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La Salvia A, Meyer ML, Hirsch FR, Kerr KM, Landi L, Tsao MS, Cappuzzo F. Rediscovering immunohistochemistry in lung cancer. Crit Rev Oncol Hematol 2024; 200:104401. [PMID: 38815876 DOI: 10.1016/j.critrevonc.2024.104401] [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: 01/02/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024] Open
Abstract
Several observations indicate that protein expression analysis by immunohistochemistry (IHC) remains relevant in individuals with non-small-cell lung cancer (NSCLC) when considering targeted therapy, as an early step in diagnosis and for therapy selection. Since the advent of next-generation sequencing (NGS), the role of IHC in testing for NSCLC biomarkers has been forgotten or ignored. We discuss how protein-level investigations maintain a critical role in defining sensitivity to lung cancer therapies in oncogene- and non-oncogene-addicted cases and in patients eligible for immunotherapy, suggesting that IHC testing should be reconsidered in clinical practice. We also argue how a panel of IHC tests should be considered complementary to NGS and other genomic assays. This is relevant to current clinical diagnostic practice but with potential future roles to optimize the selection of patients for innovative therapies. At the same time, strict validation of antibodies, assays, scoring systems, and intra- and interobserver reproducibility is needed.
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Affiliation(s)
- Anna La Salvia
- National Center for Drug Research and Evaluation, National Institute of Health (ISS), Rome 00161, Italy
| | - May-Lucie Meyer
- Center for Thoracic Oncology/Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fred R Hirsch
- Center for Thoracic Oncology/Tisch Cancer Institute and Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Keith M Kerr
- Aberdeen University School of Medicine & Aberdeen Royal Infirmary, Aberdeen, UK
| | - Lorenza Landi
- Medical Oncology, Istituto Nazionale Tumori IRCCS "Regina Elena", Rome, Italy
| | - Ming-Sound Tsao
- University Health Network, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Federico Cappuzzo
- Medical Oncology, Istituto Nazionale Tumori IRCCS "Regina Elena", Rome, Italy.
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Clavé S, Jackson JB, Salido M, Kames J, Gerding KMR, Verner EL, Kong EF, Weingartner E, Gibert J, Hardy-Werbin M, Rocha P, Riera X, Torres E, Hernandez J, Cerqueira G, Nichol D, Simmons J, Taus Á, Pijuan L, Bellosillo B, Arriola E. Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer. Front Oncol 2023; 13:1225646. [PMID: 37927472 PMCID: PMC10623306 DOI: 10.3389/fonc.2023.1225646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/28/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. Methods There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. Results The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Discussion Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.
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Affiliation(s)
- Sergi Clavé
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | | | - Marta Salido
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Jacob Kames
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Ellen L. Verner
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Eric F. Kong
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | | | - Joan Gibert
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Max Hardy-Werbin
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Pedro Rocha
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Xènia Riera
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Erica Torres
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - James Hernandez
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Gustavo Cerqueira
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Donna Nichol
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - John Simmons
- Personal Genome Diagnostics (PGDx/Labcorp), Baltimore, MD, United States
| | - Álvaro Taus
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
| | - Lara Pijuan
- Pathology Department, Hospital del Mar, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Barcelona, Spain
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Edurne Arriola
- Cancer Research Program, Hospital del Mar Medical Research Institute, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
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Athanasopoulou K, Daneva GN, Boti MA, Dimitroulis G, Adamopoulos PG, Scorilas A. The Transition from Cancer "omics" to "epi-omics" through Next- and Third-Generation Sequencing. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122010. [PMID: 36556377 PMCID: PMC9785810 DOI: 10.3390/life12122010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
Deciphering cancer etiopathogenesis has proven to be an especially challenging task since the mechanisms that drive tumor development and progression are far from simple. An astonishing amount of research has revealed a wide spectrum of defects, including genomic abnormalities, epigenomic alterations, disturbance of gene transcription, as well as post-translational protein modifications, which cooperatively promote carcinogenesis. These findings suggest that the adoption of a multidimensional approach can provide a much more precise and comprehensive picture of the tumor landscape, hence serving as a powerful tool in cancer research and precision oncology. The introduction of next- and third-generation sequencing technologies paved the way for the decoding of genetic information and the elucidation of cancer-related cellular compounds and mechanisms. In the present review, we discuss the current and emerging applications of both generations of sequencing technologies, also referred to as massive parallel sequencing (MPS), in the fields of cancer genomics, transcriptomics and proteomics, as well as in the progressing realms of epi-omics. Finally, we provide a brief insight into the expanding scope of sequencing applications in personalized cancer medicine and pharmacogenomics.
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Steeghs EM, Groen HJ, Schuuring E, Aarts MJ, Damhuis RA, Voorham QJ, consortium PATH, Ligtenberg MJ, Grünberg K. Mutation-tailored treatment selection in non-small cell lung cancer patients in daily clinical practice. Lung Cancer 2022; 167:87-97. [DOI: 10.1016/j.lungcan.2022.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 03/28/2022] [Accepted: 04/01/2022] [Indexed: 12/13/2022]
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Canterbury CR, Fernandes H, Crapanzano JP, Murty VV, Mansukhani MM, Shu CA, Szabolcs M, Saqi A. ALK Gene Rearrangements in Lung Adenocarcinomas: Concordance of Immunohistochemistry, Fluorescence In Situ Hybridization, RNA In Situ Hybridization, and RNA Next-Generation Sequencing Testing. JTO Clin Res Rep 2021; 2:100223. [PMID: 34746883 PMCID: PMC8552107 DOI: 10.1016/j.jtocrr.2021.100223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 08/05/2021] [Accepted: 08/29/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction The 2018 updated molecular testing guidelines for patients with advanced lung cancer incorporated ALK immunohistochemistry (IHC) analysis as an equivalent to fluorescence in situ hybridization (FISH) method recommended in 2013. Nevertheless, no specific recommendation for alternative methods was proposed owing to insufficient data. The aim of this study was to compare the results of ALK IHC, FISH, RNA next-generation sequencing (NGS), and RNA in situ hybridization (ISH) with available clinical data. Methods A search for lung carcinomas with ALK testing by greater than or equal to one modality (i.e., ALK IHC, FISH, NGS) was performed; a subset underwent RNA ISH. When available, clinical data were recorded. Results The results were concordant among all performed testing modalities in 86 of 90 cases (95.6%). Of the four discordant cases, two were ALK positive by FISH but negative by IHC, RNA NGS, and RNA ISH. The remaining two cases failed RNA NGS testing, one was IHC negative, FISH positive, RNA ISH negative and the second was IHC positive, FISH positive, RNA ISH equivocal. RNA NGS identified one rare and one novel ALK fusion. Sufficient therapy data were available in 10 cases treated with tyrosine kinase inhibitors; three had disease progression, including one with discordant results (FISH positive, RNA NGS negative, IHC negative, RNA ISH negative) and two with concordant ALK positivity among all modalities. Conclusions Our results reveal high concordance among IHC, RNA NGS, and RNA ISH. In cases of discordance with available RNA NGS, FISH result was positive whereas IHC and ISH results were negative. On the basis of our data, multimodality testing is recommended to identify discrepant results and patients (un)likely to respond to tyrosine kinase inhibitors.
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Affiliation(s)
- Carleigh R Canterbury
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Helen Fernandes
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - John P Crapanzano
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Vundavalli V Murty
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Mahesh M Mansukhani
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Catherine A Shu
- Division of Hematology/Oncology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Matthias Szabolcs
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Anjali Saqi
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
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Dziadziuszko R, Mok T, Peters S, Han JY, Alatorre-Alexander J, Leighl N, Sriuranpong V, Pérol M, de Castro Junior G, Nadal E, de Marinis F, Frontera OA, Tan DSW, Lee DH, Kim HR, Yan M, Riehl T, Schleifman E, Paul SM, Mocci S, Patel R, Assaf ZJ, Shames DS, Mathisen MS, Gadgeel SM. Blood First Assay Screening Trial (BFAST) in Treatment-Naive Advanced or Metastatic NSCLC: Initial Results of the Phase 2 ALK-Positive Cohort. J Thorac Oncol 2021; 16:2040-2050. [PMID: 34311110 DOI: 10.1016/j.jtho.2021.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Accepted: 07/04/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION The Blood First Assay Screening Trial is an ongoing open-label, multicohort study, prospectively evaluating the relationship between blood-based next-generation sequencing (NGS) detection of actionable genetic alterations and activity of targeted therapies or immunotherapy in treatment-naive advanced or metastatic NSCLC. We present data from the ALK-positive cohort. METHODS Patients aged more than or equal to 18 years with stage IIIB or IV NSCLC and ALK rearrangements detected by blood-based NGS using hybrid capture technology (FoundationACT) received alectinib 600 mg twice daily. Asymptomatic or treated central nervous system (CNS) metastases were permitted. Primary end point was investigator-assessed objective response rate (ORR; Response Evaluation Criteria in Solid Tumors version 1.1). Secondary end points were independent review facility-assessed ORR, duration of response, progression-free survival (PFS), overall survival, and safety. Exploratory end points were investigator-assessed ORR in patients with baseline CNS metastases and relationship between circulating biomarkers and response. RESULTS In total, 2219 patients were screened and blood-based NGS yielded results in 98.6% of the cases. Of these, 119 patients (5.4%) had ALK-positive disease; 87 were enrolled and received alectinib. Median follow-up was 12.6 months (range: 2.6-18.7). Confirmed ORR was 87.4% (95% confidence interval [CI]: 78.5-93.5) by investigator and 92.0% (95% CI: 84.1-96.7) by independent review facility. Investigator-confirmed 12-month duration of response was 75.9% (95% CI: 63.6-88.2). In 35 patients (40%) with baseline CNS disease, investigator-assessed ORR was 91.4% (95% CI: 76.9-98.2). Median PFS was not reached; 12-month investigator-assessed PFS was 78.4% (95% CI: 69.1-87.7). Safety data were consistent with the known tolerability profile of alectinib. CONCLUSIONS These results reveal the clinical application of blood-based NGS as a method to inform clinical decision-making in ALK-positive NSCLC.
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Affiliation(s)
- Rafal Dziadziuszko
- Department of Oncology and Radiotherapy, Medical University of Gdansk, Gdansk, Poland
| | - Tony Mok
- State Key Laboratory of Translational Oncology, Chinese University of Hong Kong, Shatin, Hong Kong
| | - Solange Peters
- Oncology Department, University Hospital (CHUV), University of Lausanne, Switzerland
| | - Ji-Youn Han
- Center for Lung Cancer, National Cancer Center, Goyang, South Korea
| | | | - Natasha Leighl
- Division of Medical Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Virote Sriuranpong
- Faculty of Medicine, Chulalongkorn University and the King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Maurice Pérol
- Department of Medical Oncology, Léon Bérard Cancer Center, Lyon, France
| | | | - Ernest Nadal
- Catalan Institute of Oncology, L'Hospitalet, Barcelona, Spain
| | - Filippo de Marinis
- European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan, Italy
| | | | - Daniel S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Dae Ho Lee
- Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Centre, Yonsei University College of Medicine, Seoul, South Korea
| | - Mark Yan
- F. Hoffmann-La Roche, Mississauga, Canada
| | - Todd Riehl
- Genentech, Inc., South San Francisco, California
| | | | - Sarah M Paul
- Genentech, Inc., South San Francisco, California
| | | | - Rajesh Patel
- Genentech, Inc., South San Francisco, California
| | | | | | | | - Shirish M Gadgeel
- Department of Internal Medicine, Henry Ford Cancer Institute, Henry Ford Health System, Detroit, Michigan.
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Concordance Analysis of ALK Gene Fusion Detection Methods in Patients with Non-Small-Cell Lung Cancer from Chile, Brazil, and Peru. J Mol Diagn 2021; 23:1127-1137. [PMID: 34186175 DOI: 10.1016/j.jmoldx.2021.05.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 05/08/2021] [Accepted: 05/27/2021] [Indexed: 11/23/2022] Open
Abstract
About 4% to 7% of the non-small-cell lung cancer patients have anaplastic lymphoma kinase (ALK) rearrangements, and specific targeted therapies improve patients' outcomes significantly. ALK gene fusions are detected by immunohistochemistry or fluorescent in situ hybridization as gold standards in South America. Next-generation sequencing-based assays are a reliable alternative, able to perform simultaneous detection of multiple events from a single sample. We analyzed 4240 non-small-cell lung cancer samples collected in 37 hospitals from Chile, Brazil, and Peru, where ALK rearrangements were determined as part of their standard of care (SofC) using either immunohistochemistry or fluorescent in situ hybridization. A subset of 1450 samples was sequenced with the Oncomine Focus Assay (OFA), and the concordance with the SofC tests was measured. An orthogonal analysis was performed using a real-time quantitative PCR echinoderm microtubule-associated protein-like 4-ALK fusion detection kit. ALK fusion prevalence is similar for Chile (3.67%; N = 2142), Brazil (4.05%; N = 1013), and Peru (4.59%; N = 675). Although a comparison between OFA and SofC assays showed similar sensitivity, OFA had significantly higher specificity and higher positive predictive value, which opens new opportunities for a more specific determination of ALK gene rearrangements.
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Status quo of ALK testing in lung cancer: results of an EQA scheme based on in-situ hybridization, immunohistochemistry, and RNA/DNA sequencing. Virchows Arch 2021; 479:247-255. [PMID: 34173019 PMCID: PMC8364534 DOI: 10.1007/s00428-021-03106-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 04/07/2021] [Accepted: 04/21/2021] [Indexed: 12/16/2022]
Abstract
With this external quality assessment (EQA) scheme, we aim to investigate the diagnostic performance of the currently available methods for the detection of ALK alterations in non-small cell lung cancer on a national scale, namely, in situ hybridization (ISH), immunohistochemistry (IHC), and RNA/DNA sequencing (NGS). The EQA scheme cohort consisted of ten specimens, including four ALK positive and six ALK negative samples, which were thoroughly pretested using IHC, ISH, and RNA/DNA NGS. Unstained tumor sections were provided to the 57 participants, and the results were retrieved via an online questionnaire. ISH was used by 29, IHC by 38, and RNA/DNA sequencing by 19 participants. Twenty-eight institutions (97%) passed the ring trial using ISH, 33 (87%) by using IHC, and 18 (95%) by using NGS. The highest sensitivity and interrater agreement (Fleiss ‘ kappa) was observed for RNA/DNA sequencing (99%, 0.975), followed by ISH (94%, 0.898) and IHC (92%, 0.888). However, the proportion of samples that were not evaluable due to bad tissue quality was also higher for RNA/DNA sequencing (4%) compared with ISH (0.7%) and IHC (0.5%). While all three methods produced reliable results between the different institutions, the highest sensitivity and concordance were observed for RNA/DNA sequencing. These findings encourage the broad implementation of this method in routine diagnostic, although the application might be limited by technical capacity, economical restrictions, and tissue quality of formalin-fixed samples.
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Orlov SV, Iyevleva AG, Filippova EA, Lozhkina AM, Odintsova SV, Sokolova TN, Mitiushkina NV, Tiurin VI, Preobrazhenskaya EV, Romanko AA, Martianov AS, Ivantsov AO, Aleksakhina SN, Togo AV, Imyanitov EN. Efficacy of lorlatinib in lung carcinomas carrying distinct ALK translocation variants: The results of a single-center study. Transl Oncol 2021; 14:101121. [PMID: 34030112 PMCID: PMC8144735 DOI: 10.1016/j.tranon.2021.101121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022] Open
Abstract
In patients with ALK-rearranged NSCLC who received lorlatinib within the compassionate use program, the objective tumor response (OR) and disease control (DC) were observed in 43% and 94% cases, respectively. Lorlatinib showed particularly high efficacy against brain metastases, with OR and DC for intracranial disease reaching 81% and 100%, respectively. Patients with V.1 and V.3 ALK translocations had similar response to the therapy. Complete lack of adverse events tended to correlate with poor outcome of lorlatinib treatment.
Background Lorlatinib is a novel potent ALK inhibitor, with only a few studies reporting the results of its clinical use. Methods This study describes the outcomes of lorlatinib treatment for 35 non-small cell lung cancer patients with ALK rearrangements, who had 2 (n = 5), 1 (n = 26) or none (n = 4) prior tyrosine kinase inhibitors and received lorlatinib mainly within the compassionate use program. Results Objective tumor response (OR) and disease control (DC) were registered in 15/35 (43%) and 33/35 (94%) patients, respectively; brain metastases were particularly responsive to the treatment (OR: 22/27 (81%); DC: 27/27 (100%)). Median progression free survival (PFS) was estimated to be 21.8 months, and median overall survival (OS) approached to 70.1 months. Only 4 out of 35 patients experienced no adverse effects; two of them were the only subjects who had no clinical benefit from lorlatinib. PFS and OS in the no-adverse-events lorlatinib users were strikingly lower as compared to the remaining patients (1.1 months vs. 23.7 months and 10.5 months vs. not reached, respectively; p < 0.0001 for both comparisons). ALK translocation variants were known for 28 patients; there was no statistical difference between patients with V.1 and V.3 rearrangements with regard to the OS or PFS. Conclusion Use of lorlatinib results in excellent disease outcomes, however caution must be taken for patients experiencing no adverse effects from this drug.
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Affiliation(s)
- Sergey V Orlov
- I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg 197022, Russia; Institute of Medical Primatology, Sochi 354376, Russia
| | - Aglaya G Iyevleva
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia.
| | - Elena A Filippova
- I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg 197022, Russia
| | - Alexandra M Lozhkina
- I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg 197022, Russia
| | - Svetlana V Odintsova
- I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg 197022, Russia
| | | | | | - Vladislav I Tiurin
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Elena V Preobrazhenskaya
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr A Romanko
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr S Martianov
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr O Ivantsov
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Svetlana N Aleksakhina
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Alexandr V Togo
- N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Imyanitov
- I.P. Pavlov St.-Petersburg State Medical University, St.-Petersburg 197022, Russia; Institute of Medical Primatology, Sochi 354376, Russia; N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; St.-Petersburg State Pediatric Medical University, St.-Petersburg 194100, Russia; I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia
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Fusion transcript discovery using RNA sequencing in formalin-fixed paraffin-embedded specimen. Crit Rev Oncol Hematol 2021; 160:103303. [DOI: 10.1016/j.critrevonc.2021.103303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
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Jöhrens K, von Wasielewski R, Kreipe HH, Forberger A, Jurmeister P, Dietel M, Stenzinger A, Fischer J. [Quality assurance in diagnostic in situ hybridization-experience of QuIP]. DER PATHOLOGE 2021; 41:614-620. [PMID: 32945916 DOI: 10.1007/s00292-020-00832-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The Quality Assurance Initiative Pathology (QuIP) gives pathologists the opportunity to check the methodological processes of immunohistological and molecular diagnostics in a result-oriented manner and obtain a certificate reflecting the quality. For in situ hybridization (ISH), 5 round robin tests were organized in 2019, two recurrent (HER2-ISH gastric carcinomas and HER2-ISH breast carcinomas) and three prototypical (ROS1-NSCLC, ALK1-NSCLC, NTRK). The different round robin tests, which were provided by QuIP, are based on the development in diagnostics and the importance of the therapeutic relevance of the molecules which are tested. The results of the round robin tests in 2019 showed a sensitivity of at least 94.4%, a specificity of at least 96.6%, and a success rate of 85-99%. This reflected the high standard of quality of the round robin test and the participating institutes.
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Affiliation(s)
- Korinna Jöhrens
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Deutschland. .,Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland.
| | | | - Hans-H Kreipe
- Institut für Pathologie, Medizinische Hochschule Hannover, Hannover, Deutschland
| | - Almuth Forberger
- Institut für Pathologie, Universitätsklinikum Carl Gustav Carus, TU Dresden, Dresden, Deutschland
| | - Philipp Jurmeister
- Institut für Pathologie, Universitätsklinikum Charité Berlin, Berlin, Deutschland
| | - Manfred Dietel
- Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland.,Institut für Pathologie, Universitätsklinikum Charité Berlin, Berlin, Deutschland
| | - Albrecht Stenzinger
- Institut für Allgemeine Pathologie und Pathologische Anatomie, Universitätsklinikum Heidelberg, Heidelberg, Deutschland
| | - Josephine Fischer
- Qualitätssicherungs-Initiative Pathologie QuIP GmbH, Berlin, Deutschland
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Bruno R, Fontanini G. Next Generation Sequencing for Gene Fusion Analysis in Lung Cancer: A Literature Review. Diagnostics (Basel) 2020; 10:E521. [PMID: 32726941 PMCID: PMC7460167 DOI: 10.3390/diagnostics10080521] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
Gene fusions have a pivotal role in non-small cell lung cancer (NSCLC) precision medicine. Several techniques can be used, from fluorescence in situ hybridization and immunohistochemistry to next generation sequencing (NGS). Although several NGS panels are available, gene fusion testing presents more technical challenges than other variants. This is a PubMed-based narrative review aiming to summarize NGS approaches for gene fusion analysis and their performance on NSCLC clinical samples. The analysis can be performed at DNA or RNA levels, using different target enrichment (hybrid-capture or amplicon-based) and sequencing chemistries, with both custom and commercially available panels. DNA sequencing evaluates different alteration types simultaneously, but large introns and repetitive sequences can impact on the performance and it does not discriminate between expressed and unexpressed gene fusions. RNA-based targeted approach analyses and quantifies directly fusion transcripts and is more accurate than DNA panels on tumor tissue, but it can be limited by RNA quality and quantity. On liquid biopsy, satisfying data have been published on circulating tumor DNA hybrid-capture panels. There is not a perfect method for gene fusion analysis, but NGS approaches, though still needing a complete standardization and optimization, present several advantages for the clinical practice.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy
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Liu Y, Wu S, Shi X, Lu L, Zhu L, Guo Y, Zhang L, Zeng X. Clinical evaluation of the effectiveness of fusion-induced asymmetric transcription assay-based reverse transcription droplet digital PCR for ALK detection in formalin-fixed paraffin-embedded samples from lung cancer. Thorac Cancer 2020; 11:2252-2261. [PMID: 32543087 PMCID: PMC7396369 DOI: 10.1111/1759-7714.13535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Accurate detection of anaplastic lymphoma kinase (ALK) rearrangement is the prerequisite for anti-ALK therapy for the patient with non-small cell lung cancer (NSCLC). Fusion-induced asymmetric transcription assay (FIATA)-based reverse transcription droplet digital PCR (RT-ddPCR) was developed and performed for ALK status survey in NSCLC samples. METHODS A total of 269 cases of formalin-fixed paraffin-embedded (FFPE) specimens from NSCLC, in which ALK status was confirmed by both fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC), were analyzed by FIATA-based RT-ddPCR. RESULTS In the ALK-positive group, the 3' ALK transcript copies range was 336.6-107 955.4, and the R3 [(the ratio of the 3' ALK transcript copy numbers to the internal reference gene transcript copy numbers) × 100] was 17.23-672.77. In the ALK-negative group, the 3' ALK transcript copies range was 3.7-1370.6, and the R3 range was 0.10-15.57. The lowest R3 level in the ALK-positive group was significantly higher than the highest R3 level in the ALK-negative group. A positive correlation between the proportion of cancer cells in the tissue section and ALK RNA expression level (R3) was found (P < 0.05). There was no relationship between the percentage of FISH positive cells or FISH positive signal patterns and R3 level of the ALK gene. Compared with FISH and IHC, the clinical sensitivity and specificity of FIATA-based RT-ddPCR for ALK detection were 100%, respectively. CONCLUSIONS An absolute quantitative FIATA-based RT-ddPCR was developed and validated for ALK fusion detection in NSCLC. This method can rapidly, accurately, and objectively classify ALK types and help with individual therapy.
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Affiliation(s)
- Yuanyuan Liu
- Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Shafei Wu
- Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaohua Shi
- Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
| | - Linping Lu
- TargetingOne Corporation, Beijing, China
| | - Lingxiang Zhu
- National Research Institute for Family Planning, Beijing, China
| | - Yong Guo
- Department of Biomedical Engineering, School of Medicine, Tsinghua University, Beijing, China
| | - Li Zhang
- Department of Respiratory Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Xuan Zeng
- Department of Pathology, Peking Union Medical College Hospital, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing, China
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Heyer EE, Blackburn J. Sequencing Strategies for Fusion Gene Detection. Bioessays 2020; 42:e2000016. [DOI: 10.1002/bies.202000016] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/11/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Erin E. Heyer
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
| | - James Blackburn
- The Kinghorn Cancer CentreGarvan Institute of Medical Research 384 Victoria Street Darlinghurst NSW 2010 Australia
- Faculty of Medicine, St. Vincent's Clinical SchoolUNSW, St Vincent's Hospital Victoria Street Darlinghurst NSW 2010 Australia
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Peng R, Zhang R, Zhang J, Tan P, Han Y, Zhang K, Lin G, Xie J, Li J. Continual Improvement of the Reliability of EML4-ALK Rearrangement Detection in Non-Small-Cell Lung Cancer: A Long-Term Comparison of ALK Detection in China. J Mol Diagn 2020; 22:876-884. [PMID: 32302779 DOI: 10.1016/j.jmoldx.2020.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/24/2019] [Accepted: 03/30/2020] [Indexed: 12/01/2022] Open
Abstract
The results of EML4-ALK testing are critical to manage ALK tyrosine kinase receptor inhibitor treatment. Thus, the accurate detection of ALK rearrangement is increasingly becoming a matter of serious concern. To address this issue, a long-term EML4-ALK proficiency testing (PT) scheme was launched in China in 2015, serving as an educational tool for assessing and improving the testing quality of EML4-ALK fusion detection. Responses across 20 different PT samples interrogating three different variants and wild-type samples were collected between 2015 and 2019. Performance was analyzed by evaluating the detection methods, kits, and pre-analytic practices used to further display the landscape of changing conditions of the reliability of EML4-ALK testing. During the 5 years, 3224 results reported from 988 laboratories were evaluated, with an overall error rate of 5.36%. Along with an increasing number of participating laboratories, the error rate within each of the different methods showed a significantly downward trend over the years. No obvious differences in the error rates were found regarding the testing methods or kit manufacturers. Moreover, the individual performance of the laboratories improved when they participated in more PT scheme rounds. The data demonstrated that the performance of individual Chinese laboratories for EML4-ALK testing continuously improved over time by participating PT schemes, regardless of their method. However, care must be taken in standardized operations and validations.
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Affiliation(s)
- Rongxue Peng
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiawei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Tan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.
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Pinsolle J, McLeer-Florin A, Giaj Levra M, de Fraipont F, Emprou C, Gobbini E, Toffart AC. Translating Systems Medicine Into Clinical Practice: Examples From Pulmonary Medicine With Genetic Disorders, Infections, Inflammations, Cancer Genesis, and Treatment Implication of Molecular Alterations in Non-small-cell Lung Cancers and Personalized Medicine. Front Med (Lausanne) 2019; 6:233. [PMID: 31737634 PMCID: PMC6828737 DOI: 10.3389/fmed.2019.00233] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/03/2019] [Indexed: 12/30/2022] Open
Abstract
Non-small-cell lung cancers (NSCLC) represent 85% of all lung cancers, with adenocarcinoma as the most common subtype. Since the 2000's, the discovery of molecular alterations including epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) rearrangements together with the development of specific tyrosine kinase inhibitors (TKIs) has facilitated the development of personalized medicine in the management of this disease. This review focuses on the biology of molecular alterations in NSCLC as well as the diagnostic tools and therapeutic alternatives available for each targetable alteration. Rapid and sensitive methods are essential to detect gene alterations, using tumor tissue biopsies or liquid biopsies. Massive parallel sequencing or Next Generation Sequencing (NGS) allows to simultaneously analyze numerous genes from relatively low amounts of DNA. The detection of oncogenic fusions can be conducted using fluorescence in situ hybridization, reverse-transcription polymerase chain reaction, immunohistochemistry, or NGS. EGFR mutations, ALK and ROS1 rearrangements, MET (MET proto-oncogenereceptor tyrosine kinase), BRAF (B-Raf proto-oncogen serine/threonine kinase), NTRK (neurotrophic tropomyosin receptor kinase), and RET (ret proto-oncogene) alterations are described with their respective TKIs, either already authorized or still in development. We have herein paid particular attention to the mechanisms of resistance to EGFR and ALK-TKI. As a wealth of diagnostic tools and personalized treatments are currently under development, a close collaboration between molecular biologists, pathologists, and oncologists is crucial.
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Affiliation(s)
- Julian Pinsolle
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
| | - Anne McLeer-Florin
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
| | - Matteo Giaj Levra
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Florence de Fraipont
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
- Department of Biochemistry, Molecular Biology and Environmental Toxicology, CHU Grenoble Alpes, Grenoble, France
| | - Camille Emprou
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- Departement of Pathological Anatomy and Cytology, Pôle de Biologie et Pathologie, CHU Grenoble Alpes, Grenoble, France
| | - Elisa Gobbini
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Cancer Research Center Lyon, Centre Léon Bérard, Lyon, France
| | - Anne-Claire Toffart
- Department of Pneumology, CHU Grenoble Alpes, Grenoble, France
- Medicine Faculty, Université Grenoble Alpes, Grenoble, France
- UGA/INSERM U1209/CNRS 5309-Institute for Advanced Biosciences - Université Grenoble Alpes, Grenoble, France
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Tachon G, Cortes U, Richard S, Martin S, Milin S, Evrard C, Lamour C, Karayan-Tapon L. Targeted RNA-sequencing assays: a step forward compared to FISH and IHC techniques? Cancer Med 2019; 8:7556-7566. [PMID: 31651105 PMCID: PMC6912030 DOI: 10.1002/cam4.2599] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/20/2019] [Accepted: 09/28/2019] [Indexed: 11/11/2022] Open
Abstract
Introduction ALK and ROS1 rearrangements are molecular targets of several tyrosine kinase inhibitors. RNA‐sequencing approaches are regarded as the new standard for fusion gene detection, representing an alternative to standard immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) techniques. Patients and Methods We aimed to compare two recent amplicon‐based RNA‐sequencing techniques: FusionPlex® Alk Ret Ros1 v2 Kit (Archer®) with FHS‐003Z‐12—Human Lung Cancer Panel (Qiagen®) and assessed the accuracy of the data for therapy management. Thirty‐seven formalin‐fixed paraffin‐embedded non‐small cell carcinoma (NSCC) lesions initially explored by IHC and FISH were selected for RNA‐sequencing analysis. Results Qiagen® and Archer® kits produced similar results and correctly identified 85.1% (23/27) and 81.5% (22/27) of IHC/FISH ALK‐ and ROS1‐positive samples, respectively, and 100% (6/6) of the negative samples. With regard to the ambiguous IHC‐positive/FISH‐negative cases, RNA‐sequencing confirmed 75% (3/4) of the FISH conclusion. Although not statistically significant, patients with common EML4‐ALK variants presented shorter overall survival and progression‐free survival compared with patients harboring rare variants. Conclusion Our findings assessed the implementation of RNA‐sequencing approaches to explore ALK and ROS1 rearrangements from formalin‐fixed paraffin‐embedded samples. We highlighted the similarities between Qiagen® and Archer® kits in terms of handling time, cost, and outcomes. We confirmed the feasibility of molecular testing in routine organization and its possible use not only as an alternative for standard IHC and FISH techniques, but as a supplementary technique helping to classify discrepant cases.
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Affiliation(s)
- Gaëlle Tachon
- Laboratoire de Neurosciences Expérimentales et Cliniques, Inserm U1084, Poitiers, France.,Université de Poitiers, Poitiers, France.,Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Ulrich Cortes
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Sophie Richard
- Université de Poitiers, Poitiers, France.,Service d'Anatomo-Cytopathologie, CHU de Poitiers, Poitiers, France
| | - Sébastien Martin
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
| | - Serge Milin
- Service d'Anatomo-Cytopathologie, CHU de Poitiers, Poitiers, France
| | | | | | - Lucie Karayan-Tapon
- Laboratoire de Neurosciences Expérimentales et Cliniques, Inserm U1084, Poitiers, France.,Université de Poitiers, Poitiers, France.,Laboratoire de Cancérologie Biologique, CHU de Poitiers, Poitiers, France
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Fluorescence in Situ Hybridization (FISH) for Detecting Anaplastic Lymphoma Kinase ( ALK) Rearrangement in Lung Cancer: Clinically Relevant Technical Aspects. Int J Mol Sci 2019; 20:ijms20163939. [PMID: 31412611 PMCID: PMC6720438 DOI: 10.3390/ijms20163939] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/08/2019] [Accepted: 08/11/2019] [Indexed: 02/06/2023] Open
Abstract
In 2011, the Vysis Break Apart ALK fluorescence in situ hybridization (FISH) assay was approved by the United States Food and Drug Administration as a companion diagnostic for detecting ALK rearrangement in lung cancer patients who may benefit from treatment of tyrosine kinase inhibitor therapy. This assay is the current “gold standard”. According to updated ALK testing guidelines from the College of American Pathologists, the International Association for the Study of Lung Cancer and the Association for Molecular Pathology published in 2018, ALK immunohistochemistry is formally an alternative to ALK FISH, and simultaneous detection of multiple hot spots, including, at least, ALK, ROS1, RET, MET, ERBB2, BRAF and KRAS genes is also recommended while performing next generation sequencing (NGS)-based testing. Therefore, ALK status in a specimen can be tested by different methods and platforms, even in the same institution or laboratory. In this review, we discuss several clinically relevant technical aspects of ALK FISH, including pros and cons of the unique two-step (50- to 100-cell) analysis approach employed in the Vysis Break Apart ALK FISH assay, including: the preset cutoff value of ≥15% for a positive result; technical aspects and biology of discordant results obtained by different methods; and incidental findings, such as ALK copy number gain or amplification and co-existent driver mutations. These issues have practical implications for ALK testing in the clinical laboratory following the updated guidelines.
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