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Joshi P, Gogte P, Pai T, Gurav M, Dhanawade D, Karnik N, Deshpande G, Kaushal R, Shetty O. Microfluidics-based EGFR mutation detection and its implication in the resource-limited clinical setting. Int J Exp Pathol 2024; 105:90-99. [PMID: 38717047 PMCID: PMC11129959 DOI: 10.1111/iep.12503] [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: 07/31/2023] [Revised: 02/28/2024] [Accepted: 03/14/2024] [Indexed: 05/29/2024] Open
Abstract
Management of lung cancer today obligates a mutational analysis of the epidermal growth factor receptor (EGFR) gene particularly when Tyrosine Kinase Inhibitor (TKI) therapy is being considered as part of prognostic stratification. This study evaluates the performance of automated microfluidics-based EGFR mutation detection and its significance in clinical diagnostic settings. Formalin-fixed, paraffin-embedded (FFPE) samples from NSCLC patients (n = 174) were included in a two-phase study. Phase I: Validation of the platform by comparing the results with conventional real-time PCR and next-generation sequencing (NGS) platform. Phase II: EGFR mutation detection on microfluidics-based platform as part of routine diagnostics workup. The microfluidics-based platform demonstrates 96.5% and 89.2% concordance with conventional real-time PCR and NGS, respectively. The system efficiently detects mutations across the EGFR gene with 88.23% sensitivity and 100% specificity. Out of 144 samples analysed in phase II, the platform generated valid results in 94% with mutation detected in 41% of samples. This microfluidics-based platform can detect as low as 5% mutant allele fractions from the FFPE samples. Therefore the microfluidics-based platform is a rapid, complete walkaway, with minimum tissue requirement (two sections of 5 μ thickness) and technical skill requirement. The method can detect clinically actionable EGFR mutations efficiently and can be considered a reliable diagnostic platform in resource-limited settings. From receiving samples to reporting the results this platform provides accurate data without much manual intervention. The study helped to devise an algorithm that emphasizes effective screening of the NSCLC cases for EGFR mutations with varying tumour content. Thus it helps in triaging the cases judiciously before proceeding with multigene testing.
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Affiliation(s)
- Pradnya Joshi
- Molecular Pathology Division, Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Prachi Gogte
- Molecular Pathology Division, Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Trupti Pai
- Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Mamta Gurav
- Molecular Pathology Division, Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Dipika Dhanawade
- Molecular Pathology Division, Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Nupur Karnik
- Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Gauri Deshpande
- Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Rajiv Kaushal
- Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
| | - Omshree Shetty
- Molecular Pathology Division, Department of PathologyTata Memorial Hospital, Homi Bhabha National InstituteMumbaiIndia
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Zhang MS, Yeh YC, Huang HN, Lin LW, Huang YL, Wang LC, Yao LJ, Hung TC, Tseng YF, Lee YH, Liao WY, Shih JY, Hsieh MS. The association of EGFR amplification with aberrant exon 20 insertion report using the cobas EGFR Mutation Test v2. PLoS One 2024; 19:e0301120. [PMID: 38687753 PMCID: PMC11060574 DOI: 10.1371/journal.pone.0301120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
Determining the exact type of epidermal growth factor receptor (EGFR) exon 20 insertion (ex20ins) mutation in lung cancer has become important. We found that not all ex20ins mutations reported by cobas EGFR test v2 could be validated by Sanger sequencing even using surgical specimens with high tumor contents. This study aimed to validate the ex20ins results reported by the cobas test and to determine whether there were clinicopathological factors associated with aberrant cobas ex20ins report. In total, 123 cobas-reported cases with ex20ins were retrospectively collected and validated by Sanger sequencing and Idylla assay. Clinicopathological features between ex20ins cobas+/Sanger+ group (n = 71) and cobas+/Sanger- group (n = 52) were compared. The Idylla assay detected ex20ins in 82.6% of cobas+/Sanger+ cases but only in 4.9% of cobas+/Sanger- cases. The cobas+/Sanger- group was significantly associated with higher tumor contents, poorly differentiated patterns, tumor necrosis, and a lower internal control cycle threshold value reported by the Idylla which suggesting the presence of increased EGFR gene copy numbers. EGFR fluorescence in situ hybridization (FISH) revealed the majority of cobas+/Sanger- group had EGFR high copy number gain (16%) or amplification (76%) according to the Colorado criteria. Among cases reported to have concomitant classic EGFR and ex20ins mutations by the cobas, the classic EGFR mutations were all detected by Sanger sequencing and Idylla, while the ex20ins mutations were undetected by Sanger sequencing (0%) or rarely reported by Idylla assay (3%). FISH revealed high EGFR copy number gain (17.9%) and amplification (79.5%) in cases reported having concomitant classic EGFR and ex20ins mutations by the cobas. This study demonstrated an unusually high frequency of EGFR amplification in cases with aberrant cobas ex20ins report which could not be validated by Sanger sequencing or Idylla assay. Ex20ins reported by the cobas test should be validated using other methods especially those reported having concomitant ex20ins and classic EGFR mutations.
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Affiliation(s)
- Man-San Zhang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Chen Yeh
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Hsien-Neng Huang
- Department of Pathology, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan
- Graduate Institute of Pathology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Long-Wei Lin
- Department of Pathology, National Taiwan University Hospital Yunlin Branch, Yunlin, Taiwan
| | - Yen-Lin Huang
- Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan
| | - Lei-Chi Wang
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Lai-Jin Yao
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Tze-Chun Hung
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Fen Tseng
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Hsuan Lee
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Yu Liao
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jin-Yuan Shih
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Min-Shu Hsieh
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Pathology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Pathology, National Taiwan University Cancer Center, Taipei, Taiwan
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3
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Hawkins P, Stevenson T, Powari M. Use of cytology fluid samples for predictive biomarker testing in lung cancer patients. Cytopathology 2024; 35:242-249. [PMID: 38041234 DOI: 10.1111/cyt.13344] [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: 07/16/2023] [Revised: 09/19/2023] [Accepted: 11/21/2023] [Indexed: 12/03/2023]
Abstract
OBJECTIVE To provide a method of directly using cytology fluid samples for predictive biomarker testing in lung cancer patients and to determine the efficacy of a variety of fluid sample types. METHOD A review of our in-house data from a range of cytology samples including endobronchial ultrasound (EBUS) fine-needle aspirate (FNA) needle washings (NW) and serous effusions tested on the Biocartis Idylla platform. All fluid samples were originally tested using Sanger sequencing. RESULTS Using our method for fluid samples all of our cytology samples tested for epithelial growth factor receptor (EGFR) yielded valid results on this platform and all variant cases identified. The data showed serous fluids provided the best quality DNA, and variant genotype reports were obtained within 150 minutes. CONCLUSION Cytology fluid samples can be used for predictive biomarker testing for lung cancer patients to provide in-house results with all fluids providing good-quality DNA.
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Affiliation(s)
- Paul Hawkins
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Tracey Stevenson
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
| | - Manish Powari
- Royal Devon University Healthcare NHS Foundation Trust, Exeter, UK
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Michaelidou K, Karniadakis I, Pantelaion V, Koutoulaki C, Boukla E, Folinas K, Dimaras P, Papadaki MA, Koutsopoulos AV, Mavroudis D, Vourlakou C, Mavridis K, Agelaki S. Rapid and reliable testing for clinically actionable EGFR mutations in non-small cell lung cancer using the Idylla TM platform: a real-world two-center experience in Greece. Expert Rev Mol Diagn 2024; 24:89-98. [PMID: 38193169 DOI: 10.1080/14737159.2024.2303320] [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: 09/29/2023] [Accepted: 12/22/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND Limited information exists on epidermal growth factor receptor (EGFR) molecular epidemiology in Greece. Next-generation sequencing (NGS) is the recommended method for EGFR genotyping in NSCLC. The Idylla Biocartis platform is a fully automated system for actionable EGFR mutation detection. RESEARCH DESIGN AND METHODS We describe the prevalence of EGFR mutations in NSCLC patients in two high-volume clinical centers in Greece and compare key methods used for their determination. Eight hundred and fifty-seven FFPE samples from NSCLC patients were tested for EGFR mutations at University of Crete (UoC; n = 324) and at Evangelismos Hospital, Athens (Evangelismos; n = 503). RESULTS The prevalence of EGFR mutations was 11.1% in the whole cohort (11.5% in non-squamous). The detection rate was 11.0% by NGS, 9.8% by Sanger and 11.3% by Idylla for the whole cohort (12.0% in non-squamous). The agreement between Idylla and Sanger was 93.2%. A targetable EGFR mutation was detected in 10.0% using tissue NGS alone, and in 16.0% using concurrent Idylla ctEGFR testing. CONCLUSION The frequency of EGFR mutations was as expected for a Caucasian population. The Idylla EGFR test performance is comparable to reference methods and with a shorter TAT. Adding a concurrent plasma Idylla test to tissue NGS testing increases the detection rate of EGFR mutations in NSCLC.
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Affiliation(s)
- Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
| | - Ioannis Karniadakis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
| | | | - Chara Koutoulaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
| | - Eleni Boukla
- Department of Medical Oncology, University General Hospital of Heraklion, Crete, Greece
| | | | - Pantelis Dimaras
- Department of Medical Oncology, University General Hospital of Heraklion, Crete, Greece
| | - Maria A Papadaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
| | | | - Dimitrios Mavroudis
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, Crete, Greece
| | | | - Konstantinos Mavridis
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), Heraklion, Crete, Greece
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Crete, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, Crete, Greece
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5
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Léonce C, Guerriau C, Chalabreysse L, Duruisseaux M, Couraud S, Brevet M, Bringuier PP, Poncet DA. Comparison and Validation of Rapid Molecular Testing Methods for Theranostic Epidermal Growth Factor Receptor Alterations in Lung Cancer: Idylla versus Digital Droplet PCR. Int J Mol Sci 2023; 24:15684. [PMID: 37958668 PMCID: PMC10648419 DOI: 10.3390/ijms242115684] [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: 10/06/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Targeting EGFR alterations, particularly the L858R (Exon 21) mutation and Exon 19 deletion (del19), has significantly improved the survival of lung cancer patients. From now on, the issue is to shorten the time to treatment. Here, we challenge two well-known rapid strategies for EGFR testing: the cartridge-based platform Idylla™ (Biocartis) and a digital droplet PCR (ddPCR) approach (ID_Solution). To thoroughly investigate each testing performance, we selected a highly comprehensive cohort of 39 unique del19 (in comparison, the cbioportal contains 40 unique del19), and 9 samples bearing unique polymorphisms in exon 19. Additional L858R (N = 24), L861Q (N = 1), del19 (N = 63), and WT samples (N = 34) were used to determine clear technical and biological cutoffs. A total of 122 DNA samples extracted from formaldehyde-fixed samples was used as input. No false positive results were reported for either of the technologies, as long as careful droplet selection (ddPCR) was ensured for two polymorphisms. ddPCR demonstrated higher sensitivity in detecting unique del19 (92.3%, 36/39) compared to Idylla (67.7%, 21/31). However, considering the prevalence of del19 and L858R in the lung cancer population, the adjusted theranostic values were similar (96.51% and 95.26%, respectively). ddPCR performs better for small specimens and low tumoral content, but in other situations, Idylla is an alternative (especially if a molecular platform is absent).
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Affiliation(s)
- Camille Léonce
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, 69008 Lyon, France
| | - Clémence Guerriau
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) Laboratory, Team Chromatin Dynamics, Nuclear Domains, Virus, 69008 Lyon, France
| | - Lara Chalabreysse
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
| | - Michaël Duruisseaux
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
- Cancer Research Center of Lyon, UMR INSERM 1052 CNRS 5286, 69008 Lyon, France
- Respiratory Department and Early Phase, Louis Pradel Hospital, Hospices Civils de Lyon Cancer Institute, 69100 Lyon, France
| | - Sébastien Couraud
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
- Department of Pulmonology and Thoracic Oncology, Lyon Sud Hospital, 69495 Pierre Bénite, France
| | - Marie Brevet
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
| | - Pierre-Paul Bringuier
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
| | - Delphine Aude Poncet
- Department of Pathology, Tumor Molecular Biology Unit, Groupement Hospitalier Est, Hospices Civils de Lyon, 69394 Bron, France; (C.L.); (C.G.); (L.C.); (M.B.); (P.-P.B.)
- University of Lyon, Université Claude Bernard Lyon 1, 69100 Lyon, France; (M.D.); (S.C.)
- CNRS UMR 5261, INSERM U 1315, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), Pathophysiology and Genetics of the Neuron and Muscle (PGNM) Laboratory, Team Chromatin Dynamics, Nuclear Domains, Virus, 69008 Lyon, France
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6
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Khalifa E, Chapusot C, Tournier B, Sentis J, Marion E, Remond A, Aubry M, Pioche C, Bergeron A, Primois C, Blanchard L, Millière A, Boucheix M, Léger Y, Bairrao M, Brouste V, Martin L, Soubeyran I. Idylla EGFR assay on extracted DNA: advantages, limits and place in molecular screening according to the latest guidelines for non-small-cell lung cancer (NSCLC) patients. J Clin Pathol 2023; 76:698-704. [PMID: 35820776 DOI: 10.1136/jcp-2022-208325] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/28/2022] [Indexed: 11/04/2022]
Abstract
AIMS Idylla epidermal growth factor receptor (EGFR) is a fast and fully automated mutation assay that is easy to implement. However, under the Biocartis-recommended technical conditions, tissue sections are directly introduced into the cartridge, at the risk of exhausting the tumour sample. In this study, we evaluate the performance of Idylla EGFR on extracted DNA and discuss its place within the global non-small-cell lung cancer (NSCLC) screening strategy. METHODS 577 comparative tests between Idylla EGFR on extracted DNA and next-generation sequencing (NGS) were performed across two centres. RESULTS Preanalytical thresholds were established (20% tumour cell content, 50 ng DNA input) and challenged prospectively in routine practice. 16.8% of samples referred for screening were considered non eligible for Idylla EGFR testing. Due to discordant by design cases, Idylla EGFR sensitivity was 86.9% for currently actionable EGFR mutations. Idylla EGFR specificity was 100% in first-line screening. NGS was always feasible on the same DNA. CONCLUSION Idylla EGFR on extracted DNA is feasible and enables tumour material to be saved compared with tissue section use. It is not necessary to replace the analytical thresholds of the Biocartis algorithm. Due to both the limits of the mutational repertoire and the high increase of targetable genes in NSCLC, the use of Idylla EGFR should be restricted to clinical emergency situations accompanied by NGS.
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Affiliation(s)
| | - Caroline Chapusot
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Benjamin Tournier
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Julie Sentis
- Biopathology, Institut Bergonié, Bordeaux, France
| | | | - Alicia Remond
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Manon Aubry
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Célia Pioche
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Anthony Bergeron
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | - Alice Millière
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | | | | | | | - Véronique Brouste
- Research and Clinical Epidemiology Unit - Biostatistics, Institut Bergonié, Bordeaux, France
| | - Laurent Martin
- Platform of Somatic Oncology of Burgundy, Centre Hospitalier Universitaire de Dijon, Dijon, France
- Department of Pathology, Centre Hospitalier Universitaire de Dijon, Dijon, France
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Mondelo-Macía P, Lago-Lestón RM, Rodríguez-Casanova A, Abalo A, Díaz-Lagares Á, García-González J, León-Mateos L, Díaz-Peña R, Muinelo-Romay L. Rapid Idylla mutational testing to detect EGFR mutations in plasma samples and to monitor therapy in advanced non-small cell lung cancer patients. Pathology 2023; 55:698-703. [PMID: 37037720 DOI: 10.1016/j.pathol.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/09/2022] [Accepted: 01/06/2023] [Indexed: 03/17/2023]
Affiliation(s)
- Patricia Mondelo-Macía
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
| | - Ramón Manuel Lago-Lestón
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Aitor Rodríguez-Casanova
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Alicia Abalo
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Ángel Díaz-Lagares
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain
| | - Jorge García-González
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain; Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain; Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Luis León-Mateos
- Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain; Department of Medical Oncology, Complexo Hospitalario Universitario de Santiago de Compostela (SERGAS), Santiago de Compostela, Spain; Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Roberto Díaz-Peña
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Fundación Pública Galega de Medicina Xenómica, SERGAS; Grupo de Medicina Xenomica-USC, Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain.
| | - Laura Muinelo-Romay
- Liquid Biopsy Analysis Unit, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain; Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Santiago de Compostela, Spain.
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8
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Suda K, Sakai K, Ohira T, Chikugo T, Satou T, Matsubayashi J, Nagao T, Ikeda N, Tsutani Y, Mitsudomi T, Nishio K. Performance of Ultra-Rapid Idylla™ EGFR Mutation Test in Non-Small-Cell Lung Cancer and Its Potential at Clinical Molecular Screening. Cancers (Basel) 2023; 15:cancers15092648. [PMID: 37174112 PMCID: PMC10177517 DOI: 10.3390/cancers15092648] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND The Idylla™ EGFR Mutation Test is an ultra-rapid single-gene test that detects epidermal growth factor receptor (EGFR) mutations using formalin-fixed paraffin-embedded specimens. Here, we compared the performance of the Idylla EGFR Mutation Test with the Cobas® EGFR Mutation Test v2. METHODS Surgically resected NSCLC specimens obtained at two Japanese institutions (N = 170) were examined. The Idylla EGFR Mutation Test and the Cobas EGFR Mutation Test v2 were performed independently and the results were compared. For discordant cases, the Ion AmpliSeq Colon and Lung Cancer Research Panel V2 was performed. RESULTS After the exclusion of five inadequate/invalid samples, 165 cases were evaluated. EGFR mutation analysis revealed 52 were positive and 107 were negative for EGFR mutation in both assays (overall concordance rate: 96.4%). Analyses of the six discordant cases revealed that the Idylla EGFR Mutation Test was correct in four and the Cobas EGFR Mutation Test v2 was correct in two. In a trial calculation, the combination of the Idylla EGFR Mutation Test followed by a multi-gene panel test will reduce molecular screening expenses if applied to a cohort with EGFR mutation frequency >17.9%. CONCLUSIONS We demonstrated the accuracy and potential clinical utility of the Idylla EGFR Mutation Test as a molecular screening platform in terms of turnaround time and molecular testing cost if applied to a cohort with a high EGFR mutation incidence (>17.9%).
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Affiliation(s)
- Kenichi Suda
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Tatsuo Ohira
- Department of Surgery, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Kindai University Hospital, Osakasayama 589-8511, Japan
| | - Takao Satou
- Department of Diagnostic Pathology, Kindai University Hospital, Osakasayama 589-8511, Japan
| | - Jun Matsubayashi
- Department of Anatomic Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Toshitaka Nagao
- Department of Anatomic Pathology, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Norihiko Ikeda
- Department of Surgery, Tokyo Medical University, Shinjuku-ku, Tokyo 160-0023, Japan
| | - Yasuhiro Tsutani
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Tetsuya Mitsudomi
- Division of Thoracic Surgery, Department of Surgery, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osakasayama 589-8511, Japan
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Naso J, Lo YC, Sholl LM. Updates in pathology and molecular diagnostics to inform the evolving landscape of thoracic surgery and oncology. J Surg Oncol 2023; 127:244-257. [PMID: 36630101 DOI: 10.1002/jso.27184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/08/2022] [Accepted: 12/12/2022] [Indexed: 01/12/2023]
Abstract
The pathologic assessment of lung cancers provides essential guidance to the surgeon and oncologist who are considering the best treatment strategies for patients with both early and advanced-stage disease. The management of patients with lung cancer is predicated first and foremost on access to an accurate diagnosis, even when the sample size is limited, as is often the case with use of modern, minimally invasive sampling techniques. Once the diagnosis and disease stage are established, predictive biomarker testing may be essential, particularly for those patients with nonsmall cell lung carcinoma (NSCLC) being considered for immunotherapy or genomic biomarker-driven targeted therapy. This review will discuss the best practices for the diagnosis of NSCLC using morphology and immunohistochemistry, thus providing the surgeon with needed information to understand and critically evaluate pathology reports. Controversial and evolving topics including tumor spread through airspaces, evaluation of multiple tumors, and staging based on invasive tumor size will be addressed. Clinical genomic profiling in NSCLC is driven by published guidelines and reflects evidence based on clinical trials and regulatory approvals. In this fast-moving space, surgeons should be aware of the critical immunohistochemical and genomic biomarkers that drive systemic therapy decisions and anticipate when such testing will be required, both to ensure adequate sampling and to advise the pathologist when tumor material will be required for biomarker analysis. The basic approaches to and sample requirements for molecular biomarker testing will be addressed. As biomarker testing moves exclusively from advanced-stage patients into earlier stage disease, the surgeon should be aware of the relevant markers and work with the pathologist and oncologist to ensure that this information is available to facilitate timely access to therapies not just in the advanced setting, but in consideration of neoadjuvant and adjuvant care.
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Affiliation(s)
- Julia Naso
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ying-Chun Lo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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10
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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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11
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LILLEY CULLENM, DELILLE MINERVE, MIRZA KAMRANM, PARILLA MEGAN. Toward a More Just System of Care in Molecular Pathology. Milbank Q 2022; 100:1192-1242. [PMID: 36454130 PMCID: PMC9836258 DOI: 10.1111/1468-0009.12587] [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: 02/02/2022] [Revised: 05/09/2022] [Accepted: 06/23/2022] [Indexed: 12/02/2022] Open
Abstract
Policy Points American health care policy must be critically assessed to establish the role it plays in sustaining and alleviating the health disparities that currently exist in molecular genetic testing. It is critical to understand the economic and sociocultural influences that drive patients to undergo or forgo molecular testing, especially in marginalized patient populations. A multipronged solution with actions necessary from multiple stakeholders is required to reduce the cost of health care, rebalance regional disparities, encourage physician engagement, reduce data bias, and earn patients' trust. CONTEXT The health status of a population is greatly influenced by both biological processes and external factors. For years, minority and low socioeconomic patient populations have faced worse outcomes and poorer health in the United States. Experts have worked extensively to understand the issues and find solutions to alleviate this disproportionate burden of disease. As a result, there have been some improvements and successes, but wide gaps still exist. Diagnostic molecular genetic testing and so-called personalized medicine are just now being integrated into the current American health care system. The way in which these tests are integrated can either exacerbate or reduce health disparities. METHODS We provide case scenarios-loosely based on real-life patients-so that nonexperts can see the impacts of complex policy decisions and unintentional biases in technology without needing to understand all the intricacies. We use data to explain these findings from an extensive literature search examining both peer-reviewed and gray literature. FINDINGS Access to diagnostic molecular genetic testing is not equitable or sufficient, owing to at least five major factors: (1) cost to the patient, (2) location, (3) lack of provider buy-in, (4) data-set bias, and (5) lack of public trust. CONCLUSIONS Molecular genetic pathology can be made more equitable with the concerted efforts of multiple stakeholders. Confronting the five major factors identified here may help us usher in a new era of precision medicine without its discriminatory counterpart.
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Affiliation(s)
| | | | - KAMRAN M. MIRZA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
| | - MEGAN PARILLA
- Loyola University Chicago, Strich School of Medicine
- Loyola Medical Center
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Pujol N, Heeke S, Bontoux C, Boutros J, Ilié M, Hofman V, Marquette CH, Hofman P, Benzaquen J. Molecular Profiling in Non-Squamous Non-Small Cell Lung Carcinoma: Towards a Switch to Next-Generation Sequencing Reflex Testing. J Pers Med 2022; 12:1684. [PMID: 36294823 PMCID: PMC9605324 DOI: 10.3390/jpm12101684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/05/2022] Open
Abstract
Molecular diagnosis of lung cancer is a constantly evolving field thanks to major advances in precision oncology. The wide range of actionable molecular alterations in non-squamous non-small cell lung carcinoma (NS-NSCLC) and the multiplicity of mechanisms of resistance to treatment resulted in the need for repeated testing to establish an accurate molecular diagnosis, as well as to track disease evolution over time. While assessing the increasing complexity of the molecular composition of tumors at baseline, as well as over time, has become increasingly challenging, the emergence and implementation of next-generation sequencing (NGS) testing has extensively facilitated molecular profiling in NS-NSCLC. In this review, we discuss recent developments in the molecular profiling of NS-NSCLC and how NGS addresses current needs, as well as how it can be implemented to address future challenges in the management of NS-NSCLC.
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Affiliation(s)
- Nina Pujol
- Centre Antoine-Lacassagne, Department of Radiation Oncology, Côte d’Azur University, 06000 Nice, France
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Jacques Boutros
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Charles-Hugo Marquette
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Jonathan Benzaquen
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
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13
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Hanbazazh M, Morlote D, Mackinnon AC, Harada S. Utility of Single-Gene Testing in Cancer Specimens. Clin Lab Med 2022; 42:385-394. [DOI: 10.1016/j.cll.2022.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Performance of Idylla KRAS assay on extracted DNA and de-stained cytology smears: Can we rescue small sample? Ann Diagn Pathol 2022; 60:152023. [DOI: 10.1016/j.anndiagpath.2022.152023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 08/01/2022] [Indexed: 11/22/2022]
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15
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Elsakka A, Petre EN, Ridouani F, Ghosn M, Bott MJ, Husta BC, Arcila ME, Alexander E, Solomon SB, Ziv E. Percutaneous Image-Guided Biopsy for a Comprehensive Hybridization Capture-Based Next-Generation Sequencing in Primary Lung Cancer: Safety, Efficacy, and Predictors of Outcome. JTO Clin Res Rep 2022; 3:100342. [PMID: 35711720 PMCID: PMC9194869 DOI: 10.1016/j.jtocrr.2022.100342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction To evaluate factors associated with successful comprehensive genomic sequencing of image-guided percutaneous needle biopsies in patients with lung cancer using a broad hybrid capture-based next-generation sequencing assay (CHCA). Methods We conducted a single-institution retrospective review of image-guided percutaneous transthoracic needle biopsies from January 2018 to December 2019. Samples with confirmed diagnosis of primary lung cancer and for which CHCA had been attempted were identified. Pathologic, clinical data and results of the CHCA were reviewed. Covariates associated with CHCA success were tested for using Fisher's exact test or Wilcoxon ranked sum test. Logistic regression was used to identify factors independently associated with likelihood of CHCA success. Results CHCA was requested for 479 samples and was successful for 433 (91%), with a median coverage depth of 659X. Factors independently associated with lower likelihood of CHCA success included small tumor size (OR = 0.26 [95% confidence interval (CI): 0.11-0.62, p = 0.002]), intraoperative inadequacy on cytologic assessment (OR = 0.18 [95% CI: 0.06-0.63, p = 0.005]), small caliber needles (≥20-gauge) (OR = 0.22 [95% CI: 0.10-0.45, p < 0.001]), and presence of lung parenchymal abnormalities (OR = 0.12 [95% CI: 0.05-0.25, p < 0.001]). Pneumothorax requiring chest tube insertion occurred in 6% of the procedures. No grade IV complications or procedure-related deaths were reported. Conclusions Percutaneous image-guided transthoracic needle biopsy is safe and has 91% success rate for CHCA in primary lung cancer. Intraoperative inadequacy, small caliber needle, presence of parenchymal abnormalities, and small tumor size (≤1 cm) are independently associated with likelihood of failure.
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Affiliation(s)
- Ahmed Elsakka
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
- Body Imaging Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena N. Petre
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fourat Ridouani
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mario Ghosn
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew J. Bott
- Thoracic Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bryan C. Husta
- Pulmonary Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E. Arcila
- Molecular Diagnostics Service, Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Erica Alexander
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stephen B. Solomon
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Etay Ziv
- Interventional Radiology Service, Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
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16
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Chu YH, Barbee J, Yang SR, Chang JC, Liang P, Mullaney K, Chan R, Salazar P, Benayed R, Offin M, Drilon A, Ladanyi M, Nafa K, Arcila ME. Clinical Utility and Performance of an Ultrarapid Multiplex RNA-Based Assay for Detection of ALK, ROS1, RET, and NTRK1/2/3 Rearrangements and MET Exon 14 Skipping Alterations. J Mol Diagn 2022; 24:642-654. [PMID: 35430374 DOI: 10.1016/j.jmoldx.2022.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/14/2022] [Accepted: 03/03/2022] [Indexed: 11/19/2022] Open
Abstract
Several kinase fusions are established targetable drivers in lung cancers. However, rapid and comprehensive detection remains challenging because of diverse partner genes and breakpoints. We assess the clinical utility and performance of a rapid microfluidic multiplex real-time PCR-based assay for simultaneous query of fusions involving ALK, ROS1, RET, and NTRK1/2/3, as well as MET exon 14 skipping, using a 3-hour automated process. Dual analytic strategies were utilized: fusion-specific amplification and 3' to 5' expression imbalance. One-hundred and forty-three independent, formalin-fixed, paraffin-embedded tumor samples (112 surgical specimens, 31 cytologic cell blocks) were analyzed: 133 with known kinase gene alterations and 10 negative samples based on clinically validated next-generation sequencing. Testing was successful in 142 (99%) cases. The assay demonstrated a sensitivity of 97% (28/29), 100% (31/31), 92% (22/24), 81% (22/27), and 100% (20/20) for ALK, RET, ROS1, and NTRK1/2/3 rearrangements and MET exon 14 skipping alterations, respectively, with 100% specificity for all. Concordant results were achieved in specimens aged up to 5 years, with >10% tumor, and inputs of at least 9 mm2 (surgical specimens) and 9000 cells (cytologic cell blocks). The assay enables rapid screening for clinically actionable kinase alterations with quicker turnaround and lower tissue requirements compared with immunohistochemistry and molecular methods, while also circumventing the infrastructure dependencies associated with next-generation sequencing and fluorescence in situ hybridization.
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Affiliation(s)
- Ying-Hsia Chu
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jada Barbee
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason C Chang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Priscilla Liang
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kerry Mullaney
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roger Chan
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Paulo Salazar
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryma Benayed
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael Offin
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander Drilon
- Thoracic Oncology Service, Division of Solid Tumor Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marc Ladanyi
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Khedoudja Nafa
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria E Arcila
- Department of Pathology and Laboratory Medicine, Molecular Diagnostic Service, Memorial Sloan Kettering Cancer Center, New York, New York.
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Nkosi D, Casler VL, Syposs CR, Oltvai ZN. Utility of Select Gene Mutation Detection in Tumors by the Idylla Rapid Multiplex PCR Platform in Comparison to Next-Generation Sequencing. Genes (Basel) 2022; 13:genes13050799. [PMID: 35627184 PMCID: PMC9141835 DOI: 10.3390/genes13050799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 02/01/2023] Open
Abstract
Testing of tumors by next generation sequencing (NGS) is impacted by relatively long turnaround times and a need for highly trained personnel. Recently, Idylla oncology assays were introduced to test for BRAF, EGFR, KRAS, and NRAS common hotspot mutations that do not require specialized trained personnel. Moreover, the interpretation of results is fully automated, with rapid turnaround time. Though Idylla testing and NGS have been shown to have high concordance in identifying EGFR, BRAF, KRAS, and NRAS hotspot mutations, there is limited experience on optimal ways the Idylla system can be used in routine practice. We retrospectively evaluated all cases with EGFR, BRAF, KRAS, or NRAS mutations identified in clinical specimens sequenced on two different NGS panels at the University of Rochester Medical Center (URMC) molecular diagnostics laboratory between July 2020 and July 2021 and assessed if these mutations would be detected by the Idylla cartridges if used. We found that the Idylla system could accurately identify Tier 1 or 2 actionable genomic alterations in select associated disease pathologies if used. Yet, in a minority of cases, we would have been unable to detect NGS-identified pathogenic mutations due to their absence on the Idylla panels. We derived algorithmic practice guidelines for the use of the Idylla cartridges. Overall, Idylla molecular testing could be implemented either as a first-line standalone diagnostic tool in select indications or for orthogonal confirmation of uncertain results.
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18
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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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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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Evaluation of the Idylla ctEGFR mutation assay to detect EGFR mutations in plasma from patients with non-small cell lung cancers. Sci Rep 2021; 11:10470. [PMID: 34006948 PMCID: PMC8131701 DOI: 10.1038/s41598-021-90091-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/26/2021] [Indexed: 01/13/2023] Open
Abstract
The assessment of EGFR mutations is recommended for the management of patients with non-small cell lung cancer (NSCLC). Presence of EGFR mutation is associated with response or resistance to EGFR tyrosine kinase inhibitors (EGFR-TKI). Liquid biopsy is nowadays widely used for the detection of resistance to EGFR-TKI. We evaluated here the performance of the Idylla ctEGFR mutation assay for the detection of EGFR mutations in circulating tumour DNA (ctDNA) in plasma from patients with NSCLC. Previously characterized plasma samples from 38 patients with NSCLC were analysed using 2 different analytical conditions (C1 and C2). The limit of detection (LOD) was evaluated using 2 mL of healthy donor plasma spiked with commercial DNA controls. Overall agreement, sensitivity and specificity were 92.1%, 86.7% and 95.7% for C1 condition respectively and 94.7%, 86.7% and 100% for C2 condition respectively. The T790M secondary resistance mutation was detected in two samples out of 3. The Idylla system was able to detect the exon 19 deletion from 6 copies/mL and up to 91 copies/mL for the G719S mutation. These results support that the Idylla ctEGFR mutation assay is a rapid option for the detection of EGFR hotspots mutations in plasma samples, however a particular attention is needed for its interpretation.
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