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Aisagbonhi O, Ghlichloo I, Hong DS, Roma A, Fadare O, Eskander R, Saenz C, Fisch KM, Song W. Comprehensive next-generation sequencing identifies novel putative pathogenic or likely pathogenic germline variants in patients with concurrent tubo-ovarian and endometrial serous and endometrioid carcinomas or precursors. Gynecol Oncol 2024; 187:241-248. [PMID: 38833993 DOI: 10.1016/j.ygyno.2024.05.027] [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: 04/28/2024] [Revised: 05/22/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Endometrial serous carcinoma (ESC) and tubo-ovarian high-grade serous carcinoma (HGSC) are characterized by late-stage presentation and high mortality. Current guidelines for prevention recommend risk-reducing salpingo-oophorectomy (RRSO) in patients with hereditary mutations in cancer susceptibility genes. However, HGSC displays extensive genetic heterogeneity with alterations in 168 genes identified in TCGA study, but current germline testing panels are often limited to the handful of recurrently mutated genes, leaving families with rare hereditary gene mutations potentially at-risk. OBJECTIVE To determine if there are rare germline mutations that may aid in early identification of more patients at-risk for ESC and/or HGSC by evaluating patients with concurrent ESC, HGSC or precursor lesions, and endometrial atypical hyperplasia (CAH) or low-grade endometrial endometrioid adenocarcinoma (LGEEA). METHODS We performed targeted next-generation sequencing using TSO 500, a 523 gene panel, on formalin-fixed paraffin-embedded tumor and matched benign non-tumor tissue blocks from 5 patients with concurrent ESC, HGSC or precursor lesions, and CAH or LGEEA. RESULTS We identified germline pathogenic, likely pathogenic or uncertain significance variants in cancer susceptibility genes in 4 of 5 patients - affected genes included GLI1, PIK3R1, FOXP1, FANCD2, INPP4B and H3F3C. Notably, none of these genes were included in the commercially available germline testing panels initially used to evaluate the patients at the time of their diagnoses. CONCLUSION Comprehensive germline testing of patients with concurrent LGEEA or CAH and ESC, HGSC or precursor lesions may aid in early identification of relatives at-risk for cancer who may be candidates for RRSO with hysterectomy.
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Affiliation(s)
- Omonigho Aisagbonhi
- Department of Pathology, University of California San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
| | - Ida Ghlichloo
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Duncan S Hong
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA; Division of Blood and Marrow Transplantation, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andres Roma
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Oluwole Fadare
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Ramez Eskander
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Saenz
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California, San Diego, La Jolla, CA, USA
| | - Wei Song
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
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Chowdhury A, Thway K, Pasquali S, Callegaro D, Gronchi A, Jones RL, Huang PH. Opportunities and Challenges in Soft Tissue Sarcoma Risk Stratification in the Era of Personalised Medicine. Curr Treat Options Oncol 2024; 25:1124-1135. [PMID: 39080193 DOI: 10.1007/s11864-024-01244-x] [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] [Accepted: 06/28/2024] [Indexed: 08/17/2024]
Abstract
OPINION STATEMENT Soft tissue sarcomas (STS) are a rare and heterogeneous group of cancers. Treatment options have changed little in the past thirty years, and the role of neoadjuvant chemotherapy is controversial. Accurate risk stratification is crucial in STS in order to facilitate clinical discussions around peri-operative treatment. Current risk stratification tools used in clinic, such as Sarculator, use clinicopathological characteristics and may be specific to anatomical site or to histology. More recently, risk stratification tools have been developed using molecular or immunological data. Combining Sarculator with other risk stratification tools may identify novel patient groups with differential clinical outcomes. There are several considerations when translating risk stratification tools into widespread clinical use, including establishing clinical utility, health economic value, being applicable to existing clinical pathways, having strong real-world performance, and being supported by investment into infrastructure. Future work may include incorporation of novel modalities and data integration techniques.
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Affiliation(s)
- Avirup Chowdhury
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road Sutton, London, SM2 5NG, UK
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road Sutton, London, SM2 5NG, UK
- The Royal Marsden NHS Foundation Trust, London, UK
| | - Sandro Pasquali
- Molecular Pharmacology, Department of Experimental Oncology, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Dario Callegaro
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Alessandro Gronchi
- Department of Surgery, Fondazione IRCCS Istituto Nazionale Dei Tumori, Milan, Italy
| | - Robin L Jones
- The Royal Marsden NHS Foundation Trust, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road Sutton, London, SM2 5NG, UK.
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Franklin M, Pollard D, Sah J, Rayner A, Sun Y, Dube F, Sutton A, Qin L. Direct and Indirect Costs of Breast Cancer and Associated Implications: A Systematic Review. Adv Ther 2024; 41:2700-2722. [PMID: 38833143 PMCID: PMC11213812 DOI: 10.1007/s12325-024-02893-y] [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: 03/14/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
INTRODUCTION Breast cancer is currently the leading cause of global cancer incidence. Breast cancer has negative consequences for society and economies internationally due to the high burden of disease which includes adverse epidemiological and economic implications. Our aim is to systematically review the estimated economic burden of breast cancer in the United States (US), Canada, Australia, and Western Europe (United Kingdom, France, Germany, Spain, Italy, Norway, Sweden, Denmark, Netherlands, and Switzerland), with an objective of discussing the policy and practice implications of our results. METHODS We included English-language published studies with cost as a focal point using a primary data source to inform resource usage of women with breast cancer. We focussed on studies published since 2017, but with reported costs since 2012. A systematic search conducted on 25 January 2023 identified studies relating to the economic burden of breast cancer in the countries of interest. MEDLINE, Embase, and EconLit databases were searched via Ovid. Study quality was assessed based on three aspects: (1) validity of cost findings; (2) completeness of direct cost findings; and (3) completeness of indirect cost findings. We grouped costs based on country, cancer stage (early compared to metastatic), and four resource categories: healthcare/medical, pharmaceutical drugs, diagnosis, and indirect costs. Costs were standardized to the year 2022 in US (US$2022) and International (Int$2022) dollars. RESULTS Fifty-three studies were included. Studies in the US (n = 19) and Canada (n = 9) were the majority (53%), followed by Western European countries (42%). Healthcare/medical costs were the focus for the majority (89%), followed by pharmaceutical drugs (25%), then diagnosis (17%) and indirect (17%) costs. Thirty-six (68%) included early-stage cancer costs, 17 (32%) included metastatic cancer costs, with 23% reporting costs across these cancer stages. No identified study explicitly compared costs across countries. Across cost categories, cost ranges tended to be higher in the US than any other country. Metastatic breast cancer was associated with higher costs than earlier-stage cancer. When indirect costs were accounted for, particularly in terms of productivity loss, they tended to be higher than any other estimated direct cost (e.g., diagnosis, drug, and other medical costs). CONCLUSION There was substantial heterogeneity both within and across countries for the identified studies' designs and estimated costs. Despite this, current empirical literature suggests that costs associated with early initiation of treatment could be offset against potentially avoiding or reducing the overall economic burden of later-stage and more severe breast cancer. Larger scale, national, economic burden studies are needed, to be updated regularly to ensure there is an ongoing and evolving perspective of the economic burden of conditions such as breast cancer to inform policy and practice.
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Affiliation(s)
- Matthew Franklin
- Sheffield Centre for Health and Related Research (SCHARR), School of Medicine and Population Health, University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK.
| | - Daniel Pollard
- Sheffield Centre for Health and Related Research (SCHARR), School of Medicine and Population Health, University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK
| | - Janvi Sah
- Oncology Business Unit, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Annabel Rayner
- Sheffield Centre for Health and Related Research (SCHARR), School of Medicine and Population Health, University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK
| | - Yuxiao Sun
- Sheffield Centre for Health and Related Research (SCHARR), School of Medicine and Population Health, University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK
| | - France Dube
- Oncology Business Unit, AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Anthea Sutton
- Sheffield Centre for Health and Related Research (SCHARR), School of Medicine and Population Health, University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK
| | - Lei Qin
- Oncology Business Unit, AstraZeneca, Gaithersburg, MD, 20878, USA
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Ott O, Tolppi S, Figueroa-Cruz J, Myagmar K, Unurbuyan K, Tripathi A. Leveraging the fundamentals of heat transfer and fluid mechanics in microscale geometries for automated next-generation sequencing library preparation. Sci Rep 2024; 14:12564. [PMID: 38822053 DOI: 10.1038/s41598-024-63014-x] [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: 01/30/2023] [Accepted: 05/23/2024] [Indexed: 06/02/2024] Open
Abstract
Next-generation sequencing (NGS) is emerging as a powerful tool for molecular diagnostics but remains limited by cumbersome and inefficient sample preparation. We present an innovative automated NGS library preparation system with a simplified mechanical design that exploits both macro- and microfluidic properties for optimizing heat transfer, reaction kinetics, mass transfer, fluid mechanics, adsorption-desorption rates, and molecular thermodynamics. Our approach introduces a unique two-cannula cylindrical capillary system connected to a programmable syringe pump and a Peltier heating element able to execute all steps with high efficiency. Automatic reagent movement, mixing, and magnetic bead-based washing with capillary-based thermal cycling (capillary-PCR) are completely integrated into a single platform. The manual 3-h library preparation process is reduced to less than 15 min of hands-on time via optimally pre-plated reagent plates, followed by less than 6 h of instrument run time during which no user interaction is required. We applied this method to two library preparation assays with different DNA fragmentation requirements (mechanical vs. enzymatic fragmentation), sufficiently limiting consumable use to one cartridge and one 384 well-plate per run. Our platform successfully prepared eight libraries in parallel, generating sequencing data for both human and Escherichia coli DNA libraries with negligible coverage bias compared to positive controls. All sequencing data from our libraries attained Phred (Q) scores > 30, mapping to reference genomes at 99% confidence. The method achieved final library concentrations and size distributions comparable with the conventional manual approach, demonstrating compatibility with downstream sequencing and subsequent data analysis. Our engineering design offers repeatability and consistency in the quality of sequence-able libraries, asserting the importance of mechanical design considerations that employ and optimize fundamental fluid mechanics and heat transfer properties. Furthermore in this work, we provide unique insights into the mechanisms of sample loss within NGS library preparation assays compared with automated adaptations and pinpoint areas in which the principles of thermodynamics, fluid mechanics, and heat transfer can improve future mechanical design iterations.
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Affiliation(s)
- Olivia Ott
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Sabrina Tolppi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Jennifer Figueroa-Cruz
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khaliun Myagmar
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Khulan Unurbuyan
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA.
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Halle MK, Hodneland E, Wagner-Larsen KS, Lura NG, Fasmer KE, Berg HF, Stokowy T, Srivastava A, Forsse D, Hoivik EA, Woie K, Bertelsen BI, Krakstad C, Haldorsen IS. Radiomic profiles improve prognostication and reveal targets for therapy in cervical cancer. Sci Rep 2024; 14:11339. [PMID: 38760387 PMCID: PMC11101482 DOI: 10.1038/s41598-024-61271-4] [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: 02/23/2024] [Accepted: 05/03/2024] [Indexed: 05/19/2024] Open
Abstract
Cervical cancer (CC) is a major global health problem with 570,000 new cases and 266,000 deaths annually. Prognosis is poor for advanced stage disease, and few effective treatments exist. Preoperative diagnostic imaging is common in high-income countries and MRI measured tumor size routinely guides treatment allocation of cervical cancer patients. Recently, the role of MRI radiomics has been recognized. However, its potential to independently predict survival and treatment response requires further clarification. This retrospective cohort study demonstrates how non-invasive, preoperative, MRI radiomic profiling may improve prognostication and tailoring of treatments and follow-ups for cervical cancer patients. By unsupervised clustering based on 293 radiomic features from 132 patients, we identify three distinct clusters comprising patients with significantly different risk profiles, also when adjusting for FIGO stage and age. By linking their radiomic profiles to genomic alterations, we identify putative treatment targets for the different patient clusters (e.g., immunotherapy, CDK4/6 and YAP-TEAD inhibitors and p53 pathway targeting treatments).
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Affiliation(s)
- Mari Kyllesø Halle
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Erlend Hodneland
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Kari S Wagner-Larsen
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway
- Section of Radiology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Njål G Lura
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway
- Section of Radiology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Kristine E Fasmer
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway
- Section of Radiology, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hege F Berg
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Tomasz Stokowy
- Genomics Core Facility, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, Bergen, Norway
| | - Aashish Srivastava
- Genomics Core Facility, Department of Clinical Science, University of Bergen, Bergen, Norway
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, Bergen, Norway
| | - David Forsse
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Erling A Hoivik
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Kathrine Woie
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Bjørn I Bertelsen
- Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Camilla Krakstad
- Centre for Cancer Biomarkers, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway.
| | - Ingfrid S Haldorsen
- Mohn Medical Imaging and Visualization Centre, Department of Radiology, Haukeland University Hospital, Bergen, Norway.
- Section of Radiology, Department of Clinical Medicine, University of Bergen, Bergen, Norway.
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Mirza M, Goerke L, Anderson A, Wilsdon T. Assessing the Cost-Effectiveness of Next-Generation Sequencing as a Biomarker Testing Approach in Oncology and Policy Implications: A Literature Review. VALUE IN HEALTH : THE JOURNAL OF THE INTERNATIONAL SOCIETY FOR PHARMACOECONOMICS AND OUTCOMES RESEARCH 2024:S1098-3015(24)02357-X. [PMID: 38729563 DOI: 10.1016/j.jval.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/21/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024]
Abstract
OBJECTIVE A key hurdle in broader next-generation sequencing (NGS) biomarker testing access in oncology is the ongoing debate on NGS's cost-effectiveness. We conducted a systematic review of existing evidence of the costs of NGS as a biomarker testing strategy in oncology and developed policy suggestions. METHODS We searched multiple databases for studies reporting cost comparisons and cost-effectiveness of NGS across oncology indications and geographies between 2017 and 2022, inclusive. Inclusion criteria were established based on indication and type of cost-effectiveness analysis provided. We validated analyses and policy recommendations with 5 payer/policy maker interviews in the United States, Europe, and United Kingdom. RESULTS Of the 634 identified studies, 29 met inclusion criteria, spanning 12 countries and 6 indications. Cost comparisons of NGS were evaluated using 3 methodologies: (1) comparison of direct testing costs, (2) comparison of holistic testing costs, and (3) comparison of long-term patient outcomes and costs. Targeted panel testing (2-52 genes) was considered cost-effective when 4+ genes were assessed, and larger panels (hundreds of genes) were generally not cost-effective. Holistic analysis demonstrated that NGS reduces turnaround time, healthcare staff requirements, number of hospital visits, and hospital costs. Finally, studies evaluating NGS testing including the cost of targeted therapies generally found the incremental cost-effectiveness ratio to be above common thresholds but highlighted valuable patient benefits. CONCLUSIONS Current literature supports NGS's cost-effectiveness as an oncology biomarker testing strategy under specific conditions. These findings underscore the need to develop policies to support holistic assessment of NGS to ensure appropriate reimbursement and access.
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Affiliation(s)
- Myriam Mirza
- Charles River Associates, Palais Leopold, Munich, Germany.
| | - Lutz Goerke
- Charles River Associates, Palais Leopold, Munich, Germany
| | | | - Tim Wilsdon
- Charles River Associates, London, England, 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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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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Parvizpour S, Beyrampour-Basmenj H, Razmara J, Farhadi F, Shamsir MS. Cancer treatment comes to age: from one-size-fits-all to next-generation sequencing (NGS) technologies. BIOIMPACTS : BI 2023; 14:29957. [PMID: 39104623 PMCID: PMC11298019 DOI: 10.34172/bi.2023.29957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 08/07/2024]
Abstract
Cancer is one of the leading causes of death worldwide and one of the greatest challenges in extending life expectancy. The paradigm of one-size-fits-all medicine has already given way to the stratification of patients by disease subtypes, clinical characteristics, and biomarkers (stratified medicine). The introduction of next-generation sequencing (NGS) in clinical oncology has made it possible to tailor cancer patient therapy to their molecular profiles. NGS is expected to lead the transition to precision medicine (PM), where the right therapeutic approach is chosen for each patient based on their characteristics and mutations. Here, we highlight how the NGS technology facilitates cancer treatment. In this regard, first, precision medicine and NGS technology are reviewed, and then, the NGS revolution in precision medicine is described. In the sequel, the role of NGS in oncology and the existing limitations are discussed. The available databases and bioinformatics tools and online servers used in NGS data analysis are also reviewed. The review ends with concluding remarks.
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Affiliation(s)
- Sepideh Parvizpour
- Research Center for Pharmaceutical Nanotechnology, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hanieh Beyrampour-Basmenj
- Department of Medical Biotechnology, School of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jafar Razmara
- Department of Computer Science, Faculty of Mathematics, Statistics and Computer Science, University of Tabriz, Tabriz, Iran
| | - Farhad Farhadi
- Food and Drug Administration, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohd Shahir Shamsir
- Bioinformatics Research Group, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Malaysia
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Li R, Wu J, Li G, Liu J, Xuan J, Zhu Q. Mdwgan-gp: data augmentation for gene expression data based on multiple discriminator WGAN-GP. BMC Bioinformatics 2023; 24:427. [PMID: 37957576 PMCID: PMC10644641 DOI: 10.1186/s12859-023-05558-9] [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: 08/04/2023] [Accepted: 11/06/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Although gene expression data play significant roles in biological and medical studies, their applications are hampered due to the difficulty and high expenses of gathering them through biological experiments. It is an urgent problem to generate high quality gene expression data with computational methods. WGAN-GP, a generative adversarial network-based method, has been successfully applied in augmenting gene expression data. However, mode collapse or over-fitting may take place for small training samples due to just one discriminator is adopted in the method. RESULTS In this study, an improved data augmentation approach MDWGAN-GP, a generative adversarial network model with multiple discriminators, is proposed. In addition, a novel method is devised for enriching training samples based on linear graph convolutional network. Extensive experiments were implemented on real biological data. CONCLUSIONS The experimental results have demonstrated that compared with other state-of-the-art methods, the MDWGAN-GP method can produce higher quality generated gene expression data in most cases.
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Affiliation(s)
- Rongyuan Li
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, China
| | - Jingli Wu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, China.
| | - Gaoshi Li
- Guangxi Key Lab of Multi-source Information Mining & Security, Guangxi Normal University, Guilin, China
| | - Jiafei Liu
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Junbo Xuan
- Key Lab of Education Blockchain and Intelligent Technology, Ministry of Education, Guangxi Normal University, Guilin, China
| | - Qi Zhu
- College of Computer Science and Engineering, Guangxi Normal University, Guilin, China
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11
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Davidson AL, Dressel U, Norris S, Canson DM, Glubb DM, Fortuno C, Hollway GE, Parsons MT, Vidgen ME, Holmes O, Koufariotis LT, Lakis V, Leonard C, Wood S, Xu Q, McCart Reed AE, Pickett HA, Al-Shinnag MK, Austin RL, Burke J, Cops EJ, Nichols CB, Goodwin A, Harris MT, Higgins MJ, Ip EL, Kiraly-Borri C, Lau C, Mansour JL, Millward MW, Monnik MJ, Pachter NS, Ragunathan A, Susman RD, Townshend SL, Trainer AH, Troth SL, Tucker KM, Wallis MJ, Walsh M, Williams RA, Winship IM, Newell F, Tudini E, Pearson JV, Poplawski NK, Mar Fan HG, James PA, Spurdle AB, Waddell N, Ward RL. The clinical utility and costs of whole-genome sequencing to detect cancer susceptibility variants-a multi-site prospective cohort study. Genome Med 2023; 15:74. [PMID: 37723522 PMCID: PMC10507925 DOI: 10.1186/s13073-023-01223-1] [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: 10/04/2022] [Accepted: 08/18/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND Many families and individuals do not meet criteria for a known hereditary cancer syndrome but display unusual clusters of cancers. These families may carry pathogenic variants in cancer predisposition genes and be at higher risk for developing cancer. METHODS This multi-centre prospective study recruited 195 cancer-affected participants suspected to have a hereditary cancer syndrome for whom previous clinical targeted genetic testing was either not informative or not available. To identify pathogenic disease-causing variants explaining participant presentation, germline whole-genome sequencing (WGS) and a comprehensive cancer virtual gene panel analysis were undertaken. RESULTS Pathogenic variants consistent with the presenting cancer(s) were identified in 5.1% (10/195) of participants and pathogenic variants considered secondary findings with potential risk management implications were identified in another 9.7% (19/195) of participants. Health economic analysis estimated the marginal cost per case with an actionable variant was significantly lower for upfront WGS with virtual panel ($8744AUD) compared to standard testing followed by WGS ($24,894AUD). Financial analysis suggests that national adoption of diagnostic WGS testing would require a ninefold increase in government annual expenditure compared to conventional testing. CONCLUSIONS These findings make a case for replacing conventional testing with WGS to deliver clinically important benefits for cancer patients and families. The uptake of such an approach will depend on the perspectives of different payers on affordability.
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Affiliation(s)
- Aimee L Davidson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Uwe Dressel
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Norris
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia
| | - Daffodil M Canson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Dylan M Glubb
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Cristina Fortuno
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Georgina E Hollway
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Michael T Parsons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Miranda E Vidgen
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - Oliver Holmes
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Lambros T Koufariotis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Vanessa Lakis
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Qinying Xu
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Amy E McCart Reed
- Centre for Clinical Research, University of Queensland, Brisbane, QLD, Australia
| | - Hilda A Pickett
- Children's Medical Research Institute, University of Sydney, Westmead, NSW, Australia
| | - Mohammad K Al-Shinnag
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Rachel L Austin
- Australian Genomics, Melbourne, VIC, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Jo Burke
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Elisa J Cops
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Cassandra B Nichols
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Annabel Goodwin
- Cancer Genetics Department, Royal Prince Alfred Hospital, Sydney, NSW, Australia
- University of Sydney, Sydney, NSW, Australia
| | - Marion T Harris
- Monash Health Familial Cancer, Monash Health, Melbourne, VIC, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Megan J Higgins
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Emilia L Ip
- Cancer Genetics, Liverpool Hospital, Sydney, NSW, Australia
| | | | - Chiyan Lau
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genomics, Pathology Queensland, Brisbane, QLD, Australia
| | - Julia L Mansour
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Michael W Millward
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
| | - Melissa J Monnik
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
| | - Nicholas S Pachter
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
- Faculty of Health and Medical Sciences, University of Western Australia, Perth, WA, Australia
| | - Abiramy Ragunathan
- Familial Cancer Services, The Crown Princess Mary Cancer Centre, Westmead Hospital, Westmead, NSW, Australia
| | - Rachel D Susman
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Sharron L Townshend
- Genetic Services of Western Australia, King Edward Memorial Hospital, Subiaco, WA, Australia
| | - Alison H Trainer
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
| | - Simon L Troth
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Katherine M Tucker
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Mathew J Wallis
- Tasmanian Clinical Genetics Service, Royal Hobart Hospital, Hobart, TAS, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia
| | - Maie Walsh
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Rachel A Williams
- Prince of Wales Clinical School, UNSW Medicine and Health, The University of New South Wales, Sydney, NSW, Australia
- Hereditary Cancer Centre, Prince of Wales Hospital, Sydney, NSW, Australia
| | - Ingrid M Winship
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
- Genomic Medicine and Familial Cancer Clinic, Royal Melbourne Hospital, Melbourne, VIC, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Emma Tudini
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Australian Genomics, Melbourne, VIC, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
| | - Nicola K Poplawski
- Adult Genetics Unit, Royal Adelaide Hospital, Adelaide, SA, Australia
- Adelaide Medical School, Faculty of Health and Medical Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Helen G Mar Fan
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
- Genetic Health Queensland, Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia.
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
| | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Robyn L Ward
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia.
- Faculty of Medicine and Health, University of Sydney, L2.22 The Quadrangle (A14), Sydney, NSW, 2006, Australia.
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12
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Darlington M, Sujobert P, Kosmider O, Luque Paz D, Kaltenbach S, Figeac M, Hayette S, Mezaour N, Coquerelle S, Alary AS, Bidet A, Le Bris Y, Delabesse E, Davi F, Preudhomme C, Durand-Zaleski I, Macintyre E, Alame M, Baran-Marzak F, Berger MG, Bories D, Caye-Eude A, Cayuela JM, Cornillet-Lefebvre P, Delhommeau F, Estienne-Felix MH, Etancelin P, Flandrin-Gresta P, Lippert E, Marzac C, Miguet L, Pastoret C, Raynaud S, Rizzo D. Targeted High-throughput Sequencing for Hematological Malignancies: A GBMHM Survey of Practice and Cost Evaluation in France. Hemasphere 2023; 7:e943. [PMID: 37637995 PMCID: PMC10455455 DOI: 10.1097/hs9.0000000000000943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
The objective of this study was to assess the clinical impact and financial costs of next-generation sequencing (NGS) in 5 categories of pediatric and adult hematological cancers. NGS prescriptions were prospectively collected from 26 laboratories, with varied technical and reporting practice (all or only significant targets). Impact was defined by the identification of (1) an actionable mutation, (2) a mutation with prognostic and/or theranostic value, and/or (3) a mutation allowing nosological refinement, reported by local investigators. A microcosting study was undertaken in 4 laboratories, identifying the types and volumes of resources required for each procedural step. Individual index prescriptions for 3961 patients were available for impact analysis on the management of myeloid disorders (two thirds) and, mainly mature B, lymphoid disorders (one third). NGS results were considered to impact the management for 73.4% of prescriptions: useful for evaluation of prognostic risk in 34.9% and necessary for treatment adaptation (actionable) in 19.6%, but having no immediate individual therapeutic impact in 18.9%. The average overall cost per sample was 191 € for the restricted mature lymphoid amplicon panel. Capture panel costs varied from 369 € to 513 €. Unit costs varied from 0.5 € to 5.7 € per kb sequenced, from 3.6 € to 11.3 € per target gene/hot-spot sequenced and from 4.3 € to 73.8 € per target gene/hot-spot reported. Comparable costs for the Amplicon panels were 5-8 € per kb and 10.5-14.7 € per target gene/hot-spot sequenced and reported, demonstrating comparable costs with greater informativity/flexibility for capture strategies. Sustainable funding of precision medicine requires a transparent discussion of its impact on care pathways and its financial aspects.
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Affiliation(s)
- Meryl Darlington
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Pierre Sujobert
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
| | - Olivier Kosmider
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
| | - Damien Luque Paz
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
| | - Sophie Kaltenbach
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
| | - Martin Figeac
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
| | - Sandrine Hayette
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
| | - Nadia Mezaour
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Séverine Coquerelle
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
| | - Anne-Sophie Alary
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
| | - Audrey Bidet
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
| | - Yannick Le Bris
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
| | - Eric Delabesse
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
| | - Frédéric Davi
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
| | - Claude Preudhomme
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
| | | | - Elizabeth Macintyre
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Université Paris Cité, CNRS, Inserm, France
| | - Mélissa Alame
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Fanny Baran-Marzak
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Marc G. Berger
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Dominique Bories
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Aurélie Caye-Eude
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Jean-Michel Cayuela
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascale Cornillet-Lefebvre
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - François Delhommeau
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Marie-Hélène Estienne-Felix
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascaline Etancelin
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Pascale Flandrin-Gresta
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Eric Lippert
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Christophe Marzac
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Laurent Miguet
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Cédric Pastoret
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - Sophie Raynaud
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
| | - David Rizzo
- DRCI‑URC Eco Ile‑de‑France, Assistance Publique-Hôpitaux de Paris (AP-HP), France
- Hospices Civils de Lyon, Hôpital Lyon Sud, Service d’hématologie biologique, France
- Hôpital Cochin, Hématologie Biologique, AP-HP, Université, Paris Cité, France
- Univ Angers, Nantes Université, CHU Angers, Inserm, CNRS, France
- Hématologie Biologique, AP-HP, Necker-Enfants Malades Hospital, Paris, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, France
- CHU de Lille, Equipe bioinfo du Plateau Commun de Biologie Moléculaire, Lille, France
- Department of Hematology Biology, Molecular Hematology, Bordeaux University Hospital, Haut-Levêque Hospital, Pessac, France
- Hématologie Biologique, Nantes University Hospital and CRCI2NA Nantes-Angers, France
- Hématologie Biologique, CHU Toulouse, Inserm 1037, CNRS, Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse, France
- AP-HP, Hôpital Pitié-Salpêtrière, Department of Biological Hematology, Sorbonne University, Paris
- Université Paris Cité, CNRS, Inserm, France
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13
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Jeon H, Ahn J, Na B, Hong S, Sael L, Kim S, Yoon S, Baek D. AIVariant: a deep learning-based somatic variant detector for highly contaminated tumor samples. Exp Mol Med 2023; 55:1734-1742. [PMID: 37524869 PMCID: PMC10474289 DOI: 10.1038/s12276-023-01049-2] [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: 02/28/2023] [Revised: 04/10/2023] [Accepted: 04/24/2023] [Indexed: 08/02/2023] Open
Abstract
The detection of somatic DNA variants in tumor samples with low tumor purity or sequencing depth remains a daunting challenge despite numerous attempts to address this problem. In this study, we constructed a substantially extended set of actual positive variants originating from a wide range of tumor purities and sequencing depths, as well as actual negative variants derived from sequencer-specific sequencing errors. A deep learning model named AIVariant, trained on this extended dataset, outperforms previously reported methods when tested under various tumor purities and sequencing depths, especially low tumor purity and sequencing depth.
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Affiliation(s)
- Hyeonseong Jeon
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Genome4me Inc., Seoul, 08826, Republic of Korea
| | - Junhak Ahn
- Genome4me Inc., Seoul, 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byunggook Na
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Soona Hong
- AIGENDRUG Co., Ltd., Seoul, 08826, Republic of Korea
| | - Lee Sael
- Department of Software and Computer Engineering, Ajou University, Suwon, 16499, Republic of Korea
| | - Sun Kim
- Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sungroh Yoon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daehyun Baek
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- Genome4me Inc., Seoul, 08826, Republic of Korea.
- School of Biological Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
- Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea.
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14
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Zhou Y, Lauschke VM. Challenges Related to the Use of Next-Generation Sequencing for the Optimization of Drug Therapy. Handb Exp Pharmacol 2023; 280:237-260. [PMID: 35792943 DOI: 10.1007/164_2022_596] [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] [Indexed: 06/15/2023]
Abstract
Over the last decade, next-generation sequencing (NGS) methods have become increasingly used in various areas of human genomics. In routine clinical care, their use is already implemented in oncology to profile the mutational landscape of a tumor, as well as in rare disease diagnostics. However, its utilization in pharmacogenomics is largely lacking behind. Recent population-scale genome data has revealed that human pharmacogenes carry a plethora of rare genetic variations that are not interrogated by conventional array-based profiling methods and it is estimated that these variants could explain around 30% of the genetically encoded functional pharmacogenetic variability.To interpret the impact of such variants on drug response a multitude of computational tools have been developed, but, while there have been major advancements, it remains to be shown whether their accuracy is sufficient to improve personalized pharmacogenetic recommendations in robust trials. In addition, conventional short-read sequencing methods face difficulties in the interrogation of complex pharmacogenes and high NGS test costs require stringent evaluations of cost-effectiveness to decide about reimbursement by national healthcare programs. Here, we illustrate current challenges and discuss future directions toward the clinical implementation of NGS to inform genotype-guided decision-making.
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Affiliation(s)
- Yitian Zhou
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Volker M Lauschke
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Dr Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.
- University of Tuebingen, Tuebingen, Germany.
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15
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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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16
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Akkari YM, Baughn LB, Dubuc AM, Smith AC, Mallo M, Dal Cin P, Diez Campelo M, Gallego MS, Granada Font I, Haase DT, Schlegelberger B, Slavutsky I, Mecucci C, Levine RL, Hasserjian RP, Solé F, Levy B, Xu X. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood 2022; 139:2273-2284. [PMID: 35167654 PMCID: PMC9710485 DOI: 10.1182/blood.2021014309] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 02/03/2022] [Indexed: 12/15/2022] Open
Abstract
Cytogenetics has long represented a critical component in the clinical evaluation of hematologic malignancies. Chromosome banding studies provide a simultaneous snapshot of genome-wide copy number and structural variation, which have been shown to drive tumorigenesis, define diseases, and guide treatment. Technological innovations in sequencing have ushered in our present-day clinical genomics era. With recent publications highlighting novel sequencing technologies as alternatives to conventional cytogenetic approaches, we, an international consortium of laboratory geneticists, pathologists, and oncologists, describe herein the advantages and limitations of both conventional chromosome banding and novel sequencing technologies and share our considerations on crucial next steps to implement these novel technologies in the global clinical setting for a more accurate cytogenetic evaluation, which may provide improved diagnosis and treatment management. Considering the clinical, logistic, technical, and financial implications, we provide points to consider for the global evolution of cytogenetic testing.
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Affiliation(s)
- Yassmine M.N. Akkari
- Departments of Cytogenetics and Molecular Pathology, Legacy Health, Portland, OR
| | - Linda B. Baughn
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Adrian M. Dubuc
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Adam C. Smith
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Mar Mallo
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Maria Diez Campelo
- Hematology Department University Hospital of Salamanca, IBSAL, Salamanca, Spain
| | - Marta S. Gallego
- Laboratory of Cytogenetics and Molecular Cytogenetics, Department of Clinical Pathology, Italian Hospital, Buenos Aires, Argentina
| | - Isabel Granada Font
- Hematology Laboratory, Germans Trias i Pujol University Hospital–Catalan Institute of Oncology, Josep Carreras Leukemia Research Institute, Barcelona, Spain
| | - Detlef T. Haase
- Clinics of Hematology and Medical Oncology, University Medical Center Göttingen, Göttingen, Germany
| | | | - Irma Slavutsky
- Laboratory Genetics of Lymphoid Malignancies, Institute of Experimental Medicine, Buenos Aires, Argentina
| | - Cristina Mecucci
- Laboratory of Cytogenetics and Molecular Medicine, Hematology University of Perugia, Perugia, Italy
| | - Ross L. Levine
- Department of Medicine, Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY
| | | | - Francesc Solé
- MDS Group, Microarrays Unit, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Brynn Levy
- College of Physicians and Surgeons, Columbia University Medical Center and the New York Presbyterian Hospital, New York, NY
| | - Xinjie Xu
- Division of Hematopathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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17
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Gayduk A, Vlasov Y, Smirnova D. Application of modern approaches in the screening and early diagnosis programs for the orphan diseases. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:30-39. [DOI: 10.17116/jnevro202212206130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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18
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Maia N, Nabais Sá MJ, Melo-Pires M, de Brouwer APM, Jorge P. Intellectual disability genomics: current state, pitfalls and future challenges. BMC Genomics 2021; 22:909. [PMID: 34930158 PMCID: PMC8686650 DOI: 10.1186/s12864-021-08227-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Intellectual disability (ID) can be caused by non-genetic and genetic factors, the latter being responsible for more than 1700 ID-related disorders. The broad ID phenotypic and genetic heterogeneity, as well as the difficulty in the establishment of the inheritance pattern, often result in a delay in the diagnosis. It has become apparent that massive parallel sequencing can overcome these difficulties. In this review we address: (i) ID genetic aetiology, (ii) clinical/medical settings testing, (iii) massive parallel sequencing, (iv) variant filtering and prioritization, (v) variant classification guidelines and functional studies, and (vi) ID diagnostic yield. Furthermore, the need for a constant update of the methodologies and functional tests, is essential. Thus, international collaborations, to gather expertise, data and resources through multidisciplinary contributions, are fundamental to keep track of the fast progress in ID gene discovery.
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Affiliation(s)
- Nuno Maia
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal. .,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal.
| | - Maria João Nabais Sá
- Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Manuel Melo-Pires
- Serviço de Neuropatologia, Centro Hospitalar e Universitário do Porto (CHUPorto), Porto, Portugal
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Paula Jorge
- Centro de Genética Médica Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
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19
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Queensland Genomics: an adaptive approach for integrating genomics into a public healthcare system. NPJ Genom Med 2021; 6:71. [PMID: 34408148 PMCID: PMC8373904 DOI: 10.1038/s41525-021-00234-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
The establishment of genomics in health care systems has been occurring for the past decade. It is recognised that implementing genomics within a health service is challenging without a system-wide approach. Globally, as clinical genomics implementation programs have matured there is a growing body of information around program design and outcomes. Program structures vary depending on local ecosystems including the health system, politics and funding availability, however, lessons from other programs are important to the design of programs in different jurisdictions. Here we describe an adaptive approach to the implementation of genomics into a publicly funded health care system servicing a population of 5.1 million people. The adaptive approach enabled flexibility to facilitate substantial changes during the program in response to learnings and external factors. We report the benefits and challenges experienced by the program, particularly in relation to the engagement of people and services, and the design of both individual projects and the program as a whole.
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20
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Bayle A, Droin N, Besse B, Zou Z, Boursin Y, Rissel S, Solary E, Lacroix L, Rouleau E, Borget I, Bonastre J. Whole exome sequencing in molecular diagnostics of cancer decreases over time: evidence from a cost analysis in the French setting. THE EUROPEAN JOURNAL OF HEALTH ECONOMICS : HEPAC : HEALTH ECONOMICS IN PREVENTION AND CARE 2021; 22:855-864. [PMID: 33765190 DOI: 10.1007/s10198-021-01293-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/16/2021] [Indexed: 05/06/2023]
Abstract
OBJECTIVES Although high-throughput sequencing is revolutionising medicine, data on the actual cost of whole exome sequencing (WES) applications are needed. We aimed at assessing the cost of WES at a French cancer institute in 2015 and 2018. METHODS Actual costs of WES application in oncology research were determined using both micro-costing and gross-costing for the years 2015 and 2018, before and after the acquisition of a new sequencer. The entire workflow process of a WES test was tracked, and the number and unit price of each resource were identified at the most detailed level, from library preparation to bioinformatics analyses. In addition, we conducted an ad hoc analysis of the bioinformatics storage costs of data issued from WES analyses. RESULTS The cost of WES has decreased substantially, from €1921 per sample (i.e. cost of €3842 per patient) in 2015 to €804 per sample (i.e. cost of €1,608 per patient) in 2018, representing a decrease of 58%. In the meantime, the cost of bioinformatics storage has increased from €19,836 to €200,711. CONCLUSION This study suggests that WES cost has decreased significantly in recent years. WES has become affordable, even though clinical utility and efficiency still need to be confirmed.
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Affiliation(s)
- Arnaud Bayle
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France.
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France.
- Université Paris-Sud, Orsay, France.
| | - N Droin
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- UMS CNRS 3655 and INSERM US23, AMMICa, Gustave Roussy, Villejuif, France
| | - B Besse
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - Z Zou
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
| | - Y Boursin
- Digital Transformation and IT System Department, Gustave Roussy Cancer Centre, 94805, Villejuif, France
| | - S Rissel
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - E Solary
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Université Paris-Sud, Orsay, France
| | - L Lacroix
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- UMS CNRS 3655 and INSERM US23, AMMICa, Gustave Roussy, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - E Rouleau
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
| | - I Borget
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
- Université Paris-Sud, Orsay, France
| | - J Bonastre
- Biostatistics and Epidemiology Unit, Gustave Roussy Cancer Centre, 114 rue Edouard Vaillant, 94805, Villejuif Cedex, France
- Centre for Research in Epidemiology and Population Health, INSERM U1018, Villejuif, France
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21
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Simons M, Van De Ven M, Coupé V, Joore M, IJzerman M, Koffijberg E, Frederix G, Uyl-De Groot C, Cuppen E, Van Harten W, Retèl V. Early technology assessment of using whole genome sequencing in personalized oncology. Expert Rev Pharmacoecon Outcomes Res 2021; 21:343-351. [PMID: 33910430 DOI: 10.1080/14737167.2021.1917386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Introduction: Personalized medicine-based treatments in advanced cancer hold the promise to offer substantial health benefits to genetic subgroups, but require efficient biomarker-based patient stratification to match the right treatment and may be expensive. Standard molecular diagnostics are currently very heterogeneous, and tests are often performed sequentially. The alternative to whole genome sequencing (WGS) i.e. simultaneously testing for all relevant DNA-based biomarkers thereby allowing immediate selection of the most optimal therapy, is more costly than current techniques. In the current implementation stage, it is important to explore the added value and cost-effectiveness of using WGS on a patient level and to assess optimal introduction of WGS on the level of the healthcare system.Areas covered: First, an overview of current worldwide initiatives concerning the use of WGS in clinical practice for cancer diagnostics is given. Second, a comprehensive, early health technology assessment (HTA) approach of evaluating WGS in the Netherlands is described, relating to the following aspects: diagnostic value, WGS-based treatment decisions, assessment of long-term health benefits and harms, early cost-effectiveness modeling, nation-wide organization, and Ethical, Legal and Societal Implications.Expert opinion: This study provides evidence to guide further development and implementation of WGS in clinical practice and the healthcare system.
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Affiliation(s)
- Martijn Simons
- Department of Clinical Epidemiology and Medical Technology Assessment, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Michiel Van De Ven
- Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Veerle Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, Amsterdam, The Netherlands
| | - Manuela Joore
- Department of Clinical Epidemiology and Medical Technology Assessment, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Maarten IJzerman
- Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands.,University of Melbourne Centre for Cancer Research, Melbourne Australia
| | - Erik Koffijberg
- Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Geert Frederix
- Division of Pharmacoepidemiology and Clinical Pharmacology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Carin Uyl-De Groot
- Erasmus School of Health Policy & Management (ESHPM), Erasmus University, Rotterdam, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht, The Netherlands.,Hartwig Medical Foundation, Amsterdam, The Netherlands
| | - Wim Van Harten
- Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands.,Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute.,Executive Board, Rijnstate General Hospital, Arnhem, The Netherlands
| | - Valesca Retèl
- Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands.,Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute
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22
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Gordon LG, Elliott TM, Forde B, Mitchell B, Russo PL, Paterson DL, Harris PNA. Budget impact analysis of routinely using whole-genomic sequencing of six multidrug-resistant bacterial pathogens in Queensland, Australia. BMJ Open 2021; 11:e041968. [PMID: 33526501 PMCID: PMC7852923 DOI: 10.1136/bmjopen-2020-041968] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
OBJECTIVE To predict the cost and health effects of routine use of whole-genome sequencing (WGS) of bacterial pathogens compared with those of standard of care. DESIGN Budget impact analysis was performed over the following 5 years. Data were primarily from sequencing results on clusters of multidrug-resistant organisms across 27 hospitals. Model inputs were derived from hospitalisation and sequencing data, and epidemiological and costing reports, and included multidrug resistance rates and their trends. SETTING Queensland, Australia. PARTICIPANTS Hospitalised patients. INTERVENTIONS WGS surveillance of six common multidrug-resistant organisms (Staphylococcus aureus, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, Enterobacter sp and Acinetobacter baumannii) compared with standard of care or routine microbiology testing. PRIMARY AND SECONDARY OUTCOMES Expected hospital costs, counts of patient infections and colonisations, and deaths from bloodstream infections. RESULTS In 2021, 97 539 patients in Queensland are expected to be infected or colonised with one of six multidrug-resistant organisms with standard of care testing. WGS surveillance strategy and earlier infection control measures could avoid 36 726 infected or colonised patients and avoid 650 deaths. The total cost under standard of care was $A170.8 million in 2021. WGS surveillance costs an additional $A26.8 million but was offset by fewer costs for cleaning, nursing, personal protective equipment, shorter hospital stays and antimicrobials to produce an overall cost savings of $30.9 million in 2021. Sensitivity analyses showed cost savings remained when input values were varied at 95% confidence limits. CONCLUSIONS Compared with standard of care, WGS surveillance at a state-wide level could prevent a substantial number of hospital patients infected with multidrug-resistant organisms and related deaths and save healthcare costs. Primary prevention through routine use of WGS is an investment priority for the control of serious hospital-associated infections.
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Affiliation(s)
- Louisa G Gordon
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
- School of Nursing, Queensland University of Technology (QUT), Brisbane, Queensland, Australia
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Thomas M Elliott
- Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Brian Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Brett Mitchell
- School of Nursing and Midwifery, The University of Newcastle, Newcastle, New South Wales, Australia
| | - Philip L Russo
- School of Nursing and Midwifery, Monash University, Melbourne, Victoria, Australia
| | - David L Paterson
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
| | - Patrick N A Harris
- The University of Queensland, Centre for Clinical Research, Brisbane, Queensland, Australia
- Pathology Queensland, Queensland Health, Brisbane, Queensland, Australia
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