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Xu Y, Jia L, Zhang L, Wang H, Jiang L, Feng X, Wei R, Yao Q, Ren M, Xue T, Li Y, Zhu X, Zhou X, Bai Q. Comprehensive analysis of next generation sequencing and ARMS-PCR for detecting EGFR exon 20 insertion (ex20ins) mutations in Chinese non-small cell lung cancer patients. Transl Lung Cancer Res 2024; 13:986-997. [PMID: 38854943 PMCID: PMC11157361 DOI: 10.21037/tlcr-23-848] [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: 12/25/2023] [Accepted: 04/22/2024] [Indexed: 06/11/2024]
Abstract
Background Amivantamab (JNJ-372) and mobocertinib (TAK-788) have been reported to have favorable therapeutic effect for non-small cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutations. Thus, accurate detection of EGFR ex20ins mutations is crucial for subsequent individualized therapy. The aim of this study was to compare the two common methods of next generation sequencing (NGS) and amplification refractory mutation system polymerase chain reaction (ARMS-PCR) for detecting EGFR ex20ins mutations in Chinese NSCLC patients. Methods We retrospectively analyzed EGFR mutations, especially for ex20ins, in 3,606 NSCLC patients detected by NGS and 1,785 patients by ARMS. Results Among the 3,606 NGS patients, a total of 2,077 EGFR mutations and 95 EGFR ex20ins were identified, accounting for 57.6% and 2.6%, respectively. While 48.4% of EGFR mutations and 1.1% of ex20ins were detected in 1,785 ARMS patients, which were significantly lower than those of NGS (P<0.01). Thirty-four unique ex20ins variants were identified by NGS, and eight of them was reported for the first time. However, ARMS was designed to detect only several known EGFR ex20ins variants, and even did not include the most common variants in Chinese NSCLC patients. Conclusions NGS is more advantageous and strongly recommended for the detection of EGFR ex20ins mutations. Considering the fast and cost-effective ARMS detection method, it is suggested that the primers design should be updated according to the characteristics of EGFR ex20ins mutations in Chinese NSCLC patients.
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Affiliation(s)
- Yuyin Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Liqing Jia
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ling Zhang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Haochen Wang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Lin Jiang
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xu Feng
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Ran Wei
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qianlan Yao
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Min Ren
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Tian Xue
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Yuan Li
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoli Zhu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
| | - Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Pathology, Fudan University, Shanghai, China
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2
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Behnke A, Cayre A, De Maglio G, Giannini G, Habran L, Tarsitano M, Chetta M, Cappellen D, Lespagnol A, Le Naoures C, Massazza G, Destro A, Bonzheim I, Rau A, Battmann A, Kah B, Watkin E, Hummel M. FACILITATE: A real-world, multicenter, prospective study investigating the utility of a rapid, fully automated real-time PCR assay versus local reference methods for detecting epidermal growth factor receptor variants in NSCLC. Pathol Oncol Res 2023; 29:1610707. [PMID: 36798672 PMCID: PMC9927408 DOI: 10.3389/pore.2023.1610707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/11/2023] [Indexed: 02/04/2023]
Abstract
Accurate testing for epidermal growth factor receptor (EGFR) variants is essential for informing treatment decisions in non-small cell lung cancer (NSCLC). Automated diagnostic workflows may allow more streamlined initiation of targeted treatments, where appropriate, while comprehensive variant analysis is ongoing. FACILITATE, a real-world, prospective, multicenter, European study, evaluated performance and analytical turnaround time of the Idylla™ EGFR Mutation Test compared with local reference methods. Sixteen sites obtained formalin-fixed paraffin-embedded biopsy samples with ≥ 10% neoplastic cells from patients with NSCLC. Consecutive 5 μm sections from patient samples were tested for clinically relevant NSCLC-associated EGFR variants using the Idylla™ EGFR Mutation Test and local reference methods; performance (concordance) and analytical turnaround time were compared. Between January 2019 and November 2020, 1,474 parallel analyses were conducted. Overall percentage agreement was 97.7% [n = 1,418; 95% confidence interval (CI): 96.8-98.3], positive agreement, 87.4% (n = 182; 95% CI: 81.8-91.4) and negative agreement, 99.2% (n = 1,236; 95% CI: 98.5-99.6). There were 38 (2.6%) discordant cases. Ninety percent of results were returned with an analytical turnaround time of within 1 week using the Idylla™ EGFR Mutation Test versus ∼22 days using reference methods. The Idylla™ EGFR Mutation Test performed well versus local methods and had shorter analytical turnaround time. The Idylla™ EGFR Mutation Test can thus support application of personalized medicine in NSCLC.
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Affiliation(s)
- Anke Behnke
- Charité-Universitätsmedizin Berlin, Institute of Pathology and Berlin Institute of Health, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anne Cayre
- Département de Pathologie, Centre Jean-Perrin, Clermont-Ferrand, France
| | - Giovanna De Maglio
- Azienda Sanitaria Universitaria Friuli Centrale, Pathology Department, Santa Maria della Misericordia Hospital, Udine, Italy
| | - Giuseppe Giannini
- Department Molecular Medicine, Università di Roma La Sapienza, Rome, Italy
| | - Lionel Habran
- Anatomopathology Department, CHU Liège, Liège, Belgium
| | - Marina Tarsitano
- Di Laboratorio, A.O.R.N. Cardarelli, Medical Genetics Laboratory, and Ospedale Antonio Cardarelli, U.O.C. di Genetica Medica, Naples, Italy
| | - Massimiliano Chetta
- Di Laboratorio, A.O.R.N. Cardarelli, Medical Genetics Laboratory, and Ospedale Antonio Cardarelli, U.O.C. di Genetica Medica, Naples, Italy
| | - David Cappellen
- Service de Biologie des Tumeurs, Centre Hospitalier Universitaire de Bordeaux, Hôpital du Haut Lévêque, Pessac, France
| | - Alexandra Lespagnol
- CHU de Rennes, Laboratoire de Génétique Somatique des Cancers, Rennes, France
| | - Cecile Le Naoures
- CHU de Rennes, Service d’Anatomie et Cytologie Pathologiques, Rennes, France
| | - Gabriella Massazza
- Dipartimento Medicina di Laboratorio Anatomia Patologica, ASST Papa Giovanni XXIII, Bergamo, BG, Italy
| | - Annarita Destro
- Pathology Department, Humanitas Clinical and Research Center—IRCCS, Milan, Italy
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Achim Rau
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Achim Battmann
- Institut für Pathologie und Zytodiagnostik am Krankenhaus Nordwest, Frankfurt, Germany
| | - Bettina Kah
- Institut für Hämatopathologie Hamburg, Hamburg, Germany
| | | | - Michael Hummel
- Charité-Universitätsmedizin Berlin, Institute of Pathology and Berlin Institute of Health, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Michael Hummel,
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3
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Liu C, Yu Y, Wang G, Liu J, Liu R, Liu L, Yang X, Li H, Gao C, Lu Y, Zhuang J. From tumor mutational burden to characteristic targets analysis: Identifying the predictive biomarkers and natural product interventions in cancer management. Front Nutr 2022; 9:989989. [PMID: 36204371 PMCID: PMC9530334 DOI: 10.3389/fnut.2022.989989] [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: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 12/24/2022] Open
Abstract
High-throughput next-generation sequencing (NGS) provides insights into genome-wide mutations and can be used to identify biomarkers for the prediction of immune and targeted responses. A deeper understanding of the molecular biological significance of genetic variation and effective interventions is required and ultimately needs to be associated with clinical benefits. We conducted a retrospective observational study of patients in two cancer cohorts who underwent NGS in a “real-world” setting. The association between differences in tumor mutational burden (TMB) and clinical presentation was evaluated. We aimed to identify several key mutation targets and describe their biological characteristics and potential clinical value. A pan-cancer dataset was downloaded as a verification set for further analysis and summary. Natural product screening for the targeted intervention of key markers was also achieved. The majority of tumor patients were younger adult males with advanced cancer. The gene identified with the highest mutation rate was TP53, followed by PIK3CA, EGFR, and LRP1B. The association of TMB (0–103.7 muts/Mb) with various clinical subgroups was determined. More frequent mutations, such as in LRP1B, as well as higher levels of ferritin and neuron-specific enolase, led to higher TMB levels. Further analysis of the key targets, LRP1B and APC, was performed, and mutations in LRP1B led to better immune benefits compared to APC. APC, one of the most frequently mutated genes in gastrointestinal tumors, was further investigated, and the potential interventions by cochinchinone B and rottlerin were clarified. In summary, based on the analysis of the characteristics of gene mutations in the “real world,” we obtained the potential association indicators of TMB, found the key signatures LRP1B and APC, and further described their biological significance and potential interventions.
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Affiliation(s)
- Cun Liu
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
| | - Yang Yu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ge Wang
- Clinical Medical Colleges, Weifang Medical University, Weifang, China
| | - Jingyang Liu
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
| | - Lijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
- Department of Special Medicine, School of Basic Medicine, Qingdao University, Qingdao, China
| | - Xiaoxu Yang
- School of Life Sciences and Technology, Weifang Medical University, Weifang, China
| | - Huayao Li
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang, China
| | - Chundi Gao
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi Lu
- Department of Clinical Nutrition, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer, Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Traditional Chinese Medicine Oncology, Zhejiang Cancer Hospital, Hangzhou, China
- *Correspondence: Yi Lu,
| | - Jing Zhuang
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, China
- Jing Zhuang,
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4
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Depoilly T, Garinet S, van Kempen LC, Schuuring E, Clavé S, Bellosillo B, Ercolani C, Buglioni S, Siemanowski J, Merkelbach-Bruse S, Tischler V, Demes MC, Paridaens H, Sibille C, de Montpreville VT, Rouleau E, Bartczak A, Pasieka-Lis M, Wei Teo RY, Chuah KL, Barbosa M, Quintana C, Biscuola M, Delgado-Garcia M, Vacirca D, Rappa A, Cashmore M, Smith M, Jasionowicz P, Meeney A, Desmeules P, Terris B, Mansuet-Lupo A. Multicenter Evaluation of the Idylla GeneFusion in Non-Small-Cell Lung Cancer. J Mol Diagn 2022; 24:1021-1030. [PMID: 35718095 DOI: 10.1016/j.jmoldx.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Targeted therapy in lung cancer requires the assessment of multiple oncogenic driver alterations, including fusion genes. This retrospective study evaluated the Idylla GeneFusion prototype, an automated and ease-of-use (<2 minutes) test, with a short turnaround time (3 hours) to detect fusions involving ALK, ROS1, RET, and NTRK1/2/3 genes and MET exon 14 skipping. This multicenter study (18 centers) included 313 tissue samples from lung cancer patients with 97 ALK, 44 ROS1, 20 RET, and 5 NTRKs fusions, 32 MET exon 14 skipping, and 115 wild-type samples, previously identified with reference methods (RNA-based next generation sequencing/fluorescence in situ hybridization/quantitative PCR). Valid results were obtained for 306 cases (98%), overall concordance between Idylla and the reference methods was 89% (273/306); overall sensitivity and specificity were 85% (165/193) and 96% (108/113), respectively. Discordances were observed in 28 samples, where Idylla did not detect the alteration identified by the reference methods; and 5 samples where Idylla identified an alteration not detected by the reference methods. All of the ALK-, ROS1-, and RET-specific fusions and MET exon 14 skipping identified by Idylla GeneFusion were confirmed by reference method. To conclude, Idylla GeneFusion is a clinically valuable test that does not require a specific infrastructure, allowing a rapid result. The absence of alteration or the detection of expression imbalance only requires additional testing by orthogonal methods.
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Affiliation(s)
- Thomas Depoilly
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Simon Garinet
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sergi Clavé
- Department of Pathology, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Cristiana Ercolani
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Janna Siemanowski
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Verena Tischler
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | | | | | | | | | - Etienne Rouleau
- Service de Génétique des Tumeurs, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
| | - Artur Bartczak
- Department of Pathomorphology, Public Specialist Hospital of Lung Diseases in Zakopane, Zakopane, Poland
| | - Monika Pasieka-Lis
- Department of Pathomorphology, Public Specialist Hospital of Lung Diseases in Zakopane, Zakopane, Poland
| | - Ryan Yee Wei Teo
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Khoon Leong Chuah
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Marta Barbosa
- Serviço de Anatomia Patológica, Hospital do Espírito Santo de Évora, Évora, Portugal
| | - Carlos Quintana
- Serviço de Anatomia Patológica, Hospital do Espírito Santo de Évora, Évora, Portugal
| | - Michele Biscuola
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Mercedes Delgado-Garcia
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Davide Vacirca
- Division of Pathology and Laboratory Medicine, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology and Laboratory Medicine, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Matthew Cashmore
- Black Country Pathology Services, New Cross Hospital, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
| | - Matthew Smith
- Pathology Department, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Piotr Jasionowicz
- Pathology Department, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Adam Meeney
- Sheffield Teaching Hospitals NHS Foundation Trust, Pathology Laboratory, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Patrice Desmeules
- Departement d'Anatomopathologie et Cytologie, Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Québec, Québec, Canada
| | - Benoit Terris
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Audrey Mansuet-Lupo
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.
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5
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Ilié M, Hofman V, Bontoux C, Heeke S, Lespinet-Fabre V, Bordone O, Lassalle S, Lalvée S, Tanga V, Allegra M, Salah M, Bohly D, Benzaquen J, Marquette CH, Long-Mira E, Hofman P. Setting Up an Ultra-Fast Next-Generation Sequencing Approach as Reflex Testing at Diagnosis of Non-Squamous Non-Small Cell Lung Cancer; Experience of a Single Center (LPCE, Nice, France). Cancers (Basel) 2022; 14:2258. [PMID: 35565387 PMCID: PMC9104603 DOI: 10.3390/cancers14092258] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 04/28/2022] [Indexed: 12/12/2022] Open
Abstract
The number of genomic alterations required for targeted therapy of non-squamous non-small cell lung cancer (NS-NSCLC) patients has increased and become more complex these last few years. These molecular abnormalities lead to treatment that provides improvement in overall survival for certain patients. However, these treated tumors inexorably develop mechanisms of resistance, some of which can be targeted with new therapies. The characterization of the genomic alterations needs to be performed in a short turnaround time (TAT), as indicated by the international guidelines. The origin of the tissue biopsies used for the analyses is diverse, but their size is progressively decreasing due to the development of less invasive methods. In this respect, the pathologists are facing a number of different challenges requiring them to set up efficient molecular technologies while maintaining a strategy that allows rapid diagnosis. We report here our experience concerning the development of an optimal workflow for genomic alteration assessment as reflex testing in routine clinical practice at diagnosis for NS-NSCLC patients by using an ultra-fast-next generation sequencing approach (Ion Torrent Genexus Sequencer, Thermo Fisher Scientific). We show that the molecular targets currently available to personalized medicine in thoracic oncology can be identified using this system in an appropriate TAT, notably when only a small amount of nucleic acids is available. We discuss the new challenges and the perspectives of using such an ultra-fast NGS in daily practice.
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Affiliation(s)
- Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Salomé Lalvée
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
| | - Virginie Tanga
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Maryline Allegra
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Myriam Salah
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Doriane Bohly
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
| | - Jonathan Benzaquen
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Pasteur Hospital, 06000 Nice, France
| | - Charles-Hugo Marquette
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Pasteur Hospital, 06000 Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (M.I.); (V.H.); (C.B.); (V.L.-F.); (O.B.); (S.L.); (S.L.); (E.L.-M.)
- Biobank-related Hospital (BB-0033-00025), Pasteur Hospital, 06000 Nice, France; (V.T.); (M.A.); (M.S.); (D.B.)
- FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06000 Nice, France; (J.B.); (C.-H.M.)
- Inserm U1081, CNRS UMR 7413, IRCAN, 06100 Nice, France
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6
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Zacharias M, Absenger G, Kashofer K, Wurm R, Lindenmann J, Terbuch A, Konjic S, Sauer S, Gollowitsch F, Gorkiewicz G, Brcic L. Reflex testing in non-small cell lung carcinoma using DNA- and RNA-based next-generation sequencing-a single-center experience. Transl Lung Cancer Res 2022; 10:4221-4234. [PMID: 35004252 PMCID: PMC8674594 DOI: 10.21037/tlcr-21-570] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022]
Abstract
Background Targeted treatment modalities for non-small cell lung carcinoma (NSCLC) patients are expanding rapidly and demand a constant adaptation of molecular testing strategies. In this regard, broad reflex testing via next-generation sequencing (NGS) might have several advantages. However, real-world data regarding practical feasibility and clinical relevance are scarce, especially for RNA-based NGS. Methods We performed a retrospective study comparing NGS use in two consecutive years (2019 and 2020). In 2019, reflex testing mainly consisted of DNA-based NGS for mutations and immunohistochemistry (IHC) for ALK, ROS1, and NTRK fusion products. At the beginning of 2020, our approach has changed, with DNA- and RNA-based NGS panels now being simultaneously performed. This change in protocol allowed us to retrospectively evaluate if broad molecular reflex testing brings additional value to lung cancer patients. Results Within the whole cohort (n=432), both DNA- and RNA-based NGS yielded almost always evaluable results. Only in 6 cases, the RNA content was too little for an appropriate analysis. After integrating RNA-based NGS in the reflex testing approach, the number of detected fusions increased significantly (2.6% vs. 8.2%; P=0.0021), but also more patients received targeted therapies. Furthermore, exceedingly rare alterations were more likely to be detected, including the so far undescribed EGFR-NUP160 fusion. Conclusions Our study demonstrates that a comprehensive approach to reflex NGS testing is practically feasible and clinically relevant. Including RNA-based panels in the reflex testing approach results in more detected fusions and more patients receiving targeted therapies. Additionally, this broad molecular profiling strategy identifies patients with emerging biomarkers, underscoring its usefulness in the rapidly evolving landscape of targeted therapies.
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Affiliation(s)
- Martin Zacharias
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Gudrun Absenger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Karl Kashofer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Robert Wurm
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Jörg Lindenmann
- Division of Thoracic Surgery and Hyperbaric Surgery, Department of Surgery, Medical University of Graz, Graz, Austria
| | - Angelika Terbuch
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Selma Konjic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Stefan Sauer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Franz Gollowitsch
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Gregor Gorkiewicz
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Luka Brcic
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Graz, Austria
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7
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Bourhis A, Remoué A, Samaison L, Uguen A. Diagnostic mutationnel rapide Idylla™ : applications théranostiques actuelles et futures. Ann Pathol 2022; 42:329-343. [DOI: 10.1016/j.annpat.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 12/07/2021] [Accepted: 12/12/2021] [Indexed: 10/19/2022]
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8
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Petiteau C, Robinet-Zimmermann G, Riot A, Dorbeau M, Richard N, Blanc-Fournier C, Bibeau F, Deshayes S, Bergot E, Gervais R, Levallet G. Contribution of the Idylla TM System to Improving the Therapeutic Care of Patients with NSCLC through Early Screening of EGFR Mutations. Curr Oncol 2021; 28:4432-4445. [PMID: 34898548 PMCID: PMC8628756 DOI: 10.3390/curroncol28060376] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 10/22/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) genotyping, a critical examen for the treatment decisions of patients with non-small cell lung cancer (NSCLC), is commonly assayed by next-generation sequencing (NGS), but this global approach takes time. To determine whether rapid EGFR genotyping tests by the IdyllaTM system guides earlier therapy decisions, EGFR mutations were assayed by both the IdyllaTM system and NGS in 223 patients with NSCLC in a bicentric prospective study. IdyllaTM demonstrated agreement with the NGS method in 187/194 cases (96.4%) and recovered 20 of the 26 (77%) EGFR mutations detected using NGS. Regarding the seven missed EGFR mutations, five were not detected by the IdyllaTM system, one was assayed in a sample with insufficient tumoral cells, and the last was in a sample not validated by the IdyllaTM system (a bone metastasis). IdyllaTM did not detect any false positives. The average time between EGFR genotyping results from IdyllaTM and the NGS method was 9.2 ± 2.2 working days (wd) (12.6 ± 4.0 calendar days (cd)). Subsequently, based on the IdyllaTM method, the timeframe from tumor sampling to the initiation of EGFR-TKI was 7.7 ± 1.2 wd (11.4 ± 3.1 cd), while it was 20.3 ± 6.7 wd (27.2 ± 8.3 cd) with the NGS method (p < 0.001). We thus demonstrated here that the IdyllaTM system contributes to improving the therapeutic care of patients with NSCLC by the early screening of EGFR mutations.
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Affiliation(s)
- Constance Petiteau
- Department of Pulmonology & Thoracic Oncology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (C.P.); (S.D.); (E.B.)
| | | | - Adèle Riot
- Department of Pathology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (A.R.); (F.B.)
| | - Marine Dorbeau
- Department of Pathology, Centre François Baclesse, F-14000 Caen, France; (G.R.-Z.); (M.D.); (C.B.-F.)
| | - Nicolas Richard
- Department of Genetics, Normandy University, UNICAEN, Caen University Hospital, EA 7450 BioTARGen, F-14000 Caen, France;
- Federative Structure of Cyto-Molecular Oncogenetics (SF-MOCAE), Centre Hospitalier Universitaire de Caen, F-14000 Caen, France
| | - Cécile Blanc-Fournier
- Department of Pathology, Centre François Baclesse, F-14000 Caen, France; (G.R.-Z.); (M.D.); (C.B.-F.)
| | - Frédéric Bibeau
- Department of Pathology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (A.R.); (F.B.)
| | - Simon Deshayes
- Department of Pulmonology & Thoracic Oncology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (C.P.); (S.D.); (E.B.)
| | - Emmanuel Bergot
- Department of Pulmonology & Thoracic Oncology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (C.P.); (S.D.); (E.B.)
- Normandy University, UNICAEN, CEA, CNRS, ISTCT Unit, GIP CYCERON, F-14000 Caen, France
| | - Radj Gervais
- Department of Thoracic Oncology, Centre François Baclesse, F-14000 Caen, France;
| | - Guénaëlle Levallet
- Department of Pathology, Centre Hospitalier Universitaire de Caen, F-14000 Caen, France; (A.R.); (F.B.)
- Federative Structure of Cyto-Molecular Oncogenetics (SF-MOCAE), Centre Hospitalier Universitaire de Caen, F-14000 Caen, France
- Normandy University, UNICAEN, CEA, CNRS, ISTCT Unit, GIP CYCERON, F-14000 Caen, France
- Correspondence:
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9
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Hawkins P, Stevenson T, Powari M. Use of the Idylla EGFR Mutation Test for Variant Detection in Non-Small Cell Lung Cancer Samples. Am J Clin Pathol 2021; 156:653-660. [PMID: 33877290 DOI: 10.1093/ajcp/aqab003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
OBJECTIVES Stratified management of patients with non-small cell lung carcinoma (NSCLC) through epithelial growth factor receptor (EGFR) variant analysis has become standard clinical practice. The Idylla system is a fully compliant European in vitro diagnostics device, a fully automated platform designed to rapidly genotype formalin-fixed paraffin-embedded tissue samples. This retrospective study aims to validate the Idylla EGFR Mutation Test for use with extracted DNA from known NSCLC samples. METHODS In this study, 20 µL of archival extracted DNA was placed directly inside the Idylla EGFR assay single-use cartridge. Idylla results were compared with the original Sanger sequencing reference method. RESULTS The Idylla EGFR Mutation Test yielded valid results for all samples tested, confirming the variants identified by the reference method that lay within the Idylla target range. No false-positive cases were noted with the Idylla assay. Variant genotype reports were obtained within 150 minutes. CONCLUSIONS The Idylla EGFR assay is sensitive for extracted DNA and can be reliably applied to cytologic specimens, enabling its implementation as an ancillary first-line test for patients with NSCLC.
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Affiliation(s)
- Paul Hawkins
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
| | - Tracey Stevenson
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
| | - Manish Powari
- Department of Cellular Pathology, Royal Devon and Exeter NHS Foundation Trust, DevonUK
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10
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Hofman P. EGFR Status Assessment for Better Care of Early Stage Non-Small Cell Lung Carcinoma: What Is Changing in the Daily Practice of Pathologists? Cells 2021; 10:2157. [PMID: 34440926 PMCID: PMC8392580 DOI: 10.3390/cells10082157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 02/08/2023] Open
Abstract
The recent emergence of novel neoadjuvant and/or adjuvant therapies for early stage (I-IIIA) non-small cell lung carcinoma (NSCLC), mainly tyrosine kinase inhibitors (TKIs) targeting EGFR mutations and immunotherapy or chemo-immunotherapy, has suddenly required the evaluation of biomarkers predictive of the efficacy of different treatments in these patients. Currently, the choice of one or another of these treatments mainly depends on the results of immunohistochemistry for PD-L1 and of the status of EGFR and ALK. This new development has led to the setup of different analyses for clinical and molecular pathology laboratories, which have had to rapidly integrate a number of new challenges into daily practice and to establish new organization for decision making. This review outlines the impact of the management of biological samples in laboratories and discusses perspectives for pathologists within the framework of EGFR TKIs in early stage NSCLC.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, CHU Nice, FHU OncoAge, Pasteur Hospital, Université Côte d’Azur, 06108 Nice, France; ; Tel.: +33-492-038-855; Fax: +33-492-8850
- CHU Nice, FHU OncoAge, Hospital-Integrated Biobank BB-0033-00025, Université Côte d’Azur, 06000 Nice, France
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11
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What Is New in Biomarker Testing at Diagnosis of Advanced Non-Squamous Non-Small Cell Lung Carcinoma? Implications for Cytology and Liquid Biopsy. JOURNAL OF MOLECULAR PATHOLOGY 2021. [DOI: 10.3390/jmp2020015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The discovery and clinical validation of biomarkers predictive of the response of non-squamous non-small-cell lung carcinomas (NS-NSCLC) to therapeutic strategies continue to provide new data. The evaluation of novel treatments is based on molecular analyses aimed at determining their efficacy. These tests are increasing in number, but the tissue specimens are smaller and smaller and/or can have few tumor cells. Indeed, in addition to tissue samples, complementary cytological and/or blood samples can also give access to these biomarkers. To date, it is recommended and necessary to look for the status of five genomic molecular biomarkers (EGFR, ALK, ROS1, BRAFV600, NTRK) and of a protein biomarker (PD-L1). However, the short- and more or less long-term emergence of new targeted treatments of genomic alterations on RET and MET, but also on others’ genomic alteration, notably on KRAS, HER2, NRG1, SMARCA4, and NUT, have made cellular and blood samples essential for molecular testing. The aim of this review is to present the interest in using cytological and/or liquid biopsies as complementary biological material, or as an alternative to tissue specimens, for detection at diagnosis of new predictive biomarkers of NS-NSCLC.
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12
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Hofman P, Boutros J, Benchetrit D, Benzaquen J, Leroy S, Tanga V, Bordone O, Allégra M, Lespinet V, Fayada J, Maniel C, Griffonnet J, Selva E, Troncone G, Portella G, Lavrut T, Chemla R, Carles M, Ilié M, Marquette C. A rapid near-patient RT-PCR test for suspected COVID-19: a study of the diagnostic accuracy. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:921. [PMID: 34350236 PMCID: PMC8263856 DOI: 10.21037/atm-21-690] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/21/2021] [Indexed: 01/02/2023]
Abstract
Background Management of large numbers of reverse transcriptase-polymerase chain reactions (RT-PCR) for diagnosis of coronavirus 2019 disease (COVID-19) requires robust infrastructures, located in dedicated premises with a high standard of biosafety procedures, and well-trained personnel. The handling of a “run-of-river sample” to obtain rapid reporting of results is challenging. Methods We studied the clinical performance of the Idylla™ SARS-CoV-2 Test (index test) on a platform capable of fully automated nucleic acid testing including extraction, amplification, and detection in a single-use cartridge to establish the diagnosis of COVID-19. The study was conducted on a prospective cohort of 112 volunteers with recent symptoms and an unknown SARS-CoV-2 status who came to free screening centers of the Nice metropolitan area. All subjects underwent bilateral nasopharyngeal sampling. One sample was processed using the index test, the other using the standard of care RT-PCR. Samples were treated blind. Results Most of the participants (70%) were sampled within 4 days of symptom onset. Forty-five (40.2%) were positive for COVID-19. No clinical symptoms were distinguished between SARS-CoV-2 RT-PCR positive and negative subjects except anosmia and dysgeusia. Positive and negative agreement between the index and the standard of care test was 100%. Conclusions The Idylla™ SARS-CoV-2 Test is very sensitive, specific, rapid and easy to use in a near-patient RT-PCR approach to distinguish between symptomatic SARS-CoV-2 positive and negative patients in selected settings.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France.,Institute of Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France
| | - Jacques Boutros
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | | | - Jonathan Benzaquen
- Institute of Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France.,Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Sylvie Leroy
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France.,CNRS UMR 7275 - Institut de Pharmacologie Moléculaire et Cellulaire - Université Côte d'Azur, Nice, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Olivier Bordone
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Maryline Allégra
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Virginie Lespinet
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Julien Fayada
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Charlotte Maniel
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Jennifer Griffonnet
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
| | - Eric Selva
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Frederico II, Naples, Italy
| | - Giuseppe Portella
- Department of Public Health, University of Naples Frederico II, Naples, Italy
| | - Thibaut Lavrut
- Laboratoire de Virologie CHU de Nice, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, Nice, France
| | | | - Michel Carles
- Department of Infectious Diseases, Université Côte d'Azur, Centre Hopsitalier Universitaire de Nice, Nice, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Université Côte d'Azur, Nice, France.,Université Côte d'Azur, FHU OncoAge, Centre Hospitalier Universitaire de Nice, Hospital-Related Biobank (BB-0033-00025), Nice, France.,Institute of Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France
| | - Charles Marquette
- Institute of Research on Cancer and Aging (IRCAN), Université Côte d'Azur, CNRS, INSERM, Nice, France.,Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Nice, France
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13
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Hofman P, Rouleau E, Sabourin JC, Denis M, Deleuze JF, Barlesi F, Laurent-Puig P. Predictive molecular pathology in non-small cell lung cancer in France: The past, the present and the perspectives. Cancer Cytopathol 2021; 128:601-610. [PMID: 32885912 DOI: 10.1002/cncy.22318] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/20/2020] [Accepted: 05/28/2020] [Indexed: 12/16/2022]
Abstract
The advent of molecular targets for novel therapeutics in oncology, notably for non-small cell lung carcinoma (NSCLC), led the French National Cancer Institute (INCa) to establish a national network of 28 hospital Molecular Genetics Centers for Cancer (MGCC) in 2007. In each University in France, laboratories were established to develop molecular biology testing to evaluate a few genomic alterations, initially a selection of genes, by using specific targeted polymerase chain reaction (PCR) assays. In a second phase, the number of studied genes was increased. In 2015, the MGCC benefited from an additional dedicated budget from the INCa to develop next-generation sequencing (NGS) technology. In the meantime, a new financial regulation for innovative testing has been established for the acts out of nomenclature. Consequently, all private and public laboratories in France have access to funding for molecular biology testing in oncology. The gene-based PCR assays or NGS tests have benefitted from reimbursement of cost testing by the INCa. Today, the laboratories consider this reimbursement to be only partial, and its use to be complex. In 2018, a strategic plan for medical genomic analyses (France Médecine Génomique 2025) was implemented to introduce more systematic sequencing into the health care pathway and oncology practice. The large panel of molecular tests should be centralized to a limited number of molecular genetic centers. This review describes the evolution of the different stages of implementation of molecular pathology testing for NSCLC patients over the last few years in France.
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Affiliation(s)
- Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, University Côte d'Azur, Nice, France.,Hospital-Related Biobank, Pasteur Hospital, University Côte d'Azur, Nice, France.,FHU OncoAge, Pasteur Hospital, University Côte d'Azur, Nice, France
| | - Etienne Rouleau
- Cancer Genetic Laboratory, Biology and Pathology Department, Gustave Roussy, Villejuif, France
| | | | - Marc Denis
- Department of Biochemistry and INSERM U1232, Nantes University Hospital, Nantes, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine, Institut de Biologie François Jacob, CEA, Université Paris Saclay, Evry, France.,Centre d'Etude du Polymorphisme Humain, Fondation Jean Dausset, Paris, France.,Centre de Référence, d'Innovation et d'Expertise (CREFIX), Paris, France
| | - Fabrice Barlesi
- Aix-Marseille University, CNRS, INSERM, CRCM, Marseille, France.,Gustave Roussy Cancer Campus, Villejuif, France
| | - Pierre Laurent-Puig
- UMR-1138, INSERM, Département de Biologie, Hôpital Européen Georges-Pompidou, Paris, France.,Université Paris Descartes, Assistance Publique-Hôpitaux de Paris, Paris, France
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14
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Nunnari J, Graziano P, Muscarella LA, Rossi A, Grillo LR, Montrone G, Di Lorenzo A, Bronzini M, Leone A. Rapid EGFR evaluation from used H&E, IHC and FISH diagnostic slides with the Idylla platform. J Clin Pathol 2021; 75:338-344. [PMID: 33597223 DOI: 10.1136/jclinpath-2020-207315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/26/2021] [Accepted: 01/29/2021] [Indexed: 12/25/2022]
Abstract
AIMS Diagnostic tumour samples are mandatory for morphologic and molecular diagnosis of non-small cell lung cancer (NSCLC) to establish the best therapeutic approach. In the presence of small tumour tissue sample, the pathologist needs to make responsible choices to achieve a correct diagnosis and save material for subsequent molecular evaluations. Nevertheless, in some instances, the diagnostic process can lead to tissue depletion. The automated Idylla epidermal growth factor receptor (EGFR) mutation test has been developed to rapidly process formalin-fixed paraffin-embedded (FFPE) pathologic material, without previous DNA extraction. This study aimed to test whether this platform is suitable for the reuse of H&E, immunohistochemistry (IHC) and fluorescence in situ hybridisation (FISH) diagnostic slides. METHODS A training set of 19 FFPE tissues with known EGFR status was revaluated on H&E slides. Fourteen of them were also tested using IHC and FISH treated specimens. An additional series of 25 H&E, IHC or FISH slides of NSCLC cases tested for EGFR mutation at an external institution was blindly assessed as a validation cohort. RESULTS Combining the two sets, 32 of 32 classical ex19dels and p.L858R were correctly identified. Three uncommon mutations (p.G719X, p.L861Q and ex20ins) were also detected. Four discrepancies were related to rare ex19del/ins not included in the Idylla list of detectable mutations. Two p.T790M variants were missed on one FFPE and two H&E slides but were detected using IHC and FISH sections from the same FFPE blocks. CONCLUSIONS The Idylla EGFR mutation test is highly reliable using differently treated tumour specimens and should be validated in larger studies.
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Affiliation(s)
- Josè Nunnari
- Anatomic Pathology Unit, San Camillo-Forlanini Hospitals, Rome, Italy
| | - Paolo Graziano
- Anatomic Pathology Unit, Scientific Institute for Research and Health Care (IRCCS) Fondazione Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Scientific Institute for Research and Health Care (IRCCS) Fondazione Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonio Rossi
- Oncology Center of Excellence, Therapeutic Science and Strategy Unit, IQVIA, Milan, Italy
| | | | - Giuseppe Montrone
- Anatomic Pathology Unit, San Camillo-Forlanini Hospitals, Rome, Italy
| | - Angela Di Lorenzo
- Anatomic Pathology Unit, San Camillo-Forlanini Hospitals, Rome, Italy
| | - Monica Bronzini
- Anatomic Pathology Unit, San Camillo-Forlanini Hospitals, Rome, Italy
| | - Alvaro Leone
- Anatomic Pathology Unit, San Camillo-Forlanini Hospitals, Rome, Italy
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15
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Momeni-Boroujeni A, Salazar P, Zheng T, Mensah N, Rijo I, Dogan S, Yao J, Moung C, Vanderbilt C, Benhamida J, Chang J, Travis W, Rekhtman N, Ladanyi M, Nafa K, Arcila ME. Rapid EGFR Mutation Detection Using the Idylla Platform: Single-Institution Experience of 1200 Cases Analyzed by an In-House Developed Pipeline and Comparison with Concurrent Next-Generation Sequencing Results. J Mol Diagn 2020; 23:310-322. [PMID: 33346146 DOI: 10.1016/j.jmoldx.2020.11.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Mutations in the epidermal growth factor receptor (EGFR) are the most common targetable alterations in lung adenocarcinoma. To facilitate rapid testing, the Idylla EGFR assay was incorporated as a screening method before next-generation sequencing (NGS). Validation and experience using an in-house developed analysis pipeline, enhanced with a manual review algorithm is described. Results are compared with corresponding NGS results. In all, 1249 samples were studied. Validation demonstrated 98.57% (69/70) concordance with the reference methods. The limit of detection varied from 2% to 5% variant allele frequency for total EGFR quantitation cycle between 20 and 23. Of the 1179 clinical cases, 23.41% were EGFR-positive by Idylla. Concurrent NGS was successfully performed on 94.9% (799/842) requests. Concordance of Idylla with NGS was 98.62% (788/799) and 98.50% (787/799) using our in-house and Idylla analysis pipelines, respectively. Discordances involved missed mutations by both assays associated with low tumor/low input. Incorporating a manual review algorithm to supplement automated calls improved accuracy from 98.62% to 99.37% and sensitivity from 94.68% to 97.58%. Overall reporting time, from receipt of material to official clinical report, ranged from 1 to 3 days. Therefore, Idylla EGFR testing enables rapid and sensitive screening without compromising subsequent comprehensive NGS, when required. Automated calling, enhanced with a manual review algorithm, reduces false-negative calls associated with low tumor/low input samples.
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Affiliation(s)
| | - Paulo Salazar
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tao Zheng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nana Mensah
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ivelise Rijo
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - JinYuan Yao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christine Moung
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chad Vanderbilt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jamal Benhamida
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason Chang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - William Travis
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Natasha Rekhtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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16
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Troncone G, Hofman P. Pathologists and the coronavirus distraction effect. J Clin Pathol 2020; 74:205-206. [PMID: 32499225 DOI: 10.1136/jclinpath-2020-206807] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 11/03/2022]
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