcriptome sequencing from FFPE-derived pediatric solid tumor and lymphoma samples has the potential to provide clinical classification of both tissue lineage and core genomic classification. Further expansion, refinement, and validation of this approach is necessary to explore whether this technology could be part of the solution of addressing the diagnostic limitations in LMIC.
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Affiliation(s)
- Kofi B Opoku
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Teresa Santiago
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, USA
| | - Priya Kumar
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, USA
| | - Sophia M Roush
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Yuri Fedoriw
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Tamiwe Tomoka
- University of Malawi College of Medicine, Blantyre, Malawi
- University of North Carolina at Chapel Hill, Chapel Hill, USA
- UNC Project Malawi, Lilongwe, Malawi
| | - Vasiliki Leventaki
- Department of Hematopathology, University of Texas MD Anderson Cancer Center, Houston, USA
| | - Larissa V Furtado
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, USA
| | - Nickhill Bhakta
- Department of Global Pediatric Medicine, St. Jude Children's Research Hospital, Memphis, USA
| | - Thomas B Alexander
- Department of Pediatrics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - Jeremy R Wang
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, USA.
- Department of Pathology and Laboratory Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, USA.
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Gallon R, Herrero-Belmonte P, Phelps R, Hayes C, Sollars E, Egan D, Spiewak H, Nalty S, Mills S, Loo PS, Borthwick GM, Santibanez-Koref M, Burn J, McAnulty C, Jackson MS. A novel colorectal cancer test combining microsatellite instability and BRAF/RAS analysis: Clinical validation and impact on Lynch syndrome screening. BJC REPORTS 2024; 2:48. [PMID: 38962168 PMCID: PMC11216981 DOI: 10.1038/s44276-024-00072-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 07/05/2024]
Abstract
Background Lynch syndrome (LS) is under-diagnosed. UK National Institute for Health and Care Excellence guidelines recommend multistep molecular testing of all colorectal cancers (CRCs) to screen for LS. However, the complexity of the pathway has resulted in limited improvement in diagnosis. Methods One-step multiplex PCR was used to generate sequencing-ready amplicons from 14 microsatellite instability (MSI) markers and 22 BRAF, KRAS, and NRAS mutation hotspots. MSI and BRAF/RAS variants were detected using amplicon-sequencing and automated analysis. The assay was clinically validated and deployed into service in northern England, followed by regional and local audits to assess its impact. Results MSI analysis achieved 99.1% sensitivity and 99.2% specificity and was reproducible (r = 0.995). Mutation hotspot analysis had 100% sensitivity, 99.9% specificity, and was reproducible (r = 0.998). Assay-use in service in 2022-2023 increased CRC testing (97.2% (2466/2536) versus 28.6% (601/2104)), halved turnaround times, and identified more CRC patients at-risk of LS (5.5% (139/2536) versus 2.9% (61/2104)) compared to 2019-2020 when a multi-test pathway was used. Conclusion A novel amplicon-sequencing assay of CRCs, including all biomarkers for LS screening and anti-EGFR therapy, achieved >95% testing rate. Adoption of this low cost, scalable, and fully automatable test will complement on-going, national initiatives to improve LS screening.
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Affiliation(s)
- Richard Gallon
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patricia Herrero-Belmonte
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Rachel Phelps
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Christine Hayes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elizabeth Sollars
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Daniel Egan
- North East and Yorkshire Genomic Laboratory Hub Central Lab, St James’s University Hospital, Leeds, UK
| | - Helena Spiewak
- North East and Yorkshire Genomic Laboratory Hub Central Lab, St James’s University Hospital, Leeds, UK
| | - Sam Nalty
- Sheffield Diagnostic Genetics Service, North East and Yorkshire Genomic Laboratory Hub, Sheffield Children’s NHS Foundation Trust, Sheffield, UK
| | - Sarah Mills
- Northumbria Healthcare NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Peh Sun Loo
- Department of Cellular Pathology, Royal Victoria Infirmary, The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gillian M. Borthwick
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mauro Santibanez-Koref
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - John Burn
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Ciaron McAnulty
- Northern Genetics Service, The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael S. Jackson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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Bayle A, Marino P, Baffert S, Margier J, Bonastre J. [Cost of high-throughput sequencing (NGS) technologies: Literature review and insights]. Bull Cancer 2024; 111:190-198. [PMID: 37852801 DOI: 10.1016/j.bulcan.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 08/02/2023] [Accepted: 08/28/2023] [Indexed: 10/20/2023]
Abstract
Although high-throughput sequencing technologies (Next-Generation Sequencing [NGS]) are revolutionizing medicine, the estimation of their production cost for pricing/tariffication by health systems raises methodological questions. The objective of this review of cost studies of high-throughput sequencing techniques is to draw lessons for producing robust cost estimates of these techniques. We analyzed, using an eleven item analysis framework, micro-costing studies of high-throughput sequencing technologies (n=17), including two studies conducted in the French context. The factors of variability between the studies that we identified were temporality (early evaluation of the innovation vs. evaluation of a mature technology), the choice of cost evaluation method (scope, micro- vs. gross-costing technique), the choice of production steps observed and the transposability of these studies. The lessons we have learned are that it is necessary to have a comprehensive vision of the sequencing production process by integrating all the steps from the collection of the biological sample to the delivery of the result to the clinician. It is also important to distinguish between what refers to the local context and what refers to the general context, by favouring the use of mixed methods to calculate costs. Finally, sensitivity analyses and periodic re-estimation of the costs of the techniques must be carried out in order to be able to revise the tariffs according to changes linked to the diffusion of the technology and to competition between reagent suppliers.
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Affiliation(s)
- Arnaud Bayle
- Gustave-Roussy, université Paris-Saclay, bureau biostatistique et épidémiologie, Villejuif, France; Inserm, université Paris-Saclay, CESP U1018 Oncostat, labelisé Ligue contre le cancer, Villejuif, France.
| | - Patricia Marino
- Institut Paoli-Calmettes, SESSTIM, équipe CAN-BIOS, Marseille, France
| | | | - Jennifer Margier
- Hospices civils de Lyon, service d'évaluation économique en santé (SEES), Lyon, France
| | - Julia Bonastre
- Gustave-Roussy, université Paris-Saclay, bureau biostatistique et épidémiologie, Villejuif, France; Inserm, université Paris-Saclay, CESP U1018 Oncostat, labelisé Ligue contre le cancer, Villejuif, France
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Mudau MM, Seymour H, Nevondwe P, Kerr R, Spencer C, Feben C, Lombard Z, Honey E, Krause A, Carstens N. A feasible molecular diagnostic strategy for rare genetic disorders within resource-constrained environments. J Community Genet 2024; 15:39-48. [PMID: 37815686 PMCID: PMC10858011 DOI: 10.1007/s12687-023-00674-8] [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: 02/03/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023] Open
Abstract
Timely and accurate diagnosis of rare genetic disorders is critical, as it enables improved patient management and prognosis. In a resource-constrained environment such as the South African State healthcare system, the challenge is to design appropriate and cost-effective assays that will enable accurate genetic diagnostic services in patients of African ancestry across a broad disease spectrum. Next-generation sequencing (NGS) has transformed testing approaches for many Mendelian disorders, but this technology is still relatively new in our setting and requires cost-effective ways to implement. As a proof of concept, we describe a feasible diagnostic strategy for genetic disorders frequently seen in our genetics clinics (RASopathies, Cornelia de Lange syndrome, Treacher Collins syndrome, and CHARGE syndrome). The custom-designed targeted NGS gene panel enabled concurrent variant screening for these disorders. Samples were batched during sequencing and analyzed selectively based on the clinical phenotype. The strategy employed in the current study was cost-effective, with sequencing and analysis done at USD849.68 per sample and achieving an overall detection rate of 54.5%. The strategy employed is cost-effective as it allows batching of samples from patients with different diseases in a single run, an approach that can be utilized with rare and less frequently ordered molecular diagnostic tests. The subsequent selective analysis pipeline allowed for timeous reporting back of patients results. This is feasible with a reasonable yield and can be employed for the molecular diagnosis of a wide range of rare monogenic disorders in a resource-constrained environment.
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Affiliation(s)
- Maria Mabyalwa Mudau
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Heather Seymour
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Patracia Nevondwe
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Robyn Kerr
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Careni Spencer
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Candice Feben
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Engela Honey
- Department of Biochemistry, Genetics and Microbiology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nadia Carstens
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Genomics Platform, South African Medical Research Council, Cape Town, South Africa
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Thangavelu T, Wirta V, Orsmark-Pietras C, Cavelier L, Fioretos T, Barbany G, Olsson-Arvidsson L, Pandzic T, Staffas A, Rosenquist R, Levin LÅ. Micro-costing of genetic diagnostics in acute leukemia in Sweden: from standard-of-care to whole-genome sequencing. J Med Econ 2024; 27:1053-1060. [PMID: 39101813 DOI: 10.1080/13696998.2024.2387515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/06/2024]
Abstract
AIMS AND BACKGROUND Whole-genome sequencing (WGS) is increasingly applied in clinical practice and expected to replace standard-of-care (SoC) genetic diagnostics in hematological malignancies. This study aims to assess and compare the fully burdened cost ('micro-costing') per patient for Swedish laboratories using WGS and SoC, respectively, in pediatric and adult patients with acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). METHODS The resource use and cost details associated with SoC, e.g. chromosome banding analysis, fluorescent in situ hybridization, and targeted sequencing analysis, were collected via activity-based costing methods from four diagnostic laboratories. For WGS, corresponding data was collected from two of the centers. A simulation-based scenario model was developed for analyzing the WGS cost based on different annual sample throughput to evaluate economy of scale. RESULTS The average SoC total cost per patient was €2,465 for pediatric AML and €2,201 for pediatric ALL, while in adults, the corresponding cost was €2,458 for AML and €1,207 for ALL. The average WGS cost (90x tumor/30x normal; sequenced on the Illumina NovaSeq 6000 platform) was estimated to €3,472 based on an annual throughput of 2,500 analyses, however, with an annual volume of 7,500 analyses the average cost would decrease by 23% to €2,671. CONCLUSION In summary, WGS is currently more costly than SoC, however the cost can be reduced by utilizing laboratories with higher throughput and by the expected decline in cost of reagents. Our data provides guidance to decision-makers for the resource allocation needed when implementing WGS in diagnostics of hematological malignancies.
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Affiliation(s)
- Tharshini Thangavelu
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
- Department of Register and Statistics, The National Board of Health and Welfare, Stockholm, Sweden
| | - Valtteri Wirta
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, School of Engineering Sciences in Chemistry Biotechnology and Health, KTH Royal Instititute of Technology, Stockholm, Sweden
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - Christina Orsmark-Pietras
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Lucia Cavelier
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Gisela Barbany
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Linda Olsson-Arvidsson
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Pathology, and Molecular Diagnostics, Office for Medical Services, Lund, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Staffas
- Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Richard Rosenquist
- Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Lars-Åke Levin
- Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
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Chen H, Wang B, Zhang Y, Shu Y, Dong H, Zhao Q, Yang C, Li J, Duan X, Zhou Q. A unified DNA- and RNA-based NGS strategy for the analysis of multiple types of variants at the dual nucleic acid level in solid tumors. J Clin Lab Anal 2023; 37:e24977. [PMID: 37877443 PMCID: PMC10681543 DOI: 10.1002/jcla.24977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/27/2023] [Accepted: 10/15/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is a powerful and suitable approach to comprehensively identify multiple types of variants in tumors. RNA-based NGS is increasingly playing an important role in precision oncology. Both parallel and sequential DNA- and RNA-based approaches are expensive, burdensome, and have long turnaround times, which can be impractical in clinical practice. A streamlined, unified DNA- and RNA-based NGS approach is urgently needed in clinical practice. METHODS A DNA/RNA co-hybrid capture sequencing (DRCC-Seq) approach was designed to capture pre-capture DNA and RNA libraries in a single tube and convert them into one NGS library. The performance of the DRCC-Seq approach was evaluated by a panel of reference standards and clinical samples. RESULTS The average depth, DNA data ratio, capture ratio, and target coverage 250 (×) of the DNA panel data had a negative correlation with an increase in the proportion of RNA probes. The SNVs, indels, fusions, and MSI status were not affected by the proportion of RNA probes, but the copy numbers of the target genes were higher than expected in the standard materials, and many unexpected gene amplifications were found using D:R (1:2) and D:R (1:4) probe panels. The optimal ratio of DNA and RNA probes in the combined probe panel was 1:1 using the DRCC-Seq approach. The DRCC-Seq approach was feasible and reliable for detecting multiple types of variants in reference standards and real-world clinical samples. CONCLUSIONS The DRCC-Seq approach is more cost-effective, with a shorter turnaround time and lower labor requirements than either parallel or sequential targeted DNA NGS and RNA NGS. It is feasible to identify multiple genetic variations at the DNA and RNA levels simultaneously in clinical practice.
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Affiliation(s)
- Huijuan Chen
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- Computer Network Information Center, Chinese Academy of SciencesBeijingChina
- WillingMed Technology Beijing Co., Ltd.BeijingChina
| | - Bing Wang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yiran Zhang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Yingshuang Shu
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Henan Dong
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Qian Zhao
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Chunyan Yang
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Jianji Li
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
| | - Xiaohong Duan
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
- Institute of Disaster and Emergency Medicine, Medical CollegeTianjin UniversityTianJinChina
| | - Qiming Zhou
- ChosenMed Clinical Laboratory (Beijing) Co. Ltd.BeijingChina
- ChosenMed Technology (Zhejiang) Co. Ltd.ZhejiangChina
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8
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Kinoo A, Caye-Eude A, Vial Y, Cavé H, Arfeuille C. Partitioning for Easy Multiplexing: A Versatile Droplet PCR Application for Clone Monitoring in Tumors. J Mol Diagn 2023; 25:592-601. [PMID: 37302461 DOI: 10.1016/j.jmoldx.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/04/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023] Open
Abstract
Clinical genome-wide next-generation sequencing (NGS) has brought new challenges to genetic laboratories. The identification of numerous patient-specific variants that may require to be screened for on multiple other samples poses an issue when striving for time and cost-effectiveness. Here, we propose d-multiSeq, a straightforward method utilizing the advantages of droplet PCR for multiplexing combined with amplicon-based NGS. By comparing d-multiSeq with a standard multiplex amplicon-based NGS, it was shown that partitioning prevents the amplification competition seen when multiplexing and leads to a homogeneous representation of each target in the total read count for up to a 40-target multiplex without the need for prior adjustment. Variant allele frequency was reliably evaluated with a sensitivity of 97.6% for variant allele frequency up to 1%. The applicability of d-multiSeq was also tested on cell-free DNA with the successful amplification of an eight-target multiplex panel. Preliminary application of the technique to assess the clonal evolution in a childhood leukemia harboring high interpatient variability in its somatic variants is shown. d-multiSeq represents a turnkey solution for analyzing large sets of patient-specific variants on low DNA amounts and cell-free DNA.
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Affiliation(s)
- Alexia Kinoo
- Molecular Genetics Unit, Genetics Department, Assistance Publique des Hôpitaux de Paris, Hôpital Robert Debré, Paris, France
| | - Aurélie Caye-Eude
- Molecular Genetics Unit, Genetics Department, Assistance Publique des Hôpitaux de Paris, Hôpital Robert Debré, Paris, France; INSERM Unité Mixte de Recherche (UMR)_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Yoann Vial
- Molecular Genetics Unit, Genetics Department, Assistance Publique des Hôpitaux de Paris, Hôpital Robert Debré, Paris, France; INSERM Unité Mixte de Recherche (UMR)_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Hélène Cavé
- Molecular Genetics Unit, Genetics Department, Assistance Publique des Hôpitaux de Paris, Hôpital Robert Debré, Paris, France; INSERM Unité Mixte de Recherche (UMR)_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France
| | - Chloé Arfeuille
- Molecular Genetics Unit, Genetics Department, Assistance Publique des Hôpitaux de Paris, Hôpital Robert Debré, Paris, France; INSERM Unité Mixte de Recherche (UMR)_S1131, Institut de Recherche Saint-Louis, Université de Paris-Cité, Paris, France.
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9
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Vingiani A, Agnelli L, Duca M, Lorenzini D, Damian S, Proto C, Niger M, Nichetti F, Tamborini E, Perrone F, Piccolo A, Manoukian S, Azzollini J, Brambilla M, Colombo E, Lopez S, Vernieri C, Marra F, Conca E, Busico A, Capone I, Bozzi F, Angelini M, Devecchi A, Salvatori R, De Micheli V, Baggi A, Pasini S, Jommi C, Ladisa V, Apolone G, De Braud F, Pruneri G. Molecular Tumor Board as a Clinical Tool for Converting Molecular Data Into Real-World Patient Care. JCO Precis Oncol 2023; 7:e2300067. [PMID: 37487147 PMCID: PMC10581623 DOI: 10.1200/po.23.00067] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/28/2023] [Accepted: 06/12/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE The investigation of multiple molecular targets with next-generation sequencing (NGS) has entered clinical practice in oncology, yielding to a paradigm shift from the histology-centric approach to the mutational model for personalized treatment. Accordingly, most of the drugs recently approved in oncology are coupled to specific biomarkers. One potential tool for implementing the mutational model of precision oncology in daily practice is represented by the Molecular Tumor Board (MTB), a multidisciplinary team whereby molecular pathologists, biologists, bioinformaticians, geneticists, medical oncologists, and pharmacists cooperate to generate, interpret, and match molecular data with personalized treatments. PATIENTS AND METHODS Since May 2020, the institutional MTB set at Fondazione IRCCS Istituto Nazionale Tumori of Milan met weekly via teleconference to discuss molecular data and potential therapeutic options for patients with advanced/metastatic solid tumors. RESULTS Up to October 2021, among 1,996 patients evaluated, we identified >10,000 variants, 43.2% of which were functionally relevant (pathogenic or likely pathogenic). On the basis of functionally relevant variants, 711 patients (35.6%) were potentially eligible to targeted therapy according to European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets tiers, and 9.4% received a personalized treatment. Overall, larger NGS panels (containing >50 genes) significantly outperformed small panels (up to 50 genes) in detecting actionable gene targets across different tumor types. CONCLUSION Our real-world data provide evidence that MTB is a valuable tool for matching NGS data with targeted treatments, eventually implementing precision oncology in clinical practice.
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Affiliation(s)
- Andrea Vingiani
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Luca Agnelli
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Matteo Duca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Daniele Lorenzini
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Silvia Damian
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Claudia Proto
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Monica Niger
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Federico Nichetti
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
- Computational Oncology Group, Molecular Precision Oncology Program, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elena Tamborini
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Federica Perrone
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Alberta Piccolo
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Siranoush Manoukian
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Jacopo Azzollini
- Unit of Medical Genetics, Department of Medical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Marta Brambilla
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Elena Colombo
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Salvatore Lopez
- Gynecologic Oncology, Department of Surgery, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Claudio Vernieri
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
- IFOM ETS, The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Francesca Marra
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Conca
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Adele Busico
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Iolanda Capone
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Fabio Bozzi
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Marta Angelini
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Devecchi
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Rebecca Salvatori
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | - Anna Baggi
- Business Integration Partners S.p.A., Milan, Italy
| | | | - Claudio Jommi
- Department of Pharmaceutical Sciences, Università del Piemonte Orientale, Novara, Italy
| | - Vito Ladisa
- Hospital Pharmacy, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giovanni Apolone
- Scientific Directorate, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Filippo De Braud
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Giancarlo Pruneri
- Department of Diagnostic Innovation, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
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10
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Soilly AL, Robert-Viard C, Besse C, Bruel AL, Gerard B, Boland A, Piton A, Duffourd Y, Muller J, Poë C, Jouan T, El Doueiri S, Faivre L, Bacq-Daian D, Isidor B, Genevieve D, Odent S, Philip N, Doco-Fenzy M, Lacombe D, Asensio ML, Deleuze JF, Binquet C, Thauvin-Robinet C, Lejeune C. Cost of exome analysis in patients with intellectual disability: a micro-costing study in a French setting. BMC Health Serv Res 2023; 23:386. [PMID: 37085862 PMCID: PMC10120135 DOI: 10.1186/s12913-023-09373-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 04/04/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND With the development of next generation sequencing technologies in France, exome sequencing (ES) has recently emerged as an opportunity to improve the diagnosis rate of patients presenting an intellectual disability (ID). To help French policy makers determine an adequate tariff for ES, we aimed to assess the unit cost per ES diagnostic test for ID from the preparation of the pre-analytical step until the report writing step and to identify its main cost drivers. METHODS A micro-costing bottom-up approach was conducted for the year 2018 in a French setting as part of the DISSEQ study, a cost-effectiveness study funded by the Ministry of Health and performed in collaboration with the GAD (Génétique des Anomalies du Développement), a genetic team from the Dijon University Hospital, and a public sequencing platform, the Centre National de Recherche en Génomique Humaine (CNRGH). The analysis was conducted from the point of view of these two ES stakeholders. All of the resources (labor, equipment, disposables and reagents, reusable material) required to analyze blood samples were identified, collected and valued. Several sensitivity analyses were performed. RESULTS The unit nominal cost per ES diagnostic test for ID was estimated to be €2,019.39. Labor represented 50.7% of the total cost. The analytical step (from the preparation of libraries to the analysis of sequences) represented 88% of the total cost. Sensitivity analyses suggested that a simultaneous price decrease of 20% for the capture kit and 50% for the sequencing support kit led to an estimation of €1,769 per ES diagnostic test for ID. CONCLUSION This is the first estimation of ES cost to be done in the French setting of ID diagnosis. The estimation is especially influenced by the price of equipment kits, but more generally by the organization of the centers involved in the different steps of the analysis and the time period in which the study was conducted. This information can now be used to define an adequate tariff and assess the efficiency of ES. TRIAL REGISTRATION ClinicalTrials.gov identifier NCT03287206 on September 19, 2017.
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Affiliation(s)
- A L Soilly
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, USMR, F-21000, Dijon, France
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
| | - C Robert-Viard
- CHU Dijon Bourgogne, Délégation à la Recherche Clinique et à l'Innovation, Unité Innovation, F-21000, Dijon, France
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A L Bruel
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - B Gerard
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - A Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - A Piton
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
| | - Y Duffourd
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - J Muller
- Laboratoires de Diagnostic Génétique, Hôpitaux Universitaires de Strasbourg, Institut de Génétique Médicale d'Alsace (IGMA), 67000, Strasbourg, France
- Unité Fonctionnelle de Bioinformatique Médicale appliquée au diagnostic (UF7363), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Inserm UMRS_1112, Institut de Génétique Médicale d'Alsace, Université de Strasbourg, France et CHRU, Strasbourg, France
| | - C Poë
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - T Jouan
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
| | - S El Doueiri
- CHU Dijon Bourgogne, Service financier, 21000, Dijon, France
| | - L Faivre
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - D Bacq-Daian
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - B Isidor
- Service de Génétique Médicale, CHU de Nantes, Nantes, France
| | - D Genevieve
- Département de Génétique Médicale, Centre de Référence Maladies Rares, Anomalies du Développement et Syndromes Malformatifs Sud-Languedoc Roussillon, Hôpital Arnaud de Villeneuve, Montpellier, France
| | - S Odent
- Service de Génétique Clinique, Centre Hospitalier Universitaire Rennes, F-35203, Rennes, France
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 6290, Institut Génétique et Développement de Rennes, Université de Rennes 1, F-35203, Rennes, France
| | - N Philip
- Département de Génétique Médicale, Hôpital d'Enfants de La Timone, Marseille, France
| | - M Doco-Fenzy
- Service de Génétique, CHU de Reims, EA3801, Reims, France
- CRMR Anddi-Rares constitutif, CLAD-EST, CHU Reims, Reims, France
| | - D Lacombe
- CHU de Bordeaux, Génétique Médicale, INSERM U1211, Laboratoire MRGM, Université de Bordeaux, Bordeaux, France
| | - M L Asensio
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - J F Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - C Binquet
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France
| | - C Thauvin-Robinet
- Inserm, Université Bourgogne-Franche-Comté, UMR1231, équipe GAD, Dijon, France
- CHU Dijon-Bourgogne, Centres de Référence Maladies Rares « Anomalies du Développement et syndromes malformatif de l'Est » et « Déficiences intellectuelles de causes rares », Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD), Dijon, France
| | - C Lejeune
- CHU Dijon Bourgogne, Inserm, Université de Bourgogne, CIC 1432, Module Épidémiologie Clinique, F21000, Dijon, France.
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11
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Neuzillet C, Artru P, Assenat E, Edeline J, Adhoute X, Sabourin JC, Turpin A, Coriat R, Malka D. Optimizing Patient Pathways in Advanced Biliary Tract Cancers: Recent Advances and a French Perspective. Target Oncol 2023; 18:51-76. [PMID: 36745342 PMCID: PMC9928940 DOI: 10.1007/s11523-022-00942-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/07/2023]
Abstract
Biliary tract cancers (BTCs) are a heterogeneous group of tumors that are rare in Western countries and have a poor prognosis. Three subgroups are defined by their anatomical location (intrahepatic cholangiocarcinoma, extrahepatic cholangiocarcinoma and gallbladder carcinoma) and exhibit distinct clinical, molecular, and epidemiologic characteristics. Most patients are diagnosed at an advanced disease stage and are not eligible for curative-intent resection. In addition to first- and second-line chemotherapies (CisGem and FOLFOX, respectively), biologic therapies are now available that target specific genomic alterations identified in BTC. To date, targets include alterations in the genes for isocitrate dehydrogenase (IDH) 1, fibroblast growth factor receptor (FGFR) 2, v-raf murine sarcoma viral oncogene homolog B1 (BRAF), human epidermal growth factor receptor 2 (HER2 or ERRB2), and neurotrophic tyrosine receptor kinase (NTRK), and for those leading to DNA mismatch repair deficiency. Therapies targeting these genomic alterations have demonstrated clinical benefit for patients with BTC. Despite these therapeutic advancements, genomic diagnostic modalities are not widely used in France, owing to a lack of clinician awareness, local availability of routine genomic testing, and difficulties in obtaining health insurance reimbursement. The addition of durvalumab, a monoclonal antibody targeting the immune checkpoint programmed cell death ligand-1, to CisGem in the first-line treatment of advanced BTC has shown an overall survival benefit in the TOPAZ-1 trial. Given the high mortality rates associated with BTC and the life-prolonging therapeutic options now available, it is hoped that the data presented here will support updates to the clinical management of BTC in France.
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Affiliation(s)
| | | | | | | | | | | | | | - Romain Coriat
- CHU Cochin, Service de Gastroentérologie, Hôpital Cochin, Université de Paris, Paris, France
| | - David Malka
- Department of Medical Oncology, Institut Mutualiste Montsouris, 42 Boulevard Jourdan, 75674, Paris Cedex 14, France.
- Université Paris-Saclay, Villejuif, France.
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12
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Zhao J, Wu Y, Chen MJ, Xu Y, Zhong W, Wang MZ. Characterization of driver mutations in Chinese non-small cell lung cancer patients using a novel targeted sequencing panel. J Thorac Dis 2022; 14:4669-4684. [PMID: 36647494 PMCID: PMC9840037 DOI: 10.21037/jtd-22-909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/04/2022] [Indexed: 12/05/2022]
Abstract
Background The identification of driver mutations has greatly promoted the precise diagnosis and treatment of non-small cell lung cancer (NSCLC), but there is lack of targeted sequencing panels specifically designed and applied to Chinese NSCLC patients. This study aimed to design and validate of a novel sequencing panel for comprehensive characterization of driver mutations in Chinese NSCLC patients, facilitating further exploration of downstream pathway alterations and therapeutic utility. Methods A novel target sequencing panel including 21 driver genes was designed and examined in a cohort of 260 Chinese NSCLC patients who underwent surgery in Peking Union Medical College Hospital (PUMCH). Genetic alterations were identified and further analyzed for driver mutations, downstream pathways and therapeutic utilities. Results The most frequently identified driver mutations in PUMCH NSCLC cohort were on genes TP53 (28%), EGFR (27%) and PIK3CA (19%) for lung adenocarcinoma (LUAD), and TP53 (41%), PIK3CA (14%) and CDKN2A (13%) for lung squamous cell carcinoma (LUSC), respectively. Downstream pathway analysis revealed common pathways like G1_AND_S1_PHASES pathway were shared not only between LUAD and LUSC patients, but also among three different NSCLC cohorts, while other pathways were subtype-specific, like the unique enrichment of SHC1_EVENT_IN_EGFR_SIGNALING pathway in LUAD patients, and P38_ALPHA_BETA_DOWNSTREAM pathway in LUSC patients, respectively. About 60% of both LUAD and LUSC patients harbored driver mutations as sensitive biomarkers for different targeted therapies, covering not only frequent mutations like EGFR L858R mutation, but also rare mutations like BRAF D594N mutation. Conclusions Our study provides a novel target sequencing panel suitable for Chinese NSCLC patients, which can effectively identify driver mutations, analyze downstream pathway alterations and predict therapeutic utility. Overall it is promising to further optimize and apply this panel in clinic with convenience and effectiveness.
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Affiliation(s)
- Jing Zhao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Yang Wu
- School of Medicine, Tsinghua University, Beijing, China
| | - Min-Jiang Chen
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Yan Xu
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Wei Zhong
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Meng-Zhao Wang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China
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13
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Hayashi N, Fukada I, Ohmoto A, Yamazaki M, Wang X, Hosonaga M, Takahashi S. Evaluation of an inflammation-based score for identification of appropriate patients for comprehensive genomic profiling. Discov Oncol 2022; 13:109. [PMID: 36260237 PMCID: PMC9582079 DOI: 10.1007/s12672-022-00574-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/10/2022] [Indexed: 11/19/2022] Open
Abstract
Performance status (PS) is widely used as an assessment of general condition in patients before performing comprehensive genomic profiling (CGP). However, PS scoring is dependent on each physician, and there is no objective and universal indicator to identify appropriate patients for CGP. Overall, 263 patients were scored using the modified Glasgow prognostic score (mGPS) from 0 to 2 based on the combination of serum albumin and c-reactive protein (CRP): 0, albumin ≥ 3.5 g/dl and CRP ≤ 0.5 mg/dl; 1, albumin < 3.5 g/dl or CRP > 0.5 mg/dl; and 2, albumin < 3.5 g/dl and CRP > 0.5 mg/dl. Overall survival was compared between mGPS 0-1 and mGPS 2 groups. The prognosis of patients with PS 0-1 and mGPS 2 was also evaluated. Thirty-nine patients (14.8%) were mGPS 2. Patients with mGPS 2 had significant shorter survival (14.7 months vs 4.6 months, p < 0.01). Twenty-eight patients were PS 0-1 and mGPS 2, and their survival was also short (5.6 months). Evaluation of mGPS is a simple and useful method for identifying patients with adequate prognosis using CGP.
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Affiliation(s)
- Naomi Hayashi
- Department of Genomic Medicine, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan.
- Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan.
| | - Ippei Fukada
- Department of Genomic Medicine, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
- Breast Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Akihiro Ohmoto
- Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Masumi Yamazaki
- Department of Genomic Medicine, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
- The Center for Advanced Medical Development, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Xiaofei Wang
- Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Mari Hosonaga
- Breast Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Shunji Takahashi
- Department of Genomic Medicine, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto, Tokyo, 135-8550, Japan
- Medical Oncology, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
- The Center for Advanced Medical Development, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
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14
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Ogusu S, Ariyasu R, Akita T, Kiritani A, Tsugitomi R, Amino Y, Uchibori K, Kitazono S, Yanagitani N, Nishio M. EGFR-TKI re-administration after osimertinib failure in T790M mutation loss cases with re-biopsy. Invest New Drugs 2022; 40:1342-1349. [PMID: 36152107 DOI: 10.1007/s10637-022-01301-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022]
Abstract
Data on the re-administration of epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) after osimertinib failure in patients with T790M-positive non-small cell lung cancer (NSCLC) is limited. EGFR-TKI re-administration efficacy may vary between patients with T790M loss and those with T790M persistent with re-biopsy after osimertinib treatment. Patients who received EGFR-TKI re-administration (gefitinib, erlotinib, afatinib, dacomitinib, and osimertinib) after osimertinib failure were identified from our database. T790M mutation status before EGFR-TKI re-administration was analyzed via repeat biopsy. We retrospectively evaluated the efficacy of EGFR-TKI re-administration, especially differences according to the T790M mutation status, via repeat biopsy. Until June 2020, 28 patients received EGFR-TKI re-administration and 17 underwent repeat biopsy after osimertinib failure. Patients were divided into three groups, including the T790M loss group, where active mutation persisted and T790M was lost (13/17); T790M remaining group, where both the active mutation and T790M persisted (3/17); and active mutation loss group where both the active mutation and T790M were lost (1/17). The overall response rate (ORR) of EGFR-TKI re-administration in the T790M loss group was 31% and the disease control rate (DCR) was 54%, which were higher than the ORR of 21% and DCR of 43% in the entire patient population. ORR and DCR of the not re-biopsy group were low (9% and 27%, respectively). The therapeutic effect of EGFR-TKI re-administration in patients with T790M-positive NSCLC after osimertinib failure is limited. EGFR-TKI re-administration may be considered in cases of T790M loss after repeat biopsy.
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Affiliation(s)
- Shinsuke Ogusu
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
- Division of Hematology, Respiratory Medicine and Oncology, Department of Internal Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Ryo Ariyasu
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Takahiro Akita
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ayu Kiritani
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryosuke Tsugitomi
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yoshiaki Amino
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ken Uchibori
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Satoru Kitazono
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Noriko Yanagitani
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Makoto Nishio
- Department of Thoracic Medical Oncology, the Cancer Institute Hospital, Japanese Foundation for Cancer Research, Tokyo, Japan.
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15
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Costs of Next-Generation Sequencing Assays in Non-Small Cell Lung Cancer: A Micro-Costing Study. Curr Oncol 2022; 29:5238-5246. [PMID: 35892985 PMCID: PMC9330154 DOI: 10.3390/curroncol29080416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 07/10/2022] [Accepted: 07/16/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Next-generation sequencing (NGS) of tumor genomes has changed and improved cancer treatment over the past few decades. It can inform clinicians on the optimal therapeutic approach in many of the solid and hematologic cancers, including non-small lung cancer (NSCLC). Our study aimed to determine the costs of NGS assays for NSCLC diagnostics. Methods: We performed a micro-costing study of four NGS assays (Trusight Tumor 170 Kit (Illumina), Oncomine Focus (Thermo Fisher), QIAseq Targeted DNA Custom Panel and QIASeq Targeted RNAscan Custom Panel (Qiagen), and KAPA HyperPlus/SeqCap EZ (Roche)) at the StemCore Laboratories, the Ottawa Hospital, Canada. We used a time-and-motion approach to measure personnel time and a pre-defined questionnaire to collect resource utilization. The unit costs were based on market prices. The cost data were reported in 2019 Canadian dollars. Results: Based on a case throughput of 500 cases per year, the per-sample cost for TruSight Tumor 170 Kit, QIASeq Targeted DNA Custom Panel and QIASeq Targeted RNAscan Custom Panel, Oncomine Focus, and HyperPlus/SeqCap EZ were CAD 1778, CAD 599, CAD 1100 and CAD 1270, respectively. The key cost drivers were library preparation (34–60%) and sequencing (31–51%), followed by data analysis (6–13%) and administrative support (2–7%). Conclusions: Trusight Tumor 170 Kit was the most expensive NGS assay for NSCLC diagnostics; however, an economic evaluation is required to identify the most cost-effective NGS assay. Our study results could help inform decisions to select a robust platform for NSCLC diagnostics from fine needle aspirates, and future economic evaluations of the NGS platforms to guide treatment selections for NSCLC patients.
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16
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Pedrini E, Negro A, Di Brino E, Pecoraro V, Sculco C, Abelli E, Gnoli M, Magrelli A, Sangiorgi L, Cicchetti A. Real-World Data and Budget Impact Analysis (BIA): Evaluation of a Targeted Next-Generation Sequencing Diagnostic Approach in Two Orthopedic Rare Diseases. Front Pharmacol 2022; 13:785705. [PMID: 35734413 PMCID: PMC9207266 DOI: 10.3389/fphar.2022.785705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Next-generation sequencing (NGS) technology, changing the diagnostic approach, has become essential in clinical settings, and its adoption by public health laboratories is now the practice. Despite this, as technological innovations, its intake requires an evaluation of both the clinical utility and the economic investment, especially considering the rare disease scenario. This study evaluated the analytical validity and the budget impact of an NGS-Ion Torrent™ approach for the molecular germline diagnosis of two musculoskeletal rare diseases.Methods: Two cohorts of 200 and 199 patients with suspect or clinical diagnosis of multiple osteochondromas (MO) and osteogenesis imperfecta (OI) previously evaluated with a single-gene diagnostic protocol were re-analyzed using a targeted NGS assay. Analytical validity was assessed by comparing NGS and single-gene protocol. A budget impact analysis using real-world cost data-considering the healthcare perspective— was performed by applying activity-based costing (ABC). The cost considered consumables, personnel, and equipment. Additional costs not related to NGS activities were not considered. Sensitivity analysis was performed.Results: The NGS method showed a higher (for MO) and comparable (for OI) diagnostic sensitivity than the traditional techniques, apart from always reducing the time and costs of diagnosis. Overall, the cost saving per patient is € 765 for OI and € 74 for MO. Materials represented the highest cost driver of the NGS process. A time saving—proportional to the panel size—has been assessed in both cases.Conclusions: Our targeted NGS diagnostic approach decreases time to diagnosis and costs, appearing to be beneficial and recommended both for patients and from a healthcare perspective in routine diagnosis also considering very small gene panels and a low patient flow. The adequate analytical sensitivity always required the additional Sanger sequencing step of the low- and non-covered regions. A more accurate strategy evaluation is suggested in the case of ultra-rare/complex diseases, large gene-panel, or non-reference diagnostic centers.
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Affiliation(s)
- Elena Pedrini
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Antonella Negro
- Regional Agency for Health and Social Care of Emilia-Romagna, Bologna, Italy
| | - Eugenio Di Brino
- Università Cattolica del Sacro Cuore, Graduate School of Health Economics and Management, Rome, Italy
| | - Valentina Pecoraro
- Regional Agency for Health and Social Care of Emilia-Romagna, Bologna, Italy
| | - Camilla Sculco
- School of Economics and Management, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Elisabetta Abelli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Maria Gnoli
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Armando Magrelli
- National Center for Drug Research and Evaluation, National Institute of Health (ISS), Rome, Italy
| | - Luca Sangiorgi
- Department of Rare Skeletal Disorders, IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
- *Correspondence: Luca Sangiorgi,
| | - Americo Cicchetti
- Università Cattolica del Sacro Cuore, Graduate School of Health Economics and Management, Rome, Italy
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17
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Brandner S, McAleenan A, Jones HE, Kernohan A, Robinson T, Schmidt L, Dawson S, Kelly C, Leal ES, Faulkner CL, Palmer A, Wragg C, Jefferies S, Vale L, Higgins JPT, Kurian KM. Diagnostic accuracy of 1p/19q codeletion tests in oligodendroglioma: A comprehensive meta-analysis based on a Cochrane systematic review. Neuropathol Appl Neurobiol 2022; 48:e12790. [PMID: 34958131 PMCID: PMC9208578 DOI: 10.1111/nan.12790] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/29/2022]
Abstract
Codeletion of chromosomal arms 1p and 19q, in conjunction with a mutation in the isocitrate dehydrogenase 1 or 2 gene, is the molecular diagnostic criterion for oligodendroglioma, IDH mutant and 1p/19q codeleted. 1p/19q codeletion is a diagnostic marker and allows prognostication and prediction of the best drug response within IDH-mutant tumours. We performed a Cochrane review and simple economic analysis to establish the most sensitive, specific and cost-effective techniques for determining 1p/19q codeletion status. Fluorescent in situ hybridisation (FISH) and polymerase chain reaction (PCR)-based loss of heterozygosity (LOH) test methods were considered as reference standard. Most techniques (FISH, chromogenic in situ hybridisation [CISH], PCR, real-time PCR, multiplex ligation-dependent probe amplification [MLPA], single nucleotide polymorphism [SNP] array, comparative genomic hybridisation [CGH], array CGH, next-generation sequencing [NGS], mass spectrometry and NanoString) showed good sensitivity (few false negatives) for detection of 1p/19q codeletions in glioma, irrespective of whether FISH or PCR-based LOH was used as the reference standard. Both NGS and SNP array had a high specificity (fewer false positives) for 1p/19q codeletion when considered against FISH as the reference standard. Our findings suggest that G banding is not a suitable test for 1p/19q analysis. Within these limits, considering cost per diagnosis and using FISH as a reference, MLPA was marginally more cost-effective than other tests, although these economic analyses were limited by the range of available parameters, time horizon and data from multiple healthcare organisations.
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Affiliation(s)
- Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and NeurosurgeryUniversity College London Hospitals NHS Foundation TrustLondonUK
- Department of Neurodegenerative Disease, Queen Square Instituite of NeurologyUniversity College LondonLondonUK
| | - Alexandra McAleenan
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Hayley E. Jones
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Ashleigh Kernohan
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Tomos Robinson
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Lena Schmidt
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Sarah Dawson
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Claire Kelly
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | | | - Claire L. Faulkner
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Abigail Palmer
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | - Christopher Wragg
- Bristol Genetics Laboratory, Pathology SciencesSouthmead HospitalBristolUK
| | | | - Luke Vale
- Population Health Sciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Julian P. T. Higgins
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
| | - Kathreena M. Kurian
- Population Health Sciences, Bristol Medical SchoolUniversity of BristolBristolUK
- Bristol Medical School: Brain Tumour Research Centre, Public Health SciencesUniversity of BristolBristolUK
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18
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Zischke J, White N, Gordon L. Accounting for Intergenerational Cascade Testing in Economic Evaluations of Clinical Genomics: A Scoping Review. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2022; 25:944-953. [PMID: 35667782 DOI: 10.1016/j.jval.2021.11.1353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/25/2021] [Accepted: 11/03/2021] [Indexed: 06/15/2023]
Abstract
OBJECTIVES Clinical genomics is emerging as a diagnostic tool in the identification of blood relatives at risk of developing heritable diseases. Our objective was to identify how genetic cascade screening has been incorporated into health economic evaluations. METHODS A scoping review was conducted to identify how multiple generations of a family were included in economic evaluations of clinical genomic sequencing, how many and which relatives were included, and uptake rates. Databases were searched for full economic evaluations of genetic interventions that screened multiple generations of families and were in English language, and no restrictions were made for disease or publication type. Data were synthesized using a narrative approach. RESULTS Twenty-five studies were included covering a range of diseases in various countries. Markov cohort models were mostly used with hypothetical populations and unsupported by clinical evidence. Cascade testing was either the primary intervention or secondary to the index cases. The number and type of relatives were based on assumptions or identified through population or family records, clinical registry data, or clinical literature. Studies included only immediate family members and the uptake of testing ranged between 20% and 100%. All interventions were reported as cost-effective, and a higher number of relatives was a key driver. CONCLUSIONS Several economic evaluations have considered the impacts of cascade testing interventions within clinical genomics. Ideally, models supported with high-quality clinical data are needed and, in their absence, transparent and justifiable assumptions of uptake rates and choices about including relatives. Consideration of more appropriate modeling types is required.
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Affiliation(s)
- Jason Zischke
- Health Economics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Public Health and Social Work, Queensland University of Technology, Brisbane, Australia.
| | - Nicole White
- Centre for Healthcare Transformation, School of Public Health and Social Work and Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, Australia
| | - Louisa Gordon
- Health Economics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia; School of Nursing, Queensland University of Technology, Brisbane, Australia; School of Public Health, The University of Queensland, Brisbane, Australia
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19
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Perdrizet K, Stockley TL, Law JH, Smith A, Zhang T, Fernandes R, Shabir M, Sabatini P, Youssef NA, Ishu C, Li JJ, Tsao MS, Pal P, Cabanero M, Schwock J, Ko HM, Boerner S, Ruff H, Shepherd FA, Bradbury PA, Liu G, Sacher AG, Leighl NB. Integrating comprehensive genomic sequencing of non-small cell lung cancer into a public healthcare system. Cancer Treat Res Commun 2022; 31:100534. [PMID: 35278845 DOI: 10.1016/j.ctarc.2022.100534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVES Standard molecular testing for patients with stage IV non-small cell lung cancer (NSCLC) in the Canadian publicly funded health system includes single gene testing for EGFR, ALK, and ROS-1. Comprehensive genomic profiling (CGP) may broaden treatment options for patients. This study examined the impact of CGP in a publicly funded health system. METHODS Consenting patients with stage IV NSCLC without known targetable alterations underwent CGP on diagnostic samples. Patients that had progressed on targeted therapy were also eligible. The CGP assay was a hybrid capture next generation sequencing (NGS) panel (Oncomine Comprehensive Assay Version 3, ThermoFisher). The number of actionable alterations, changes in treatment, clinical trial eligibility and costs as a result of CGP were evaluated and patient willingness-to-pay. RESULTS Of 182 screened patients,134 (74%) had successful CGP testing. Twenty percent had received prior targeted therapy. Incremental actionable alterations were identified in 31% of patients. The most common novel targets identified were mutations in ERBB2 (exon 20 insertions), MET (exon 14 skipping) and KRAS (G12C). At data cut off (31/12/2020), 16% of patients had a change in treatment as a result of CGP. Additional clinical trial options were identified for 75% of patients. The incremental direct laboratory cost for CGP beyond public reimbursement for single gene tests was $747 CAD/case. CONCLUSION CGP identifies additional actionable targets beyond single gene tests with a direct impact on patient treatment and increased clinical trial eligibility. These benefits highlight the value of CGP in patients with NSCLC in public health systems.
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Affiliation(s)
- Kirstin Perdrizet
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; William Osler Health System, Brampton, Ontario, Canada.
| | - Tracy L Stockley
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Jennifer H Law
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Adam Smith
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Tong Zhang
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Roxanne Fernandes
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Muqdas Shabir
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Peter Sabatini
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Nadia Al Youssef
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Christine Ishu
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada; Advanced Molecular Diagnostics Laboratory, University Health Network, Toronto, Canada
| | - Janice Jn Li
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Prodipto Pal
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Michael Cabanero
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Joerg Schwock
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Hyang Mi Ko
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Scott Boerner
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Heather Ruff
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | | | - Geoffrey Liu
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Adrian G Sacher
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada
| | - Natasha B Leighl
- Princess Margaret Cancer Centre/University Health Network, Toronto, Canada.
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20
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Hussen BM, Abdullah ST, Salihi A, Sabir DK, Sidiq KR, Rasul MF, Hidayat HJ, Ghafouri-Fard S, Taheri M, Jamali E. The emerging roles of NGS in clinical oncology and personalized medicine. Pathol Res Pract 2022; 230:153760. [PMID: 35033746 DOI: 10.1016/j.prp.2022.153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/29/2021] [Accepted: 01/06/2022] [Indexed: 02/07/2023]
Abstract
Next-generation sequencing (NGS) has been increasingly popular in genomics studies over the last decade, as new sequencing technology has been created and improved. Recently, NGS started to be used in clinical oncology to improve cancer therapy through diverse modalities ranging from finding novel and rare cancer mutations, discovering cancer mutation carriers to reaching specific therapeutic approaches known as personalized medicine (PM). PM has the potential to minimize medical expenses by shifting the current traditional medical approach of treating cancer and other diseases to an individualized preventive and predictive approach. Currently, NGS can speed up in the early diagnosis of diseases and discover pharmacogenetic markers that help in personalizing therapies. Despite the tremendous growth in our understanding of genetics, NGS holds the added advantage of providing more comprehensive picture of cancer landscape and uncovering cancer development pathways. In this review, we provided a complete overview of potential NGS applications in scientific and clinical oncology, with a particular emphasis on pharmacogenomics in the direction of precision medicine treatment options.
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Affiliation(s)
- Bashdar Mahmud Hussen
- Department Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Erbil, Iraq; Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq
| | - Sara Tharwat Abdullah
- Department of Pharmacology and Toxicology, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Abbas Salihi
- Center of Research and Strategic Studies, Lebanese French University, Kurdistan Region, Erbil, Iraq; Department of Biology, College of Science, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Dana Khdr Sabir
- Department of Medical Laboratory Sciences, Charmo University, Kurdistan Region, Iraq
| | - Karzan R Sidiq
- Department of Biology, College of Education, University of Sulaimani, Sulaimani 334, Kurdistan, Iraq
| | - Mohammed Fatih Rasul
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Kurdistan Region, Erbil, Iraq
| | - Hazha Jamal Hidayat
- Department of Biology, College of Education, Salahaddin University, Kurdistan Region, Erbil, Iraq
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Elena Jamali
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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21
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Economic evaluation of genomic/genetic tests: a review and future directions. Int J Technol Assess Health Care 2022; 38:e67. [DOI: 10.1017/s0266462322000484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Abstract
It has been suggested that health economists need to improve their methods in order to meet the challenges of evaluating genomic/genetic tests. In this article, we set out twelve challenges identified from a rapid review of the literature and suggest solutions to the challenges identified. Two challenges were common to all economic evaluations: choice of perspective and time-horizon. Five challenges were relevant for all diagnostic technologies: complexity of analysis; range of costs; under-developed evidence base; behavioral aspects; and choice of outcome metrics. The final five challenges were pertinent for genomic tests and only these may require methodological development: heterogeneity of tests and platforms, increasing stratification, capturing personal utility; incidental findings; and spillover effects. Current methods of economic evaluation are generally able to cope with genomic/genetic tests, although a renewed focus on specific decision-makers’ needs and a willingness to move away from cost-utility analysis may be required. Certain analysts may be constrained by reference cases developed primarily for the assessment of pharmaceuticals. The combined impact of multiple challenges may require analysts to be particularly careful in setting the scope of their analysis in order to ensure that feasibility is balanced with usefulness to the decision maker. A key issue is the under-developed evidence-base and it may be necessary to rethink translation processes to ensure sufficient, relevant evidence is available to support economic evaluation and adoption of genomic/genetic tests.
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22
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Yoon S, Kim M, Hong YS, Kim HS, Kim ST, Kim J, Yun H, Yoo C, Ahn HK, Kim HS, Lee IH, Kim IH, Park I, Jeong JH, Cheon J, Kim JW, Yun J, Lim SM, Cha Y, Jang SJ, Zang DY, Kim TW, Kang JH, Kim JH. Recommendations for the Use of Next-Generation Sequencing and the Molecular Tumor Board for Patients with Advanced Cancer: A Report from KSMO and KCSG Precision Medicine Networking Group. Cancer Res Treat 2021; 54:1-9. [PMID: 34902959 PMCID: PMC8756119 DOI: 10.4143/crt.2021.1115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/08/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is becoming essential in the fields of precision oncology. With implementation of NGS in daily clinic, the needs for continued education, facilitated interpretation of NGS results and optimal treatment delivery based on NGS results have been addressed. Molecular tumor board (MTB) is multidisciplinary approach to keep pace with the growing knowledge of complex molecular alterations in patients with advanced solid cancer. Although guidelines for NGS use and MTB have been developed in western countries, there is limitation for reflection of Korea’s public health environment and daily clinical practice. These recommendations provide a critical guidance from NGS panel testing to final treatment decision based on MTB discussion.
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Affiliation(s)
- Shinkyo Yoon
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Miso Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Yong Sang Hong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Sang Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jihun Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hongseok Yun
- Department of Genomic Medicine, Seoul National University Hospital, College of Medicine, Seoul, Korea
| | - Changhoon Yoo
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hee Kyung Ahn
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Hyo Song Kim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - In Hee Lee
- Department of Oncology/Hematology, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - In-Ho Kim
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Inkeun Park
- Division of Medical Oncology, Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Jae Ho Jeong
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jaekyung Cheon
- Department of Medical Oncology, CHA Bundang Medical Center, CHA University School of Medicine, Seongnam, Korea
| | - Jin Won Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
| | - Jina Yun
- Division of Medical Oncology, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Korea
| | - Yongjun Cha
- Center for Colorectal Cancer, National Cancer Center, Research Institute and Hospital, Goyang, Korea
| | - Se Jin Jang
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dae Young Zang
- Department of Internal Medicine, Hallym University Medical Center, Hallym University, Anyang, Korea
| | - Tae Won Kim
- Department of Oncology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin Hyoung Kang
- Division of Medical Oncology, Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University of Korea College of Medicine, Seoul, Korea
| | - Jee Hyun Kim
- Division of Hematology/Medical Oncology, Department of Internal Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam, Korea
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23
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Pisapia P, Pepe F, Baggi A, Barberis M, Galvano A, Gristina V, Mastrilli F, Novello S, Pagni F, Pasini S, Perrone G, Righi D, Russo A, Troncone G, Malapelle U. Next generation diagnostic algorithm in non-small cell lung cancer predictive molecular pathology: The KWAY Italian multicenter cost evaluation study. Crit Rev Oncol Hematol 2021; 169:103525. [PMID: 34813925 DOI: 10.1016/j.critrevonc.2021.103525] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/21/2022] Open
Abstract
AIMS The KWAY project aims to investigate the economic sustainability of the up-front NGS technologies adoption in the analysis of clinically relevant molecular alterations in NSCLC patients. METHODS The diagnostic workflow and the related sustained costs of five Italian referral centers were assessed in four different evolving scenarios were analyzed. For each scenario, two alternative testing strategies were evaluated: the Maximized Standard strategy and the Maximized NGS strategy. RESULTS For each center, the robustness of obtained results was verified through a deterministic sensitivity analysis, observing the variation of total costs based on a variation of ±20 % of the input parameters and ensuring that results would present a consistent behavior compared to the original ones. CONCLUSIONS our project, highlighted that the adoption of NGS allows to save personnel time dedicated to testing activities and to reduce the overall cost of testing per patient.
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Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Anna Baggi
- Business Integration Partners (BIP), Life Sciences Division, Italy
| | - Massimo Barberis
- Unit of Histopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Antonio Galvano
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Fabrizio Mastrilli
- Medical Director, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | - Silvia Novello
- Department of Oncology, San Luigi Hospital, University of Turin, Orbassano, Italy
| | - Fabio Pagni
- Department of Pathology, University of Milan-Bicocca (UNIMIB), 20900, Monza, Italy
| | - Silvia Pasini
- Business Integration Partners (BIP), Life Sciences Division, Italy
| | - Giuseppe Perrone
- Predictive Molecular Diagnostic Division, Department of Pathology, Campus Bio-Medico, University of Rome, Italy
| | - Daniela Righi
- Predictive Molecular Diagnostic Division, Department of Pathology, Campus Bio-Medico, University of Rome, Italy
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
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24
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Bonneville-Levard A, Frappaz D, Tredan O, Lavergne E, Corset V, Agrapart V, Chabaud S, Pissaloux D, Wang Q, Attignon V, Cartalat S, Ducray F, Thomas-Maisonneuve L, Honnorat J, Meyronet D, Taillandier L, Blonski M, Viari A, Baudet C, Sohier E, Lantuejoul S, Paindavoine S, Treilleux I, Rodriguez C, Pérol D, Blay JY. Molecular profile to guide personalized medicine in adult patients with primary brain tumors: results from the ProfiLER trial. Med Oncol 2021; 39:4. [PMID: 34739635 DOI: 10.1007/s12032-021-01536-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 06/15/2021] [Indexed: 11/30/2022]
Abstract
Immunohistochemistry and recent molecular technologies progressively guided access to personalized anti-tumoral therapies. We explored the feasibility, efficacy, and the impact of molecular profiling in patients with advanced brain tumors. This multicentric prospective trial ProfiLER enrolled patients with primary brain tumors, who have been pre-treated with at least one line of anti-cancer treatment, and for whom molecular profiles had been achieved using next-generation sequencing and/or comparative genomic hybridization on fresh or archived samples from tumor, relapse, or biopsies. A molecular tumor board weekly analyzed results and proposed molecular-based recommended therapy (MBRT). From February 2013 to December 2015, we enrolled 141 patients with primary brain tumor and analyzed 105 patients for whom tumor genomic profiles had been achieved. Histology mainly identified glioblastoma (N = 46, 44%), low-grade glioma (N = 26, 25%), high-grade glioma (N = 12, 11%), and atypical and anaplastic meningioma (N = 8, 8%). Forty-three (41%) patients presented at least one actionable molecular alteration. Out of 61 alterations identified, the most frequent alterations occurred in CDKN2A (N = 18), EGFR (N = 12), PDGFRa (N = 8), PTEN (N = 8), CDK4 (N = 7), KIT (N = 6), PIK3CA (N = 5), and MDM2 (N = 3). Sixteen (15%) patients could not be proposed for a MBRT due to early death (N = 5), lack of available clinical trials (N = 9), or inappropriate results (N = 2). Only six (6%) of the 27 (26%) patients for whom a MBRT had been proposed finally initiated MBRT (everolimus (N = 3), erlotinib (N = 1), ruxolitinib (N = 1), and sorafenib (N = 1)), but discontinued treatment for toxicity (N = 4) or clinical progression (N = 2). High-throughput sequencing in patients with brain tumors may be routinely performed, especially when macroscopic surgery samples are available; nevertheless delays should be reduced. Criteria for clinical trial enrollment should be reconsidered in patients with brain tumors, and a panel of genes specifically dedicated to neurologic tumors should be developed to help decision-making in clinical practice.
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Affiliation(s)
- Alice Bonneville-Levard
- Department of Medical Oncology, Leon Bérard Cancer Centre, 28, rue Laennec, 69373, Lyon, France.
| | - Didier Frappaz
- Department of Medical Oncology, Leon Bérard Cancer Centre, 28, rue Laennec, 69373, Lyon, France
| | - Olivier Tredan
- Department of Medical Oncology, Leon Bérard Cancer Centre, 28, rue Laennec, 69373, Lyon, France
| | - Emilie Lavergne
- Department of Clinical Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Véronique Corset
- Department of Clinical Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Vincent Agrapart
- Department of Clinical Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Sylvie Chabaud
- Department of Clinical Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Daniel Pissaloux
- Department of Translational Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Qing Wang
- Department of Translational Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Valery Attignon
- Department of Translational Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | | | - François Ducray
- Department of Neuro-Oncology, Hospices Civils de Lyon, Lyon, France
| | | | - Jérôme Honnorat
- Department of Neuro-Oncology, Hospices Civils de Lyon, Lyon, France
| | - David Meyronet
- Department of Neuropathology, Hospices Civils de Lyon, Lyon, France
| | - Luc Taillandier
- Department of Neuro-Oncology, Central Hospital, Nancy, France
| | - Marie Blonski
- Department of Neuro-Oncology, Central Hospital, Nancy, France
| | - Alain Viari
- Synergie Lyon Cancer, Bio-Informatics Platform, Léon Bérard Cancer Centre, Lyon, France
| | - Christian Baudet
- Synergie Lyon Cancer, Bio-Informatics Platform, Léon Bérard Cancer Centre, Lyon, France
| | - Emilie Sohier
- Synergie Lyon Cancer, Bio-Informatics Platform, Léon Bérard Cancer Centre, Lyon, France
| | | | | | | | | | - David Pérol
- Department of Clinical Research and Innovation, Léon Bérard Cancer Centre, Lyon, France
| | - Jean-Yves Blay
- Department of Medical Oncology, Leon Bérard Cancer Centre, 28, rue Laennec, 69373, Lyon, France
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25
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Normanno N, Apostolides K, de Lorenzo F, Beer PA, Henderson R, Sullivan R, Biankin AV, Horgan D, Lawler M. Cancer Biomarkers in the era of precision oncology: Addressing the needs of patients and health systems. Semin Cancer Biol 2021; 84:293-301. [PMID: 34389490 DOI: 10.1016/j.semcancer.2021.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 07/30/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Cancer Biomarkers are the key to unlocking the promise of precision oncology, selecting which patients will respond to a more personalised treatment while sparing non-responders the therapy-related toxicity. In this paper, we highlight the primacy of cancer biomarkers, but focus on their importance to patients and to health systems. We also highlight how cancer biomarkers represent value for money. We emphasise the need for cancer biomarkers infrastructure to be embedded into European health systems. We also highlight the need to deploy multiple biomarker testing to deliver the optimal benefit for patients and health systems and consider cancer biomarkers from the perspective of cost, value and regulation. Cancer biomarkers must also be situated in the context of the upcoming In Vitro Diagnostics Regulation, which may pose certain challenges (e.g. non-compliance of laboratory developed tests, leading to cancer biomarker shortages and increased costs) that need to be overcome. Cancer biomarkers must be embedded in the real world of oncology delivery and testing must be implemented across Europe, with the intended aim of narrowing, not widening the inequity gap for patients. Cancer patients must be placed firmly at the centre of a cancer biomarker informed precision oncology care agenda.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - "Fondazione G. Pascale", Napoli, Italy
| | - Kathi Apostolides
- European Cancer Patient Coalition, Rue Montoyer 40, 1000, Brussels, Belgium
| | | | - Philip A Beer
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Raymond Henderson
- Diaceutics PLC, Belfast, United Kingdom; Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom
| | - Richard Sullivan
- King's College London, Institute of Cancer Policy, Guy's Hospital, Great Maze Pond, London, SE1 9RT, United Kingdom
| | - Andrew V Biankin
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow, Scotland, G61 1QH, United Kingdom; West of Scotland Pancreatic Unit, Glasgow Royal Infirmary, Glasgow, G31 2ER, United Kingdom; South Western Sydney Clinical School, Goulburn St, Liverpool, NSW, 2170, Australia
| | - Denis Horgan
- European Alliance for Personalised Medicine, Avenue de l'Armee Legerlaan 10, 1040, Brussels, Belgium
| | - Mark Lawler
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, United Kingdom.
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26
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Pasmans CTB, Tops BBJ, Steeghs EMP, Coupé VMH, Grünberg K, de Jong EK, Schuuring EMD, Willems SM, Ligtenberg MJL, Retèl VP, van Snellenberg H, de Bruijn E, Cuppen E, Frederix GWJ. Micro-costing diagnostics in oncology: from single-gene testing to whole- genome sequencing. Expert Rev Pharmacoecon Outcomes Res 2021; 21:413-414. [PMID: 33852815 DOI: 10.1080/14737167.2021.1917385] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Purpose: Predictive diagnostics play an increasingly important role in personalized medicine for cancer treatment. Whole-genome sequencing (WGS)-based treatment selection is expected to rapidly increase worldwide. This study aimed to calculate and compare the total cost of currently used diagnostic techniques and of WGS in treatment of non-small cell lung carcinoma (NSCLC), melanoma, colorectal cancer (CRC), and gastrointestinal stromal tumor (GIST) in the Netherlands.Methods: The activity-based costing (ABC) method was conducted to calculate total cost of included diagnostic techniques based on data provided by Dutch pathology laboratories and the Dutch-centralized cancer WGS facility. Costs were allocated to four categories: capital costs, maintenance costs, software costs, and operational costs.Results: The total cost per cancer patient per technique varied from € 58 (Sanger sequencing, three amplicons) to € 2925 (paired tumor-normal WGS). The operational costs accounted for the vast majority (over 90%) of the total per cancer patient technique costs.Conclusion: This study outlined in detail all costing aspects and cost prices of current and new diagnostic modalities used in treatment of NSCLC, melanoma, CRC, and GIST in the Netherlands. Detailed cost differences and value comparisons between these diagnostic techniques enable future economic evaluations to support decision-making.
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Affiliation(s)
- Clémence T B Pasmans
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Bilthoven, The Netherlands
| | - Elisabeth M P Steeghs
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, The Netherlands
| | - Katrien Grünberg
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Eiko K de Jong
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ed M D Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.,PALGA Foundation, Houten, The Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Valesca P Retèl
- Department of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Health Technology and Services Research, University of Twente, Enschede, The Netherlands
| | | | | | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, The Netherlands.,Center for Molecular Medicine and Cancer Genomics Netherlands, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Geert W J Frederix
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
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27
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Palmieri G, Rozzo CM, Colombino M, Casula M, Sini MC, Manca A, Pisano M, Doneddu V, Paliogiannis P, Cossu A. Are Molecular Alterations Linked to Genetic Instability Worth to Be Included as Biomarkers for Directing or Excluding Melanoma Patients to Immunotherapy? Front Oncol 2021; 11:666624. [PMID: 34026645 PMCID: PMC8132875 DOI: 10.3389/fonc.2021.666624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 12/28/2022] Open
Abstract
The improvement of the immunotherapeutic potential in most human cancers, including melanoma, requires the identification of increasingly detailed molecular features underlying the tumor immune responsiveness and acting as disease-associated biomarkers. In recent past years, the complexity of the immune landscape in cancer tissues is being steadily unveiled with a progressive better understanding of the plethora of actors playing in such a scenario, resulting in histopathology diversification, distinct molecular subtypes, and biological heterogeneity. Actually, it is widely recognized that the intracellular patterns of alterations in driver genes and loci may also concur to interfere with the homeostasis of the tumor microenvironment components, deeply affecting the immune response against the tumor. Among others, the different events linked to genetic instability—aneuploidy/somatic copy number alteration (SCNA) or microsatellite instability (MSI)—may exhibit opposite behaviors in terms of immune exclusion or responsiveness. In this review, we focused on both prevalence and impact of such different types of genetic instability in melanoma in order to evaluate whether their use as biomarkers in an integrated analysis of the molecular profile of such a malignancy may allow defining any potential predictive value for response/resistance to immunotherapy.
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Affiliation(s)
- Giuseppe Palmieri
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Carla Maria Rozzo
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Maria Colombino
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Milena Casula
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Maria Cristina Sini
- Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Antonella Manca
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Marina Pisano
- Institute of Genetic and Biomedical Research (IRGB), National Research Council (CNR), Sassari, Italy
| | - Valentina Doneddu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Panagiotis Paliogiannis
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Cossu
- Department of Medical, Surgical, and Experimental Sciences, University of Sassari, Sassari, Italy
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28
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Bekaii-Saab TS, Bridgewater J, Normanno N. Practical considerations in screening for genetic alterations in cholangiocarcinoma. Ann Oncol 2021; 32:1111-1126. [PMID: 33932504 DOI: 10.1016/j.annonc.2021.04.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/06/2021] [Accepted: 04/18/2021] [Indexed: 12/14/2022] Open
Abstract
Cholangiocarcinoma (CCA) encompasses diverse epithelial tumors historically associated with poor outcomes due to an aggressive disease course, late diagnosis, and limited benefit of standard chemotherapy for advanced disease. Comprehensive molecular profiling has revealed a diverse landscape of genomic alterations as oncogenic drivers in CCA. TP53 mutations, CDKN2A/B loss, and KRAS mutations are the most common genetic alterations in CCA. However, intrahepatic CCA (iCCA) and extrahepatic CCA (eCCA) differ substantially in the frequency of many alterations. This includes actionable alterations, such as isocitrate dehydrogenase 1 (IDH1) mutations and a large variety of FGFR2 rearrangements, which are found in up to 29% and ∼10% of patients with iCCA, respectively, but are rare in eCCA. FGFR2 rearrangements are currently the only genetic alteration in CCA for which a targeted therapy, the fibroblast growth factor receptor 1-3 inhibitor pemigatinib, has been approved. However, favorable phase III results for IDH1-targeted therapy with ivosidenib in iCCA have been published, and numerous other alterations are actionable by targeted therapies approved in other indications. Recent advances in next-generation sequencing (NGS) have led to the development of assays that allow comprehensive genomic profiling of large gene panels within 2-3 weeks, including in vitro diagnostic tests approved in the United States. These assays vary regarding acceptable source material (tumor tissue or peripheral whole blood), genetic source for library construction (DNA or RNA), target selection technology, gene panel size, and type of detectable genomic alterations. While some large commercial laboratories offer rapid and comprehensive genomic profiling services based on proprietary assay platforms, clinical centers may use commercial genomic profiling kits designed for clinical research to develop their own customized laboratory-developed tests. Large-scale genomic profiling based on NGS allows for a detailed and precise molecular diagnosis of CCA and provides an important opportunity for improved targeted treatment plans tailored to the individual patient's genetic signature.
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Affiliation(s)
| | - J Bridgewater
- University College London Cancer Institute, London, UK
| | - N Normanno
- Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Naples, Italy
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29
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Zhang W, Zhang Z, Krushkal J, Liu A. Group testing can improve the cost-efficiency of prospective-retrospective biomarker studies. BMC Med Res Methodol 2021; 21:55. [PMID: 33740890 PMCID: PMC7977501 DOI: 10.1186/s12874-021-01239-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 02/24/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cancer treatment is increasingly dependent on biomarkers for prognostication and treatment selection. Potential biomarkers are frequently evaluated in prospective-retrospective studies in which biomarkers are measured retrospectively on archived specimens after completion of prospective clinical trials. In light of the high costs of some assays, random sampling designs have been proposed that measure biomarkers for a random sub-sample of subjects selected on the basis of observed outcome and possibly other variables. Compared with a standard design that measures biomarkers on all subjects, a random sampling design can be cost-efficient in the sense of reducing the cost of the study substantially while achieving a reasonable level of precision. METHODS For a biomarker that indicates the presence of some molecular alteration (e.g., mutation in a gene), we explore the use of a group testing strategy, which involves physically pooling specimens across subjects and assaying pooled samples for the presence of the molecular alteration of interest, for further improvement in cost-efficiency beyond random sampling. We propose simple and general approaches to estimating the prognostic and predictive values of biomarkers with group testing, and conduct simulation studies to validate the proposed estimation procedures and to assess the cost-efficiency of the group testing design in comparison to the standard and random sampling designs. RESULTS Simulation results show that the proposed estimation procedures perform well in realistic settings and that a group testing design can have considerably higher cost-efficiency than a random sampling design. CONCLUSIONS Group testing can be used to improve the cost-efficiency of biomarker studies.
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Affiliation(s)
- Wei Zhang
- LSC, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, China
| | - Zhiwei Zhang
- Biometric Research Program, Division of Cancer Treatment and Diagnostics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Julia Krushkal
- Biometric Research Program, Division of Cancer Treatment and Diagnostics, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Aiyi Liu
- Biostatistics and Bioinformatics Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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30
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Hofman P, Rouleau E, Sabourin JC, Denis M, Deleuze JF, Barlesi F, Laurent-Puig P. Predictive molecular pathology in non-small cell lung cancer in France: The past, the present and the perspectives. Cancer Cytopathol 2021; 128:601-610. [PMID: 32885912 DOI: 10.1002/cncy.22318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022]
Abstract
The advent of molecular targets for novel therapeutics in oncology, notably for non-small cell lung carcinoma (NSCLC), led the French National Cancer Institute (INCa) to establish a national network of 28 hospital Molecular Genetics Centers for Cancer (MGCC) in 2007. In each University in France, laboratories were established to develop molecular biology testing to evaluate a few genomic alterations, initially a selection of genes, by using specific targeted polymerase chain reaction (PCR) assays. In a second phase, the number of studied genes was increased. In 2015, the MGCC benefited from an additional dedicated budget from the INCa to develop next-generation sequencing (NGS) technology. In the meantime, a new financial regulation for innovative testing has been established for the acts out of nomenclature. Consequently, all private and public laboratories in France have access to funding for molecular biology testing in oncology. The gene-based PCR assays or NGS tests have benefitted from reimbursement of cost testing by the INCa. Today, the laboratories consider this reimbursement to be only partial, and its use to be complex. In 2018, a strategic plan for medical genomic analyses (France Médecine Génomique 2025) was implemented to introduce more systematic sequencing into the health care pathway and oncology practice. The large panel of molecular tests should be centralized to a limited number of molecular genetic centers. This review describes the evolution of the different stages of implementation of molecular pathology testing for NSCLC patients over the last few years in France.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, University Côte d'Azur, Nice, France.,Hospital-Related Biobank, Pasteur Hospital, University Côte d'Azur, Nice, France.,FHU OncoAge, Pasteur Hospital, University Côte d'Azur, Nice, France
| | - Etienne Rouleau
- Cancer Genetic Laboratory, Biology and Pathology Department, Gustave Roussy, Villejuif, France
| | | | - Marc Denis
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris Saclay, Evry, France.,Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France.,Centre de Référence, d'Innovation et d'Expertise (CREFIX), Paris, France
| | - Fabrice Barlesi
- Aix-Marseille University, CNRS, INSERM, CRCM, Marseille, France.,Gustave Roussy Cancer Campus, Villejuif, France
| | - Pierre Laurent-Puig
- UMR-1138, INSERM, Département de Biologie, Hôpital Européen Georges-Pompidou, Paris, France.,Université Paris Descartes, Assistance Publique-Hôpitaux de Paris, Paris, France
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31
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van de Ven M, Koffijberg H, Retèl V, Monkhorst K, Smit E, van Harten W, IJzerman M. Real-World Utilization of Biomarker Testing for Patients with Advanced Non-Small Cell Lung Cancer in a Tertiary Referral Center and Referring Hospitals. J Mol Diagn 2021; 23:484-494. [PMID: 33493663 DOI: 10.1016/j.jmoldx.2021.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 12/21/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022] Open
Abstract
The continued introduction of biomarkers and innovative testing methods makes already complex diagnosis in patients with stage IV non-small-cell lung cancer (NSCLC) even more complex. This study primarily analyzed variations in biomarker testing in clinical practice in patients referred to a comprehensive cancer center in the Netherlands. The secondary aim was to compare the cost of biomarker testing with the cost of whole-genome sequencing. The cohort included 102 stage IV NSCLC patients who received biomarker testing in 2017 or 2018 at the comprehensive cancer center. The complete biomarker testing history of the cohort was identified using linked data from the comprehensive cancer center and the nationwide network and registry of histopathology and cytopathology in the Netherlands. Unique biomarker-test combinations, costs, turnaround times, and test utilization were examined. The results indicate substantial variation in test utilization and sequences. The mean cost per patient of biomarker testing was 2259.92 ± 1217.10 USD, or 1881.23 ± 1013.15 EUR. Targeted gene panels were most frequently conducted, followed by IHC analysis for programmed cell death protein ligand 1. Typically, the most common biomarkers were assessed within the first tests, and emerging biomarkers were tested further down the test sequence. At the cost of current biomarker testing, replacing current testing with whole-genome sequencing would have led to cost-savings in only two patients (2%).
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Affiliation(s)
- Michiel van de Ven
- Health Technology and Services Research, TechMed Center, University of Twente, Enschede, the Netherlands
| | - Hendrik Koffijberg
- Health Technology and Services Research, TechMed Center, University of Twente, Enschede, the Netherlands
| | - Valesca Retèl
- Health Technology and Services Research, TechMed Center, University of Twente, Enschede, the Netherlands; Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Department of Pathology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Egbert Smit
- Department of Thoracic Oncology, Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, the Netherlands
| | - Wim van Harten
- Health Technology and Services Research, TechMed Center, University of Twente, Enschede, the Netherlands; Rijnstate General Hospital, Arnhem, the Netherlands
| | - Maarten IJzerman
- Health Technology and Services Research, TechMed Center, University of Twente, Enschede, the Netherlands; Centre for Cancer Research and Centre for Health Policy, University of Melbourne, Melbourne, Australia; Peter MacCallum Cancer Centre, Melbourne, Australia.
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Gallon R, Gawthorpe P, Phelps RL, Hayes C, Borthwick GM, Santibanez-Koref M, Jackson MS, Burn J. How Should We Test for Lynch Syndrome? A Review of Current Guidelines and Future Strategies. Cancers (Basel) 2021; 13:406. [PMID: 33499123 PMCID: PMC7865939 DOI: 10.3390/cancers13030406] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/13/2022] Open
Abstract
International guidelines for the diagnosis of Lynch syndrome (LS) recommend molecular screening of colorectal cancers (CRCs) to identify patients for germline mismatch repair (MMR) gene testing. As our understanding of the LS phenotype and diagnostic technologies have advanced, there is a need to review these guidelines and new screening opportunities. We discuss the barriers to implementation of current guidelines, as well as guideline limitations, and highlight new technologies and knowledge that may address these. We also discuss alternative screening strategies to increase the rate of LS diagnoses. In particular, the focus of current guidance on CRCs means that approximately half of Lynch-spectrum tumours occurring in unknown male LS carriers, and only one-third in female LS carriers, will trigger testing for LS. There is increasing pressure to expand guidelines to include molecular screening of endometrial cancers, the most frequent cancer in female LS carriers. Furthermore, we collate the evidence to support MMR deficiency testing of other Lynch-spectrum tumours to screen for LS. However, a reliance on tumour tissue limits preoperative testing and, therefore, diagnosis prior to malignancy. The recent successes of functional assays to detect microsatellite instability or MMR deficiency in non-neoplastic tissues suggest that future diagnostic pipelines could become independent of tumour tissue.
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Affiliation(s)
| | | | | | | | | | | | | | - John Burn
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK; (P.G.); (R.L.P.); (C.H.); (G.M.B.); (M.S.-K.); (M.S.J.)
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Mosele F, Remon J, Mateo J, Westphalen CB, Barlesi F, Lolkema MP, Normanno N, Scarpa A, Robson M, Meric-Bernstam F, Wagle N, Stenzinger A, Bonastre J, Bayle A, Michiels S, Bièche I, Rouleau E, Jezdic S, Douillard JY, Reis-Filho JS, Dienstmann R, André F. Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group. Ann Oncol 2020; 31:1491-1505. [PMID: 32853681 DOI: 10.1016/j.annonc.2020.07.014] [Citation(s) in RCA: 644] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 07/20/2020] [Indexed: 02/06/2023] Open
Abstract
Next-generation sequencing (NGS) allows sequencing of a high number of nucleotides in a short time frame at an affordable cost. While this technology has been widely implemented, there are no recommendations from scientific societies about its use in oncology practice. The European Society for Medical Oncology (ESMO) is proposing three levels of recommendations for the use of NGS. Based on the current evidence, ESMO recommends routine use of NGS on tumour samples in advanced non-squamous non-small-cell lung cancer (NSCLC), prostate cancers, ovarian cancers and cholangiocarcinoma. In these tumours, large multigene panels could be used if they add acceptable extra cost compared with small panels. In colon cancers, NGS could be an alternative to PCR. In addition, based on the KN158 trial and considering that patients with endometrial and small-cell lung cancers should have broad access to anti-programmed cell death 1 (anti-PD1) antibodies, it is recommended to test tumour mutational burden (TMB) in cervical cancers, well- and moderately-differentiated neuroendocrine tumours, salivary cancers, thyroid cancers and vulvar cancers, as TMB-high predicted response to pembrolizumab in these cancers. Outside the indications of multigene panels, and considering that the use of large panels of genes could lead to few clinically meaningful responders, ESMO acknowledges that a patient and a doctor could decide together to order a large panel of genes, pending no extra cost for the public health care system and if the patient is informed about the low likelihood of benefit. ESMO recommends that the use of off-label drugs matched to genomics is done only if an access programme and a procedure of decision has been developed at the national or regional level. Finally, ESMO recommends that clinical research centres develop multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development, and prospectively capture the data that could further inform how to optimise the use of this technology.
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Affiliation(s)
- F Mosele
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - J Remon
- Department of Medical Oncology, Centro Integral Oncológico Clara Campal (HM-CIOCC), Hospital HM Delfos, HM Hospitales, Barcelona, Spain
| | - J Mateo
- Clinical Research Program, Vall Hebron Institute of Oncology (VHIO) and Vall d'Hebron University Hospital, Barcelona, Spain
| | - C B Westphalen
- Comprehensive Cancer Center Munich and Department of Medicine III, University Hospital, LMU Munich, Munich, Germany
| | - F Barlesi
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - M P Lolkema
- Department of Medical Oncology, Erasmus MC Cancer Center, Rotterdam, the Netherlands
| | - N Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, 'Fondazione G. Pascale' - IRCCS, Naples, Italy
| | - A Scarpa
- ARC-Net Research Centre and Department of Diagnostics and Public Health - Section of Pathology, University of Verona, Verona, Italy
| | - M Robson
- Breast Medicine and Clinical Genetics Services, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - N Wagle
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA
| | - A Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - J Bonastre
- Department of Biostatistics and Epidemiology, Gustave Roussy, University Paris-Saclay, Villejuif, France; Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - A Bayle
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Department of Biostatistics and Epidemiology, Gustave Roussy, University Paris-Saclay, Villejuif, France; Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - S Michiels
- Department of Biostatistics and Epidemiology, Gustave Roussy, University Paris-Saclay, Villejuif, France; Oncostat U1018, Inserm, University Paris-Saclay, labeled Ligue Contre le Cancer, Villejuif, France
| | - I Bièche
- Department of Genetics, Institut Curie, Paris Descartes University, Paris, France
| | - E Rouleau
- Cancer Genetic Laboratories, Department of Medical Biology and Pathology, Gustave Roussy Cancer Campus, Villejuif, France
| | - S Jezdic
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - J-Y Douillard
- Scientific and Medical Division, European Society for Medical Oncology, Lugano, Switzerland
| | - J S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - R Dienstmann
- Oncology Data Science Group, Molecular Prescreening Program, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - F André
- Department of Medical Oncology, Gustave Roussy, Villejuif, France; Inserm, Gustave Roussy Cancer Campus, UMR981, Villejuif, France; Paris Saclay University, Orsay, France.
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Siamoglou S, Karamperis K, Mitropoulou C, Patrinos GP. Costing Methods as a Means to Measure the Costs of Pharmacogenomics Testing. J Appl Lab Med 2020; 5:1005-1016. [PMID: 32916714 DOI: 10.1093/jalm/jfaa113] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 06/24/2020] [Indexed: 12/26/2022]
Abstract
Clinical implementation of pharmacogenomics and personalized medicine interventions relies on addressing important financial aspects of the delivery of genetic testing to the patients, be it from public or private providers. Details on how to determine the cost items of the genetic testing are often limited. The goal of this study is to present a costing methodology in order to estimate and measure the costs as far as the technical process of pharmacogenomics testing is concerned. Moreover, an overall cost mindset strategy based on the selective genotyping workflow to guide specialized laboratories of interest effectively is provided. We particularly accounted for the resources consumed within the laboratory premises such as cost of reagents for DNA isolation, cost of consumables, cost of personnel, while costs associated with patient recruitment, blood sample collection and maintenance, administration costs in the hospital, and costs of blood sample shipment were not taken into consideration. Our article presents the first-time detailed information on a costing framework for pharmacogenomic testing that could be employed to laboratories involved in routine clinical implementation of pharmacogenomics.
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Affiliation(s)
- Stavroula Siamoglou
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Kariofyllis Karamperis
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,The Golden Helix Foundation, London, UK
| | | | - George P Patrinos
- Laboratory of Pharmacogenomics and Individualized Therapy, Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE.,Zayed Center of Health Sciences, United Arab Emirates University, Al-Ain, Abu Dhabi, UAE
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35
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Gao G, Smith DI. Clinical Massively Parallel Sequencing. Clin Chem 2020; 66:77-88. [PMID: 31811004 DOI: 10.1373/clinchem.2019.303305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/24/2019] [Indexed: 01/13/2023]
Abstract
BACKGROUND The newest advances in DNA sequencing are based on technologies that perform massively parallel sequencing (MPS). Since 2006, the output from MPS platforms has increased from 20 Mb to >7 Tb. First-generation MPS platforms amplify individual DNA molecules to multiple copies and then interrogate the sequence of those molecules. Second-generation MPS analyzes single unamplified molecules to generate much longer sequence reads but with less output than first-generation MPS and lower first-pass accuracy. With MPS technologies, it is now possible to analyze genomes, exomes, a defined subset of genes, transcriptomes, and even methylation across the genome. These technologies have and will continue to completely transform the clinical practice. CONTENT The major first- and second-generation MPS platforms and how they are used in clinical practice are discussed. SUMMARY The ability to sequence terabases of DNA per run on an MPS platform will dramatically change how DNA sequencing is used in clinical practice. Currently, MPS of targeted gene panels is the most common use of this technology clinically, but as the cost for genome sequencing inches downward to $100, this may soon become the method of choice (with the caveat that, at least in the near term, clinical-grade genome sequencing with interpretation may cost much more than $100). Other uses of this technology include sequencing of a mixture of bacterial and viral species (metagenomics), as well as the characterization of methylation across the genome.
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Affiliation(s)
- Ge Gao
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - David I Smith
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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36
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Coquerelle S, Darlington M, Michel M, Durand M, Borget I, Baffert S, Marino P, Perrier L, Durand-Zaleski I. Impact of Next Generation Sequencing on Clinical Practice in Oncology in France: Better Genetic Profiles for Patients Improve Access to Experimental Treatments. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2020; 23:898-906. [PMID: 32762992 DOI: 10.1016/j.jval.2020.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/11/2020] [Accepted: 03/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVES We evaluated how next generation sequencing (NGS) can modify care pathways in an observational impact study in France. METHODS All patients with lung cancer, colorectal cancer, or melanoma who had NGS analyses of somatic genomic alterations done in 1 of 7 biomolecular platforms certified by the French National Cancer Institute (INCa) between 2013 and 2016 were eligible. We compared patients' pathways before and after their NGS results. Endpoints consisted of the turnaround time in obtaining results, the number of patients with at least 1 genomic alteration identified, the number of actionable alterations, the impact of the genomic multidisciplinary tumor board on care pathways, the number of changes in the treatment plan, and the survival outcome up to 1 year after NGS analyses. RESULTS 1213 patients with a request for NGS analysis were included. NGS was performed for 1155 patients, identified at least 1 genomic alteration for 867 (75%), and provided an actionable alteration for 614 (53%). Turnaround time between analyses and results was on average 8 days (Min: 0; Max: 95) for all cancer types. Before NGS analysis, 33 of 614 patients (5%) were prescribed a targeted therapy compared with 54 of 614 patients (8%) after NGS analysis. Proposition of inclusion in clinical trials with experimental treatments increased from 5% (n = 31 of 614) before to 28% (n = 178 of 614) after NGS analysis. Patients who benefited from a genotype matched treatment after NGS analysis tended to have a better survival outcome at 1 year than patients with nonmatched treatment: 258 days (±107) compared with 234 days (±106), (P = .41). CONCLUSIONS NGS analyses resulted in a change in patients' care pathways for 20% of patients (n = 232 of 1155).
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Affiliation(s)
- Séverine Coquerelle
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Centre of Research in Epidemiology and Statistics, Institut National de la Santé et de la Recherche Médicale-Joint Research Units, Paris, France.
| | - Meryl Darlington
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Morgane Michel
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France; Institut National de la Santé et de la Recherche Médicale, Epidémiologie Clinique et Evaluation Economique, Paris, France
| | - Manon Durand
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Isabelle Borget
- Etudes et Recherche en Economie de la Santé, Gustave Roussy Institute, Villejuif, France
| | | | - Patricia Marino
- Institut Paoli Calmettes, Sciences Economiques et Sociales de la Santé et Traitement de l'information Médicale, Marseille, France
| | - Lionel Perrier
- Université de Lyon, Centre Léon Bérard, Groupe d'Analyse de Théorie Economique, Lyon Saint-Etienne-Joint Research Units, Lyon, France
| | - Isabelle Durand-Zaleski
- Unité de Recherche Clinique en Économie de la Santé d'Ile de France, Assistance Publique Hôpitaux de Paris, Paris, France; Centre of Research in Epidemiology and Statistics, Institut National de la Santé et de la Recherche Médicale-Joint Research Units, Paris, France; Public Health Department, Hôpital Henri-Mondor, Assistance Publique Hôpitaux de Paris, Créteil, France
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37
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Personalized Nutrition for Management of Micronutrient Deficiency-Literature Review in Non-bariatric Populations and Possible Utility in Bariatric Cohort. Obes Surg 2020; 30:3570-3582. [PMID: 32564308 PMCID: PMC7378102 DOI: 10.1007/s11695-020-04762-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023]
Abstract
Background Bariatric surgery can effectively treat morbid obesity; however, micronutrient deficiencies are common despite recommendations for high-dose supplements. Genetic predisposition to deficiencies underscores necessary identification of high-risk candidates. Personalized nutrition (PN) can be a tool to manage these deficiencies. Methods Medline, PubMed, and Google Scholar were searched. Articles involving genetic testing, micronutrient metabolism, and bariatric surgery were included. Results Studies show associations between genetic variants and micronutrient metabolism. Research demonstrates genetic testing to be a predictor for outcomes among obesity and bariatric surgery populations. There is limited research in bariatric surgery and micronutrient genetic variants. Conclusion Genotype-based PN is becoming feasible to provide an effective treatment of micronutrient deficiencies associated with bariatric surgery. The role of genomic technology in micronutrient recommendations needs further investigation.
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Miao X, Li B, Shen Y, Yu H, Zhu G, Liang C, Fu X, Wang C, Li S, Zhang B. Development and Verification of an Economical Method of Custom Target Library Construction. ACS OMEGA 2020; 5:13087-13095. [PMID: 32548494 PMCID: PMC7288555 DOI: 10.1021/acsomega.0c01014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/21/2020] [Indexed: 05/13/2023]
Abstract
Although technological advances have greatly reduced the cost of DNA sequencing, sample preparation time and reagent costs remain the limiting factors for many studies. Based on low-cost targeted amplification, we developed an economical method for custom target library construction based on DNA nanoball (DNB) technology and two-step polymerase chain reaction (PCR). Here, we refer to this method as the two-step PCR, which was compared to traditional multiplex PCR methods in three aspects, data quality, efficiency, and specificity to humans. The results confirmed that two-step PCR reduces to finishing 128 sequencing libraries in only 2 h 24 min 59 s of the total PCR time and at a data utilization rate of 0.44 at a cost of approximately $1.70 per sample for targeted sequencing via the two-step PCR. The replacement of traditional multiplex PCR methods with this strategy makes the sample preparation process before sequencing relatively more cost-effective and further reduces the cost of next-generation sequencing (NGS). This method may also be free from the interference of other species and the limitations of sample type and DNA content. These findings reveal possibilities for broad applications of this approach in forensic research.
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Affiliation(s)
- Xinyao Miao
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Bowen Li
- School
of Life Sciences, Sichuan University, 610207 Chengdu, P. R. China
| | - Yuesheng Shen
- School
of Life Sciences, Northwest University, 710069 Xi’an, P. R. China
| | - Huiyun Yu
- School
of Life Sciences, Northwest A&F University, 712100 Yangling, P. R. China
| | - Guoqiang Zhu
- Key
Laboratory of Bio-Resources and Eco-Environment of Ministry of Education,
College of Life Sciences, Sichuan University, 610065 Chengdu, P. R. China
| | - Chen Liang
- School of
Mechanical Engineering, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Xiao Fu
- The
Beijing Genomics Institute (BGI)—Tianjin, 301700 Tianjin, P. R. China
| | - Chu Wang
- School
of Life Sciences, Xiamen Medical College, 361023 Xiamen, P. R. China
| | - Shengbin Li
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
| | - Bao Zhang
- School
of Forensic Sciences, Xi’an Jiaotong
University, 710049 Xi’an, P. R. China
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Estimating the costs of genomic sequencing in cancer control. BMC Health Serv Res 2020; 20:492. [PMID: 32493298 PMCID: PMC7268398 DOI: 10.1186/s12913-020-05318-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 05/11/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite the rapid uptake of genomic technologies within cancer care, few studies provide detailed information on the costs of sequencing across different applications. The objective of the study was to examine and categorise the complete costs involved in genomic sequencing for a range of applications within cancer settings. METHODS We performed a cost-analysis using gross and micro-costing approaches for genomic sequencing performed during 2017/2018 across different settings in Brisbane, Australia. Sequencing was undertaken for patients with lung, breast, oesophageal cancers, melanoma or mesothelioma. Aggregated resource data were captured for a total of 1433 patients and point estimates of per patient costs were generated. Deterministic sensitivity analyses addressed the uncertainty in the estimates. Estimated costs to the public health system for resources were categorised into seven distinct activities in the sequencing process: sampling, extraction, library preparation, sequencing, analysis, data storage and clinical reporting. Costs were also aggregated according to labour, consumables, testing, equipment and 'other' categories. RESULTS The per person costs were AU$347-429 (2018 US$240-297) for targeted panels, AU$871-$2788 (2018 US$604-1932) for exome sequencing, and AU$2895-4830 (2018 US$2006-3347) for whole genome sequencing. Cost proportions were highest for library preparation/sequencing materials (average 76.8% of total costs), sample extraction (8.1%), data analysis (9.2%) and data storage (2.6%). Capital costs for the sequencers were an additional AU$34-197 (2018 US$24-67) per person. CONCLUSIONS Total costs were most sensitive to consumables and sequencing activities driven by commercial prices. Per person sequencing costs for cancer are high when tumour/blood pairs require testing. Using the natural steps involved in sequencing and categorising resources accordingly, future evaluations of costs or cost-effectiveness of clinical genomics across cancer projects could be more standardised and facilitate easier comparison of cost drivers.
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40
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Wang HY, Chen CH, Shi S, Chung CR, Wen YH, Wu MH, Lebowitz MS, Zhou J, Lu JJ. Improving Multi-Tumor Biomarker Health Check-up Tests with Machine Learning Algorithms. Cancers (Basel) 2020; 12:E1442. [PMID: 32492934 PMCID: PMC7352838 DOI: 10.3390/cancers12061442] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tumor markers are used to screen tens of millions of individuals worldwide at annual health check-ups, especially in East Asia. Machine learning (ML)-based algorithms that improve the diagnostic accuracy and clinical utility of these tests can have substantial impact leading to the early diagnosis of cancer. METHODS ML-based algorithms, including a cancer screening algorithm and a secondary organ of origin algorithm, were developed and validated using a large real world dataset (RWD) from asymptomatic individuals undergoing routine cancer screening at a Taiwanese medical center between May 2001 and April 2015. External validation was performed using data from the same period from a separate medical center. The data set included tumor marker values, age, and gender from 27,938 individuals, including 342 subsequently confirmed cancer cases. RESULTS Separate gender-specific cancer screening algorithms were developed. For men, a logistic regression-based algorithm outperformed single-marker and other ML-based algorithms, with a mean area under the receiver operating characteristic curve (AUROC) of 0.7654 in internal and 0.8736 in external cross validation. For women, a random forest-based algorithm attained a mean AUROC of 0.6665 in internal and 0.6938 in external cross validation. The median time to cancer diagnosis (TTD) in men was 451.5, 204.5, and 28 days for the mild, moderate, and high-risk groups, respectively; for women, the median TTD was 229, 132, and 125 days for the mild, moderate, and high-risk groups. A second algorithm was developed to predict the most likely affected organ systems for at-risk individuals. The algorithm yielded 0.8120 sensitivity and 0.6490 specificity for men, and 0.8170 sensitivity and 0.6750 specificity for women. CONCLUSIONS ML-derived algorithms, trained and validated by using a RWD, can significantly improve tumor marker-based screening for multiple types of early stage cancers, suggest the tissue of origin, and provide guidance for patient follow-up.
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Affiliation(s)
- Hsin-Yao Wang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33305, Taiwan; (H.-Y.W.); (C.-H.C.); (Y.-H.W.)
- 20/20 GeneSystems, Inc., Rockville, MD 20850, USA; (S.S.); (M.S.L.)
- Program in Biomedical Engineering, Chang Gung University, Taoyuan City 33301, Taiwan
| | - Chun-Hsien Chen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33305, Taiwan; (H.-Y.W.); (C.-H.C.); (Y.-H.W.)
- Department of Information Management, Chang Gung University, Taoyuan City 33301, Taiwan
| | - Steve Shi
- 20/20 GeneSystems, Inc., Rockville, MD 20850, USA; (S.S.); (M.S.L.)
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan City 32001, Taiwan;
| | - Ying-Hao Wen
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33305, Taiwan; (H.-Y.W.); (C.-H.C.); (Y.-H.W.)
| | - Min-Hsien Wu
- Graduate Institute of Biomedical Engineering, Chang Gung University, Taoyuan City 33301, Taiwan;
| | | | - Jiming Zhou
- 20/20 GeneSystems, Inc., Rockville, MD 20850, USA; (S.S.); (M.S.L.)
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou, Taoyuan City 33305, Taiwan; (H.-Y.W.); (C.-H.C.); (Y.-H.W.)
- 20/20 GeneSystems, Inc., Rockville, MD 20850, USA; (S.S.); (M.S.L.)
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan City 33301, Taiwan
- Department of Medicine, College of Medicine, Chang Gung University, Taoyuan City 33301, Taiwan
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Next-Generation Sequencing of the Ocular Surface Microbiome: In Health, Contact Lens Wear, Diabetes, Trachoma, and Dry Eye. Eye Contact Lens 2020; 46:254-261. [DOI: 10.1097/icl.0000000000000697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Torres S, González Á, Cunquero Tomas AJ, Calabuig Fariñas S, Ferrero M, Mirda D, Sirera R, Jantus-Lewintre E, Camps C. A profile on cobas® EGFR Mutation Test v2 as companion diagnostic for first-line treatment of patients with non-small cell lung cancer. Expert Rev Mol Diagn 2020; 20:575-582. [PMID: 32011193 DOI: 10.1080/14737159.2020.1724094] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Among non-small cell lung cancer (NSCLC) patients, there is one molecularly defined subgroup harboring activating mutations in the epidermal growth factor receptor gene (EGFR), which results in constitutive activation of its intrinsic kinase activity. Consistent data have demonstrated that these patients have a better outcome when treated with specific tyrosine-kinase inhibitors (EGFR-TKIs). Therefore, analysis of EGFR mutational status for treatment guidance is mandatory in this context. AREAS COVERED Herein we review the clinical development and technical features of cobas® EGFR Mutation Test v2 as a companion diagnostic test (CDx) for therapy with EGFR-TKIs, such as gefitinib, in advanced NSCLC. We also discuss the pros and cons of the current version of the CDx and its performance in both tissue and plasma samples. EXPERT OPINION The RT-PCR based cobas® EGFR Mutation Test v2 is a reliable and rapid solution for EGFR mutational status assessment at the time of diagnosis in advanced NSCLC that allows eligibility of patients for EGFR-TKI treatment. This test determines EGFR mutations with acceptable sensitivity in tissue or plasma samples. Pre-analytical considerations like tumor cell content, tumor burden or location of metastasis should be considered to better interpret results in the clinical contexture.
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Affiliation(s)
- Susana Torres
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain.,CIBERONC , Madrid, Spain.,Mixed Unit TRIAL CIPF-FIHGUV , Valencia, Spain
| | - Álvaro González
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain
| | | | - Silvia Calabuig Fariñas
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain.,CIBERONC , Madrid, Spain.,Mixed Unit TRIAL CIPF-FIHGUV , Valencia, Spain.,Department of Pathology, Universitat de València , Valencia, Spain
| | - Macarena Ferrero
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain
| | - Danielle Mirda
- George Washington University School of Medicine and Health Sciences , Washington, DC, USA
| | - Rafael Sirera
- CIBERONC , Madrid, Spain.,Mixed Unit TRIAL CIPF-FIHGUV , Valencia, Spain.,Department of Biotechnology, Universitat Politècnica de València , Valencia, Spain
| | - Eloisa Jantus-Lewintre
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain.,CIBERONC , Madrid, Spain.,Mixed Unit TRIAL CIPF-FIHGUV , Valencia, Spain.,Department of Biotechnology, Universitat Politècnica de València , Valencia, Spain
| | - Carlos Camps
- Molecular Oncology Laboratory, General University Hospital Research Foundation , Valencia, Spain.,CIBERONC , Madrid, Spain.,Mixed Unit TRIAL CIPF-FIHGUV , Valencia, Spain.,Medical Oncology Department, General University Hospital of Valencia , Valencia, Spain.,Department of Medicine, Universitat de València , Valencia, Spain
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Cohen D, Hondelink LM, Solleveld-Westerink N, Uljee SM, Ruano D, Cleton-Jansen AM, von der Thüsen JH, Ramai SRS, Postmus PE, Graadt van Roggen JF, Hoppe BPC, Clahsen PC, Maas KW, Ahsmann EJM, Ten Heuvel A, Smedts F, van Rossem RN, van Wezel T. Optimizing Mutation and Fusion Detection in NSCLC by Sequential DNA and RNA Sequencing. J Thorac Oncol 2020; 15:1000-1014. [PMID: 32014610 DOI: 10.1016/j.jtho.2020.01.019] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Frequently, patients with locally advanced or metastatic NSCLC are screened for mutations and fusions. In most laboratories, molecular workup includes a multitude of tests: immunohistochemistry (ALK, ROS1, and programmed death-ligand 1 testing), DNA sequencing, in situ hybridization for fusion, and amplification detection. With the fast-emerging new drugs targeting specific fusions and exon-skipping events, this procedure harbors a growing risk of tissue exhaustion. METHODS In this study, we evaluated the benefit of anchored, multiplexed, polymerase chain reaction-based targeted RNA sequencing (RNA next-generation sequencing [NGS]) in the identification of gene fusions and exon-skipping events in patients, in which no pathogenic driver mutation was found by DNA-based targeted cancer hotspot NGS (DNA NGS). We analyzed a cohort of stage IV NSCLC cases from both in-house and referral hospitals, consisting 38.5% cytology samples and 61.5% microdissected histology samples, mostly core needle biopsies. We compared molecular findings in a parallel workup (DNA NGS and RNA NGS, cohort 1, n = 198) with a sequential workup (DNA NGS followed by RNA NGS in selected cases, cohort 2, n = 192). We hypothesized the sequential workup to be the more efficient procedure. RESULTS In both cohorts, a maximum of one oncogenic driver mutation was found per case. This is in concordance with large, whole-genome databases and suggests that it is safe to omit RNA NGS when a clear oncogenic driver is identified in DNA NGS. In addition, this reduced the number of necessary RNA NGS to only 53% of all cases. The tumors of never smokers, however, were enriched for fusions and exon-skipping events (32% versus 4% in former and current smokers, p = 0.00), and therefore benefited more often from the shorter median turnaround time of the parallel approach (15 d versus only 9 d in the parallel workup). CONCLUSIONS We conclude that sequentially combining DNA NGS and RNA NGS is the most efficient strategy for mutation and fusion detection in smoking-associated NSCLC, whereas for never smokers we recommend a parallel approach. This approach was shown to be feasible on small tissue samples including for cytology tests, can drastically reduce the complexity and cost of molecular workup, and also provides flexibility in the constantly evolving landscape of actionable targets in NSCLC.
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Affiliation(s)
- Danielle Cohen
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands.
| | - Liesbeth M Hondelink
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | | | - Sandra M Uljee
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | | | - Jan H von der Thüsen
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - S Rajen S Ramai
- Department of Pulmonology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | - Pieter E Postmus
- Department of Pulmonology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
| | | | - Bart P C Hoppe
- Department of Pulmonology, Alrijne Hospital, Leiderdorp, The Netherlands
| | - Pieter C Clahsen
- Department of Pathology, Haaglanden Medical Centre (HMC), Den Haag, The Netherlands
| | - Klaartje W Maas
- Department of Pulmonology, Haaglanden Medical Centre (HMC), Den Haag, The Netherlands
| | - Els J M Ahsmann
- Department of Pathology, Groene Hart Hospital (GHZ), Gouda, The Netherlands
| | | | - Frank Smedts
- Department of Pathology, Reinier de Graaf gasthuis (RdGG), Delft, The Netherlands
| | - Ronald N van Rossem
- Department of Pulmonology, Reinier de Graaf gasthuis (RdGG), Delft, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Centre (LUMC), Leiden, The Netherlands
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Song W, Platteel I, Suurmeijer AJH, van Kempen LC. Diagnostic yield of NanoString nCounter FusionPlex profiling in soft tissue tumors. Genes Chromosomes Cancer 2020; 59:318-324. [PMID: 31965673 PMCID: PMC7079105 DOI: 10.1002/gcc.22834] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/17/2020] [Accepted: 01/17/2020] [Indexed: 11/11/2022] Open
Abstract
Diagnostic histopathology of soft tissue tumors can be troublesome as many entities are quite rare and have overlapping morphologic features. Many soft tissue tumors harbor tumor‐defining gene translocations, which may provide an important ancillary tool for tumor diagnosis. The NanoString nCounter platform enables multiplex detection of pre‐defined gene fusion transcripts in formalin‐fixed and paraffin‐embedded tissue. A cohort of 104 soft tissue tumors representing 20 different histological types was analyzed for the expression of 174 unique gene fusion transcripts. A tumor‐defining gene fusion transcript was detected in 60 cases (58%). Sensitivity and specificity of the NanoString assay calculated against the result of an alternative molecular method were 85% and 100%, respectively. Highest diagnostic coverage was obtained for Ewing sarcoma, synovial sarcoma, myxoid liposarcoma, alveolar rhabdomyosarcoma, and desmoplastic small round cell tumor. For these tumor types, the NanoString assay is a rapid, cost‐effective, sensitive, and specific ancillary screening tool for molecular diagnosis. For other sarcomas, additional molecular testing may be required when a translocation transcript is not identified with the current 174 gene fusion panel.
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Affiliation(s)
- Wangzhao Song
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Inge Platteel
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Albert J H Suurmeijer
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Léon C van Kempen
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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45
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Horiuchi S, Saito Y, Matsui A, Takahashi N, Ikeya T, Hoshi E, Shimizu Y, Yasuda M. A novel loop‑mediated isothermal amplification method for efficient and robust detection of EGFR mutations. Int J Oncol 2020; 56:743-749. [PMID: 32124949 PMCID: PMC7010225 DOI: 10.3892/ijo.2020.4961] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 12/12/2019] [Indexed: 12/23/2022] Open
Abstract
The activation of somatic mutations conferring sensitivity to epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors has been widely used in the development of advanced or metastatic primary lung cancer therapy. Therefore, identification of EGFR mutations is essential. In the present study, a loop-mediated isothermal amplification (LAMP) method was used to identify EGFR mutations, and its efficiency was compared with the Therascreen quantitative PCR assay. Using LAMP and Therascreen to analyze surgically resected tissue samples from patients with pulmonary adenocarcinoma, EGFR mutations were observed in 32/59 tumor samples (LAMP) and 33/59 tumor samples (Therascreen). Notably, the LAMP assay identified one tumor as wild-type, which had previously been identified as a deletion mutation in exon 19 via the Therascreen assay (Case X). However, the direct sequencing to confirm the EGFR status of the Case X adhered to the results of the LAMP assay. Further experiments using Case X DNA identified this exon 19 deletion mutation using both methods. In addition, a novel deletion mutation in exon 19 of the EGFR was identified. Overall, the present study shows that the LAMP method may serve as a valuable alternative for the identification oncogene mutations.
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Affiliation(s)
- Sho Horiuchi
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka 350‑1298, Japan
| | - Yuichi Saito
- Department of Thoracic Surgery, Saitama Cardiovascular and Respiratory Center, Kumagaya, Saitama 360‑0197, Japan
| | - Atsuka Matsui
- Fundamental Research Laboratory, Fundamental Technology Research Department, Eiken Chemical Co., Ltd., Otawara, Tochigi 324‑0036, Japan
| | - Nobumasa Takahashi
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Tomohiko Ikeya
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Eishin Hoshi
- Department of Surgery, Teikyo University School of Medicine, Tokyo 173‑8605, Japan
| | - Yoshihiko Shimizu
- Department of Pathology, Saitama Cardiovascular and Respiratory Center, Kumagaya, Saitama 360‑0197, Japan
| | - Masanori Yasuda
- Department of Pathology, Saitama Medical University International Medical Center, Hidaka 350‑1298, Japan
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Gallon R, Sheth H, Hayes C, Redford L, Alhilal G, O'Brien O, Spiewak H, Waltham A, McAnulty C, Izuogu OG, Arends MJ, Oniscu A, Alonso AM, Laguna SM, Borthwick GM, Santibanez‐Koref M, Jackson MS, Burn J. Sequencing-based microsatellite instability testing using as few as six markers for high-throughput clinical diagnostics. Hum Mutat 2020; 41:332-341. [PMID: 31471937 PMCID: PMC6973255 DOI: 10.1002/humu.23906] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/14/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022]
Abstract
Microsatellite instability (MSI) testing of colorectal cancers (CRCs) is used to screen for Lynch syndrome (LS), a hereditary cancer-predisposition, and can be used to predict response to immunotherapy. Here, we present a single-molecule molecular inversion probe and sequencing-based MSI assay and demonstrate its clinical validity according to existing guidelines. We amplified 24 microsatellites in multiplex and trained a classifier using 98 CRCs, which accommodates marker specific sensitivities to MSI. Sample classification achieved 100% concordance with the MSI Analysis System v1.2 (Promega) in three independent cohorts, totaling 220 CRCs. Backward-forward stepwise selection was used to identify a 6-marker subset of equal accuracy to the 24-marker panel. Assessment of assay detection limits showed that the 24-marker panel is marginally more robust to sample variables than the 6-marker subset, detecting as little as 3% high levels of MSI DNA in sample mixtures, and requiring a minimum of 10 template molecules to be sequenced per marker for >95% accuracy. BRAF c.1799 mutation analysis was also included to streamline LS testing, with all c.1799T>A variants being correctly identified. The assay, therefore, provides a cheap, robust, automatable, and scalable MSI test with internal quality controls, suitable for clinical cancer diagnostics.
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Affiliation(s)
- Richard Gallon
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Harsh Sheth
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
- FRIGE's Institute of Human GeneticsFRIGE HouseAhmedabadIndia
| | - Christine Hayes
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Lisa Redford
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Ghanim Alhilal
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Ottilia O'Brien
- Northern Genetics ServiceNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUnited Kingdom
| | - Helena Spiewak
- Northern Genetics ServiceNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUnited Kingdom
| | - Amanda Waltham
- Northern Genetics ServiceNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUnited Kingdom
| | - Ciaron McAnulty
- Northern Genetics ServiceNewcastle Hospitals NHS Foundation TrustNewcastle upon TyneUnited Kingdom
| | - Osagie G. Izuogu
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - Mark J. Arends
- Division of Pathology, Institute of Genetics & Molecular MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Anca Oniscu
- Department of Molecular Pathology, Laboratory MedicineRoyal Infirmary of EdinburghEdinburghUnited Kingdom
| | - Angel M. Alonso
- Oncogenetics and Hereditary Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Instituto de Investigación Sanitaria de Navarra (IdiSNA)Universidad Pública de Navarra (UPNA)PamplonaSpain
| | - Sira M. Laguna
- Oncogenetics and Hereditary Cancer Group, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Instituto de Investigación Sanitaria de Navarra (IdiSNA)Universidad Pública de Navarra (UPNA)PamplonaSpain
| | - Gillian M. Borthwick
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | | | - Michael S. Jackson
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
| | - John Burn
- Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUnited Kingdom
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Marchetti A, Di Lorito A, Felicioni L, Buttitta F. An innovative diagnostic strategy for the detection of rare molecular targets to select cancer patients for tumor-agnostic treatments. Oncotarget 2019; 10:6957-6968. [PMID: 31857850 PMCID: PMC6916754 DOI: 10.18632/oncotarget.27343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/26/2019] [Indexed: 12/25/2022] Open
Abstract
Targeted therapies are playing an increasing role in oncology. Among them, particular attention is nowadays reserved to histology-agnostic treatments. Rare molecular alterations affecting different neoplastic forms, such as Microsatellite Instability (MSI), Neurotropic Tyrosine Receptor Kinase (NTRK) gene fusions, etc., can allow efficient treatments, irrespective of the histologic type. Developing an effective testing strategy for the detection of rare molecular alterations is challenging. We report an innovative diagnostic strategy for a rapid and economically affordable detection of this uncommon targets. Malignant tumor samples are selected at the time of histopathological diagnosis and further processed for simultaneous analysis of multiple samples on Tissue Micro Arrays (TMAs) and Tissue Slice Arrays (TSAs). The TSA approach was specifically designed for large scale screening of small biopsies. TMA sections and TSA were first screened by immunohistochemistry (IHC) for the expression of mismatch repair and TRK proteins. Positive cases were subjected to confirmation tests (fragment analysis/FISH/NGS). In a series of 1865 malignant tumors, 48 (2.6%) MSI cases and 6 (0.3%) NTRK fusion cases were detected in 9 and 4 different tumor forms, respectively. On average, the TMA/TSA screening approach enabled IHC analysis of about 20 patients simultaneously with significant saving of time and costs. In addition, we have shown that multiplex IHC can further increment the throughput. A detailed procedure for application of this diagnostic approach in clinical practice is reported. The strategy described may allow an efficient and sustainable selection of tumors carrying rare molecular targets, not to leave behind patients for effective agnostic treatments.
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Affiliation(s)
- Antonio Marchetti
- Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), University of Chieti, Chieti, Italy
- Department of Medical and Oral Sciences and Biotechnologies, University of Chieti, Chieti, Italy
- Department of Pathology, SS Annunziata Clinical Hospital, Chieti, Italy
| | - Alessia Di Lorito
- Department of Medical and Oral Sciences and Biotechnologies, University of Chieti, Chieti, Italy
| | - Lara Felicioni
- Department of Pathology, SS Annunziata Clinical Hospital, Chieti, Italy
| | - Fiamma Buttitta
- Laboratory of Diagnostic Molecular Oncology, Center for Advanced Studies and Technology (CAST), University of Chieti, Chieti, Italy
- Department of Medical and Oral Sciences and Biotechnologies, University of Chieti, Chieti, Italy
- Department of Pathology, SS Annunziata Clinical Hospital, Chieti, Italy
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48
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Fahr P, Buchanan J, Wordsworth S. A Review of the Challenges of Using Biomedical Big Data for Economic Evaluations of Precision Medicine. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2019; 17:443-452. [PMID: 30941659 PMCID: PMC6647451 DOI: 10.1007/s40258-019-00474-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
There is potential value in incorporating biomedical big data (BBD)-observational real-world patient-level genomic and clinical data in multiple sub-populations-into economic evaluations of precision medicine. However, health economists face practical and methodological challenges when using BBD in this context. We conducted a literature review to identify and summarise these challenges. Relevant articles were identified in MEDLINE, EMBASE, EconLit, University of York Centre for Reviews and Dissemination and Cochrane Library from 2000 to 2018. Articles were included if they studied issues relevant to the interconnectedness of biomedical big data, precision medicine, and health economic evaluation. Nineteen articles were included in the review. Challenges identified related to data management, data quality and data analysis. The availability of large volumes of data from multiple sources, the need to conduct data linkages within an environment of opaque data access and sharing procedures, and other data management challenges are primarily practical and may not be long-term obstacles if procedures for data sharing and access are improved. However, the existence of missing data across linked datasets, the need to accommodate dynamic data, and other data quality and analysis challenges may require an evolution in economic evaluation methods. Health economists face challenges when using BBD in economic evaluations of technologies that facilitate precision medicine. Potential solutions to some of these challenges do, however, exist. Going forward, health economists who present work that uses BBD should document challenges and the solutions they have applied to the challenges to support future researcher endeavours.
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Affiliation(s)
- Patrick Fahr
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK.
| | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Old Road Campus, Oxford, OX3 7LF, UK
- National Institute for Health Research Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
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49
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Franczak C, Dubouis L, Gilson P, Husson M, Rouyer M, Demange J, Leroux A, Merlin JL, Harlé A. Integrated routine workflow using next-generation sequencing and a fully-automated platform for the detection of KRAS, NRAS and BRAF mutations in formalin-fixed paraffin embedded samples with poor DNA quality in patients with colorectal carcinoma. PLoS One 2019; 14:e0212801. [PMID: 30811471 PMCID: PMC6392303 DOI: 10.1371/journal.pone.0212801] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 02/10/2019] [Indexed: 01/13/2023] Open
Abstract
Background KRAS and NRAS mutations are identified resistance mutations to anti-epidermal growth factor receptor monoclonal antibodies in patients with metastatic colorectal cancer. BRAF status is also routinely assessed for its poor prognosis value. In our institute, next-generation sequencing (NGS) is routinely used for gene-panel mutations detection including KRAS, NRAS and BRAF, but DNA quality is sometimes not sufficient for sequencing. In our routine practice, Idylla platform is used for the analysis of samples that don’t reach sufficient quality criteria for NGS assay. Methods In this study, data from mCRC samples analyzed from May 2017 to 2018 were retrospectively collected. All samples with a poor DNA quality for sequencing have been assessed using Idylla platform. First, KRAS Idylla assay cartridge has been used for the determination of KRAS mutational status. All KRAS wild-type samples have then been analyzed using NRAS-BRAF assay. Among 669 samples, 67 samples failed the DNA quality control and have been assessed on Idylla KRAS mutation test. Results Among 67 samples, 50 (75%) samples had a valid result with Idylla KRAS mutation test including 22 carrying a KRAS mutation. For 28 samples, NRAS and BRAF mutational statuses have been assessed using Idylla NRAS-BRAF mutation test. Among 28 samples, 27 (96%) had a valid result including 2 samples bearing a NRAS mutation and 3 samples bearing a BRAF mutation. Conclusions Our study shows that an integrated workflow using NGS and Idylla platform allows the determination of KRAS, NRAS and BRAF mutational statuses of 651/669 (97.3%) samples and retrieve 49/67 (73.1%)samples that don’t reach DNA quality requirements for NGS.
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Affiliation(s)
- Claire Franczak
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Ludovic Dubouis
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Pauline Gilson
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Marie Husson
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Marie Rouyer
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Jessica Demange
- Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Agnès Leroux
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Jean-Louis Merlin
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
| | - Alexandre Harlé
- Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Nancy, France
- * E-mail:
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50
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Laviolle B, Perche O, Gueyffier F, Bégué É, Bilbault P, Espérou H, Gaillard-Bigot F, Grenet G, Guérin JF, Guillot C, Longeray PH, Morere J, Perrier L, Sanlaville D, Thevenon J, Varoqueaux N. Apport de la génomique dans la médecine de demain, applications cliniques et enjeux. Therapie 2019; 74:1-8. [DOI: 10.1016/j.therap.2018.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 11/13/2018] [Indexed: 11/24/2022]
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