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Conde E, Hernandez S, Rodriguez Carrillo JL, Martinez R, Alonso M, Curto D, Jimenez B, Caminoa A, Benito A, Garrido P, Clave S, Arriola E, Esteban-Rodriguez I, De Castro J, Sansano I, Felip E, Rojo F, Dómine M, Abdulkader I, Garcia-Gonzalez J, Teixido C, Reguart N, Compañ D, Insa A, Mancheño N, Palanca S, Juan-Vidal O, Baixeras N, Nadal E, Cebollero M, Calles A, Martin P, Salas C, Provencio M, Aranda I, Massuti B, Lopez-Vilaro L, Majem M, Paz-Ares L, Lopez-Rios F. RET Fusion Testing in Patients With NSCLC: The RETING Study. JTO Clin Res Rep 2024; 5:100653. [PMID: 38525319 PMCID: PMC10957499 DOI: 10.1016/j.jtocrr.2024.100653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction RET inhibitors with impressive overall response rates are now available for patients with NSCLC, yet the identification of RET fusions remains a difficult challenge. Most guidelines encourage the upfront use of next-generation sequencing (NGS), or alternatively, fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction (RT-PCR) when NGS is not possible or available. Taken together, the suboptimal performance of single-analyte assays to detect RET fusions, although consistent with the notion of encouraging universal NGS, is currently widening some of the clinical practice gaps in the implementation of predictive biomarkers in patients with advanced NSCLC. Methods This situation prompted us to evaluate several RET assays in a large multicenter cohort of RET fusion-positive NSCLC (n = 38) to obtain real-world data. In addition to RNA-based NGS (the criterion standard method), all positive specimens underwent break-apart RET FISH with two different assays and were also tested by an RT-PCR assay. Results The most common RET partners were KIF5B (78.9%), followed by CCDC6 (15.8%). The two RET NGS-positive but FISH-negative samples contained a KIF5B(15)-RET(12) fusion. The three RET fusions not identified with RT-PCR were AKAP13(35)-RET(12), KIF5B(24)-RET(9) and KIF5B(24)-RET(11). All three false-negative RT-PCR cases were FISH-positive, exhibited a typical break-apart pattern, and contained a very high number of positive tumor cells with both FISH assays. Signet ring cells, psammoma bodies, and pleomorphic features were frequently observed (in 34.2%, 39.5%, and 39.5% of tumors, respectively). Conclusions In-depth knowledge of the advantages and disadvantages of the different RET testing methodologies could help clinical and molecular tumor boards implement and maintain sensible algorithms for the rapid and effective detection of RET fusions in patients with NSCLC. The likelihood of RET false-negative results with both FISH and RT-PCR reinforces the need for upfront NGS in patients with NSCLC.
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Affiliation(s)
- Esther Conde
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Susana Hernandez
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | | | - Marta Alonso
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Daniel Curto
- Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | | | | | - Pilar Garrido
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Sergi Clave
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | - Edurne Arriola
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital del Mar, Barcelona, Spain
| | | | - Javier De Castro
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Hospital Universitario La Paz, Madrid, Spain
- Instituto de Investigacion Sanitaria del Hospital Universitario La Paz (IdiPAZ), Madrid, Spain
| | - Irene Sansano
- Hospital Universitario Vall d'Hebron, Barcelona, Spain
| | | | - Federico Rojo
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
| | - Manuel Dómine
- Instituto de Investigacion Sanitaria-Fundacion Jimenez Diaz (IIS-FJD), Madrid, Spain
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - Ihab Abdulkader
- Hospital Clinico Universitario de Santiago, Santiago de Compostela, Spain
| | | | - Cristina Teixido
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | - Noemi Reguart
- Hospital Clinic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Universitat de Barcelona, Barcelona, Spain
| | | | - Amelia Insa
- Hospital Clinico Universitario, Valencia, Spain
| | - Nuria Mancheño
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sarai Palanca
- Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | | | - Nuria Baixeras
- Hospital Universitari de Bellvitge, L’Hospitalet, Barcelona, Spain
| | - Ernest Nadal
- Catalan Institute of Oncology, L’Hospitalet, Barcelona, Spain
| | - Maria Cebollero
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Antonio Calles
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Paloma Martin
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Instituto de Investigación Sanitaria Hospital Universitario Puerta de Hierro, Madrid, Spain
| | - Clara Salas
- Hospital Universitario Puerta de Hierro, Madrid, Spain
| | | | - Ignacio Aranda
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | - Bartomeu Massuti
- Hospital General Universitario Dr. Balmis – Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Alicante, Spain
| | | | | | - Luis Paz-Ares
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Fernando Lopez-Rios
- Hospital Universitario 12 de Octubre, Madrid, Spain
- Universidad Complutense, Madrid, Spain
- Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), Madrid, Spain
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2
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Russo GL, Bironzo P, Bennati C, Bonanno L, Catino A, Metro G, Petrini I, Russano M, Passaro A. Clinical evidence and adverse event management update of patients with RET- rearranged advanced non-small-cell lung cancer (NSCLC) treated with pralsetinib. Crit Rev Oncol Hematol 2024; 194:104243. [PMID: 38135019 DOI: 10.1016/j.critrevonc.2023.104243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/12/2023] [Accepted: 12/17/2023] [Indexed: 12/24/2023] Open
Abstract
Current non-small cell lung cancer (NSCLC) management relies on genome-driven precision oncology thus shifting treatment paradigm towards biomarker-guided tumor-agnostic approaches. Recently, rearranged during transfection (RET) has been endorsed as tissue-agnostic target with sensitivity to RET inhibition. There are currently two selective RET tyrosine kinase inhibitors, pralsetinib and selpercatinib. The recent introduction of pralsetinib in the treatment algorithm of RET-rearranged tumor along with the mounting clinical evidence of pralsetinib durable activity from both randomized and observational studies holds the potential to disclose new avenues in the management of RET fusion positive NSCLC patients. Our narrative review aims to discuss the available clinical evidence on pralsetinib efficacy, particularly on brain metastases, and tolerability profile. In addition, our work explores the relevance of detecting RET fusions upfront in the disease history of patients with NSCLC.
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Affiliation(s)
- Giuseppe Lo Russo
- Medical Oncology Department, Thoracic Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Bironzo
- Department of Oncology, University of Torino, Ospedale San Luigi Gonzaga, Orbassano, TO, Italy
| | - Chiara Bennati
- Department of Onco-Hematology, AUSL della Romagna, Ravenna, Italy
| | - Laura Bonanno
- Medical Oncology 2, Istituto Oncologico Veneto IOV IRCCS, Padova, Italy
| | - Annamaria Catino
- Thoracic Oncology Unit, IRCCS Istituto Tumori "Giovanni Paolo II", Bari, Italy
| | - Giulio Metro
- Medical Oncology, Santa Maria della Misericordia Hospital, Azienda Ospedaliera Perugia, Italy
| | - Iacopo Petrini
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Marco Russano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
| | - Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Milano, Italy.
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3
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Diks J, Tang Z, Altan M, Anderson S, Chen H, Rashid A, Yang RK, Routbort MJ, Patel KP, Toruner GA, Medeiros LJ, Tang G, Luthra R, Roy-Chowdhuri S. Detection of clinically actionable gene fusions by next-generation sequencing-based RNA sequencing of non-small cell lung cancer cytology specimens: A single-center experience with comparison to fluorescence in situ hybridization. Cancer Cytopathol 2024; 132:41-49. [PMID: 37747438 DOI: 10.1002/cncy.22766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/26/2023]
Abstract
BACKGROUND Genomic profiling is needed to identify actionable alterations in non-small cell lung cancer (NSCLC). Panel-based testing such as next-generation sequencing (NGS) is often preferred to interrogate multiple alterations simultaneously. In this study, we evaluate the utility of an RNA-based NGS assay to detect genomic alterations in NSCLC cytology specimens and compare these results to fluorescence in situ hybridization (FISH) testing. METHODS A retrospective review was performed of 264 NSCLC cytology specimens that were concurrently tested for gene fusions by RNA-based NGS and ALK, RET, and/or ROS1 by FISH. RESULTS Genomic alterations were detected in 29 cases by NGS, including ALK, RET, ROS1, NTRK, NUTM1, and FGFR3 fusions and MET exon 14 skipping alterations. Of the 20 cases with ALK, RET, and ROS1 fusions detected by NGS, 16 (80%) were concordant with the corresponding FISH results. Three cases showed discordance, where EML4::ALK (n = 2) and SLC34A2::ROS1 (n = 1) fusions were not detected by the corresponding FISH assay; one case with EZR::ROS1 was inadequate for FISH. No gene fusions were detected in 181 cases by NGS and 54 cases failed testing. The concordance rates for detecting ALK, RET, and ROS1 fusions using NGS and FISH were 97%, 100%, and 99.5%, respectively. CONCLUSION RNA-based NGS can be used to detect gene fusions in NSCLC cytology cases with high concordance with FISH results. However, RNA-based NGS may have high failure rates and therefore a low threshold for reflexing inadequate cases to an orthogonal testing method is essential for comprehensive genomic profiling.
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Affiliation(s)
- John Diks
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mehmet Altan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sarah Anderson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hui Chen
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Kenneth Yang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Mark J Routbort
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Keyur P Patel
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Gokce A Toruner
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Guilin Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Tiurin VI, Preobrazhenskaya EV, Mitiushkina NV, Romanko AA, Anuskina AA, Mulkidjan RS, Saitova ES, Krivosheyeva EA, Kharitonova ED, Shevyakov MP, Tryakin IA, Aleksakhina SN, Venina AR, Sokolova TN, Martianov AS, Shestakova AD, Ivantsov AO, Iyevleva AG, Imyanitov EN. Rapid and Cost-Efficient Detection of RET Rearrangements in a Large Consecutive Series of Lung Carcinomas. Int J Mol Sci 2023; 24:10530. [PMID: 37445709 DOI: 10.3390/ijms241310530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/18/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
RET-kinase-activating gene rearrangements occur in approximately 1-2% of non-small-cell lung carcinomas (NSCLCs). Their reliable detection requires next-generation sequencing (NGS), while conventional methods, such as immunohistochemistry (IHC), fluorescence in situ hybridization (FISH) or variant-specific PCR, have significant limitations. We developed an assay that compares the level of RNA transcripts corresponding to 5'- and 3'-end portions of the RET gene; this test relies on the fact that RET translocations result in the upregulation of the kinase domain of the gene and, therefore, the 5'/3'-end expression imbalance. The present study included 16,106 consecutive NSCLC patients, 14,449 (89.7%) of whom passed cDNA quality control. The 5'/3'-end unbalanced RET expression was observed in 184 (1.3%) tumors, 169 of which had a sufficient amount of material for the identification of translocation variants. Variant-specific PCR revealed RET rearrangements in 155/169 (91.7%) tumors. RNA quality was sufficient for RNA-based NGS in 10 cases, 8 of which carried exceptionally rare or novel (HOOK1::RET and ZC3H7A::RET) RET translocations. We also applied variant-specific PCR for eight common RET rearrangements in 4680 tumors, which emerged negative upon the 5'/3'-end unbalanced expression test; 33 (0.7%) of these NSCLCs showed RET fusion. While the combination of the analysis of 5'/3'-end RET expression imbalance and variant-specific PCR allowed identification of RET translocations in approximately 2% of consecutive NSCLCs, this estimate approached 120/2361 (5.1%) in EGFR/KRAS/ALK/ROS1/BRAF/MET-negative carcinomas. RET-rearranged tumors obtained from females, but not males, had a decreased level of expression of thymidylate synthase (p < 0.00001), which is a known predictive marker of the efficacy of pemetrexed. The results of our study provide a viable alternative for RET testing in facilities that do not have access to NGS due to cost or technical limitations.
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Affiliation(s)
- Vladislav I Tiurin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Elena V Preobrazhenskaya
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Natalia V Mitiushkina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Aleksandr A Romanko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Aleksandra A Anuskina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Rimma S Mulkidjan
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Evgeniya S Saitova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Elena A Krivosheyeva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Elena D Kharitonova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Mikhail P Shevyakov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Ilya A Tryakin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Svetlana N Aleksakhina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Aigul R Venina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Tatiana N Sokolova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Aleksandr S Martianov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Anna D Shestakova
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
| | - Alexandr O Ivantsov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Aglaya G Iyevleva
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, 197758 St.-Petersburg, Russia
- Department of Medical Genetics, St.-Petersburg Pediatric Medical University, 194100 St.-Petersburg, Russia
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Goldman JW, Sholl LM, Dacic S, Fishbein MC, Murciano-Goroff YR, Rajaram R, Szymczak S, Szpurka AM, Chao BH, Drilon A. Case Report: Complete pathologic response to neoadjuvant selpercatinib in a patient with resectable early-stage RET fusion-positive non-small cell lung cancer. Front Oncol 2023; 13:1178313. [PMID: 37274265 PMCID: PMC10232990 DOI: 10.3389/fonc.2023.1178313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/03/2023] [Indexed: 06/06/2023] Open
Abstract
The LIBRETTO-001 trial demonstrated the activity of the selective rearrangement during transfection (RET) inhibitor selpercatinib in advanced RET fusion-positive non-small cell lung cancer (NSCLC) and resulted in the drug's approval for this indication. A cohort that included neoadjuvant and adjuvant selpercatinib was opened on LIBRETTO-001 for early-stage RET fusion-positive NSCLC with the primary endpoint of major pathologic response. A patient with a stage IB (cT2aN0M0) KIF5B-RET fusion-positive NSCLC received 8 weeks of neoadjuvant selpercatinib at 160 mg twice daily followed by surgery. While moderate regression in the primary tumor (stable disease, Response Evaluation Criteria in Solid Tumors (RECIST) guidelines version 1.1) was observed radiologically, assessment via an Independent Pathologic Review Committee revealed a pathologic complete response (0% viable tumor). This consensus assessment by three independent pathologists was aided by RET fluorescence in situ hybridization testing of a reactive pneumocyte proliferation showing no rearrangement. Neoadjuvant selpercatinib was well-tolerated with only low-grade treatment-emergent adverse events. The activity of prospective preoperative selpercatinib in this case establishes proof of concept of the potential utility of RET inhibitor therapy in early-stage RET fusion-positive NSCLC.
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Affiliation(s)
- Jonathan W. Goldman
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lynette M. Sholl
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States
| | - Sanja Dacic
- Department of Pathology, Yale School of Medicine, New Haven, CT, United States
| | - Michael C. Fishbein
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | | | - Ravi Rajaram
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | | | - Anna M. Szpurka
- Loxo@Lilly, Eli Lilly and Company, Indianapolis, IN, United States
| | - Bo H. Chao
- Loxo@Lilly, Eli Lilly and Company, New York, NY, United States
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan-Kettering Cancer CenterNew York, NY, United States
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States
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6
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Chen M, Xue J, Sang Y, Jiang W, He W, Hong S, Lv W, Xiao H, Liu R. Highly sensitive droplet digital PCR for detection of RET fusion in papillary thyroid cancer. BMC Cancer 2023; 23:363. [PMID: 37081420 PMCID: PMC10120194 DOI: 10.1186/s12885-023-10852-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 04/15/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND Thyroid cancer is the most frequent malignancy of the endocrine system, of which papillary thyroid cancer (PTC) is the predominant form with a rapid increasing incidence worldwide. Rearranged during transfection (RET) fusions are common genetic drivers of PTC and the potent RET inhibitor selpercatinib has been recently approved for treating advanced or metastatic RET fusion-positive thyroid cancer. In this study we aimed to develop a droplet digital PCR (ddPCR) system to accurately detect RET fusion in PTC samples. METHODS The frequency and distribution of RET fusions in PTC were analyzed using genomic data of 402 PTC patients in The Cancer Genome Atlas (TCGA) database. To establish the ddPCR system for detecting CCDC6::RET fusion, a plasmid containing CCDC6::RET infusion fragment was constructed as standard template, the annealing temperature and concentrations of primers and probe were optimized. The analytical performance of ddPCR and quantitative reverse transcription PCR (qRT-PCR) were assessed in standard templates and tissue samples from 112 PTC patients. Sanger sequencing was performed in all the RET fusion-positive samples identified by ddPCR. RESULTS RET fusions were observed in 25 (6.2%) of the 402 TCGA samples, and 15 (60%) of the RET fusion-positive patients had the CCDC6::RET fusion. Compared with qRT-PCR, the ddPCR method showed a lower limit of detection (128.0 and 430.7 copies/reaction for ddPCR and qRT-PCR, respectively). When applying the two methods to 112 tissue samples of PTC, eleven (9.8%) CCDC6::RET fusion-positive samples were detected by qRT-PCR, while ddPCR identified 4 additional positive samples (15/112, 13.4%). All the CCDC6::RET fusion-positive cases identified by ddPCR were confirmed by Sanger sequencing except for one case with 0.14 copies/uL of the fusion. CONCLUSION The accurate and sensitive ddPCR method reported here is powerful to detection CCDC6::RET fusion in PTC samples, application of this method would benefit more RET fusion-positive patients in the clinic.
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Affiliation(s)
- Mengke Chen
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Junyu Xue
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Ye Sang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Wenting Jiang
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiman He
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Shubin Hong
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Weiming Lv
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China
| | - Haipeng Xiao
- Department of Endocrinology, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
| | - Rengyun Liu
- Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, No. 58, Zhongshan Second Road, Guangzhou, 510080, China.
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7
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Saigí M, Carcereny E, Morán T, Cucurull M, Domènech M, Hernandez A, Martinez-Cardús A, Pros E, Sanchez-Cespedes M. Biological and clinical perspectives of the actionable gene fusions and amplifications involving tyrosine kinase receptors in lung cancer. Cancer Treat Rev 2022; 109:102430. [DOI: 10.1016/j.ctrv.2022.102430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/20/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
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8
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Hondelink LM, Schrader AMR, Asri Aghmuni G, Solleveld-Westerink N, Cleton-Jansen AM, van Egmond D, Boot A, Ouahoud S, Khalifa MN, Wai Lam S, Morreau H, Bovee JVMG, van Wezel T, Cohen D. The sensitivity of pan-TRK immunohistochemistry in solid tumours: A meta-analysis. Eur J Cancer 2022; 173:229-237. [PMID: 35933886 DOI: 10.1016/j.ejca.2022.06.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 05/16/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Since the approval of neurotrophic tropomyosin receptor kinase (NTRK) tyrosine kinase inhibitors for fist-line advanced stage pan-cancer therapy, pathologists and molecular biologists have been facing a complex question: how should the large volume of specimens be screened for NTRK fusions? Immunohistochemistry is fast and cheap, but the sensitivity compared to RNA NGS is unclear. METHODS We performed RNA-based next-generation sequencing on 1,329 cases and stained 24 NTRK-rearranged cases immunohistochemically with pan-TRK (ERP17341). Additionally, we performed a meta-analysis of the literature. After screening 580 studies, 200 additional NTRK-rearranged cases from 13 studies, analysed with sensitive molecular diagnostics as well as pan-TRK IHC, were included. RESULTS In the included 224 NTRK-rearranged solid tumours, the sensitivity for pan-TRK IHC was 82% and the false-negative rate was 18%. NTRK3 fusions had more false negatives (27%) compared to NTRK1 (6%) and NTRK2 (14%) (p = 0.0006). Membranous, nuclear and peri-nuclear staining patterns strongly correlated with different fusion products, with membranous staining being more prevalent in NTRK1 and NTRK2, nuclear in NTRK3, and perinuclear in NTRK1. CONCLUSION Despite a reduction in the number of molecular analysis, using pan-TRK immunohistochemistry as a prescreening method to detect NTRK fusions in solid tumours will miss 18% of all NTRK-fused cases (especially involving NTRK3). Therefore, the most comprehensive and optimal option to detect NTRK fusions is to perform molecular testing on all eligible cases. However, in case of financial or logistical limitations, an immunohistochemistry-first approach is defensible in tumours with a low prevalence of NTRK fusions.
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Affiliation(s)
- Liesbeth M Hondelink
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Anne M R Schrader
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Golzar Asri Aghmuni
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | | | | | - Demi van Egmond
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Arnoud Boot
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Sarah Ouahoud
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Midia N Khalifa
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Suk Wai Lam
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Judith V M G Bovee
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands
| | - Danielle Cohen
- Department of Pathology, Leiden University Medical Center (LUMC), the Netherlands.
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9
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Thouvenin J, Van Marcke C, Decoster L, Raicevic G, Punie K, Vandenbulcke M, Salgado R, Van Valckenborgh E, Maes B, Joris S, Steichel DV, Vranken K, Jacobs S, Dedeurwaerdere F, Martens G, Devos H, Duhoux FP, Rasschaert M, Pauwels P, Geboes K, Collignon J, Tejpar S, Canon JL, Peeters M, Rutten A, Van de Mooter T, Vermeij J, Schrijvers D, Demey W, Lybaert W, Van Huysse J, Mebis J, Awada A, Claes KBM, Hebrant A, Van der Meulen J, Delafontaine B, Bempt IV, Maetens J, de Hemptinne M, Rottey S, Aftimos P, De Grève J. PRECISION: the Belgian molecular profiling program of metastatic cancer for clinical decision and treatment assignment. ESMO Open 2022; 7:100524. [PMID: 35970014 PMCID: PMC9434164 DOI: 10.1016/j.esmoop.2022.100524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022] Open
Abstract
PRECISION is an initiative from the Belgian Society of Medical Oncology (BSMO) in collaboration with several stakeholders, encompassing four programs that aim to boost genomic and clinical knowledge with the ultimate goal to offer patients with metastatic solid tumors molecularly guided treatments. The PRECISION 1 study has led to the creation of a clinico-genomic database. The Belgian Approach for Local Laboratory Extensive Tumor Testing (BALLETT) and GeNeo studies will increase the number of patients with advanced cancer that have comprehensive genotyping of their cancer. The PRECISION 2 project consists of investigator-initiated phase II studies aiming to provide access to a targeted drug for patients whose tumors harbor actionable mutations in case the matched drug is not available through reimbursement or clinical trials in Belgium.
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Affiliation(s)
- J Thouvenin
- Hospices Civils de Lyon, Medical Oncology, Lyon, France; Institut Jules Bordet, Medical Oncology Clinic, Brussels, Belgium
| | | | - L Decoster
- UZ Brussel, Medical Oncology, Brussels, Belgium
| | | | - K Punie
- KU Leuven University Hospitals Leuven, General Medical Oncology, Leuven, Belgium
| | | | - R Salgado
- GasthuisZusters Antwerpen, Pathology, Antwerp, Belgium
| | | | - B Maes
- Laboratory of Molecular Diagnostics, Jessa Hospital Campus Virga Jesse, Hasselt, Belgium
| | - S Joris
- UZ Brussel, Medical Oncology, Brussels, Belgium
| | | | - K Vranken
- Pediatric Oncology, WIV-ISP, Leuven, Belgium
| | | | | | - G Martens
- Laboratoriumgeneeskunde, AZ Delta, Roeselare, Belgium
| | - H Devos
- Laboratoriumgeneeskunde, AZ Sint-Jan, Bruges, Belgium
| | - F P Duhoux
- UCLouvain, Ottignies-Louvain-la-Neuve, Belgium
| | - M Rasschaert
- Universitair Ziekenhuis Antwerpen, Medical Oncology, Antwerpen, Belgium; Medical Oncology, AZ Monica, Deurne, Belgium
| | - P Pauwels
- Universitair Ziekenhuis Antwerpen, Pathology, Antwerpen, Belgium
| | - K Geboes
- Division of Digestive Oncology, Department of Gastroenterology, UZ Gent, Gent, Belgium; Department of Internal Medicine and Pediatrics, UZ Gent, Gent, Belgium
| | - J Collignon
- Medical Oncology, CHU de Liege - Hospital Sart Tilman, Liège, Belgium
| | | | - J-L Canon
- Grand Hôpital de Charleroi Site Notre Dame, Service d'Oncologie-Hématologie, Charleroi, Belgium
| | - M Peeters
- Universitair Ziekenhuis Antwerpen, Oncology, Antwerpen, Belgium
| | - A Rutten
- GZA Ziekenhuizen Campus Sint-Vincentius, Medical Oncology, Antwerpen, Belgium
| | - T Van de Mooter
- GZA Ziekenhuizen Campus Sint-Vincentius, Medical Oncology, Antwerpen, Belgium
| | - J Vermeij
- ZNA Middelheim, Medical Oncology, Antwerpen, Belgium
| | | | - W Demey
- AZ Klina, Medical Oncology, Brasschaat, Belgium
| | - W Lybaert
- GZA Ziekenhuizen Campus Sint-Vincentius, Medical Oncology, Antwerpen, Belgium
| | - J Van Huysse
- AZ Sint-Jan Brugge-Oostende, Pathology, Brugge, Belgium
| | - J Mebis
- Laboratory of Molecular Diagnostics, Jessa Hospital Campus Virga Jesse, Hasselt, Belgium
| | - A Awada
- Institut Jules Bordet, Medical Oncology Clinic, Anderlecht, Belgium
| | | | | | | | | | | | | | | | - S Rottey
- Medical Oncology Department, UZ Gent, Gent, Belgium
| | - P Aftimos
- Institut Jules Bordet, Medical Oncology Clinic, Anderlecht, Belgium
| | - J De Grève
- UZ Brussel, Medical Oncology, Brussels, Belgium.
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10
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Penault-Llorca F, Kerr KM, Garrido P, Thunnissen E, Dequeker E, Normanno N, Patton SJ, Fairley J, Kapp J, de Ridder D, Ryška A, Moch H. Expert opinion on NSCLC small specimen biomarker testing - Part 2: Analysis, reporting, and quality assessment. Virchows Arch 2022. [PMID: 35857103 DOI: 10.1007/s00428-022-03344-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/16/2022] [Accepted: 05/18/2022] [Indexed: 10/31/2022]
Abstract
The diagnostic work-up for non-small cell lung cancer (NSCLC) requires biomarker testing to guide therapy choices. This article is the second of a two-part series. In Part 1, we summarised evidence-based recommendations for obtaining and processing small specimen samples (i.e. pre-analytical steps) from patients with advanced NSCLC. Here, in Part 2, we summarise evidence-based recommendations relating to analytical steps of biomarker testing (and associated reporting and quality assessment) of small specimen samples in NSCLC. As the number of biomarkers for actionable (genetic) targets and approved targeted therapies continues to increase, simultaneous testing of multiple actionable oncogenic drivers using next-generation sequencing (NGS) becomes imperative, as set forth in European Society for Medical Oncology guidelines. This is particularly relevant in advanced NSCLC, where tissue specimens are typically limited and NGS may help avoid tissue exhaustion compared with sequential biomarker testing. Despite guideline recommendations, significant discrepancies in access to NGS persist across Europe, primarily due to reimbursement constraints. The use of increasingly complex testing methods also has implications for the reporting of results. Molecular testing reports should include clinical interpretation with additional commentary on sample adequacy as appropriate. Molecular tumour boards are recommended to facilitate the interpretation of complex genetic information arising from NGS, and to collaboratively determine the optimal treatment for patients with NSCLC. Finally, whichever testing modality is employed, it is essential that adequate internal and external validation and quality control measures are implemented.
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11
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Bergshoeff VE, Balkenhol MCA, Haesevoets A, Ruland A, Chenault MN, Nelissen RC, Peutz CJ, Clarijs R, Van der Laak JAWM, Takes RP, Van den Brekel MW, Van Velthuysen MF, Ramaekers FCS, Kremer B, Speel EM. Evaluation Criteria for Chromosome Instability Detection by FISH to Predict Malignant Progression in Premalignant Glottic Laryngeal Lesions. Cancers (Basel) 2022; 14. [PMID: 35805032 DOI: 10.3390/cancers14133260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/25/2022] [Accepted: 06/26/2022] [Indexed: 01/27/2023] Open
Abstract
Background: The definition of objective, clinically applicable evaluation criteria for FISH 1c/7c in laryngeal precursor lesions for the detection of chromosome instability (CI). Copy Number Variations (CNV) for chromosomes 1 and 7 reflect the general ploidy status of premalignant head and neck lesions and can therefore be used as a marker for CI. Methods: We performed dual-target FISH for chromosomes 1 and 7 centromeres on 4 µm formalin-fixed, paraffin-embedded tissue sections of 87 laryngeal premalignancies to detect CNVs. Thirty-five normal head and neck squamous cell samples were used as a control. First, the chromosome 7:1 ratio (CR) was evaluated per lesion. The normal range of CRs (≥0.84 ≤ 1.16) was based on the mean CR +/− 3 x SD found in the normal population. Second, the percentage of aberrant nuclei, harboring > 2 chromosomes of chromosome 1 and/or 7 (PAN), was established (cut-off value for abnormal PAN ≥ 10%). Results: PAN showed a stronger correlation with malignant progression than CR (resp. OR 5.6, p = 0.001 and OR 3.8, p = 0.009). PAN combined with histopathology resulted in a prognostic model with an area under the ROC curve (AUC) of 0.75 (s.e. 0.061, sensitivity 71%, specificity 70%). Conclusions: evaluation criteria for FISH 1c/7c based on PAN ≥ 10% provide the best prognostic information on the risk of malignant progression of premalignant laryngeal lesions as compared with criteria based on the CR. FISH 1c/7c detection can be applied in combination with histopathological assessment.
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12
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Wolff HB, Steeghs EMP, Mfumbilwa ZA, Groen HJM, Adang EM, Willems SM, Grünberg K, Schuuring E, Ligtenberg MJL, Tops BBJ, Coupé VMH. Cost-Effectiveness of Parallel Versus Sequential Testing of Genetic Aberrations for Stage IV Non-Small-Cell Lung Cancer in the Netherlands. JCO Precis Oncol 2022; 6:e2200201. [PMID: 35834758 PMCID: PMC9307305 DOI: 10.1200/po.22.00201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
PURPOSE A large number of targeted treatment options for stage IV nonsquamous non–small-cell lung cancer with specific genetic aberrations in tumor DNA is available. It is therefore important to optimize diagnostic testing strategies, such that patients receive adequate personalized treatment that improves survival and quality of life. The aim of this study is to assess the efficacy (including diagnostic costs, turnaround time (TAT), unsuccessful tests, percentages of correct findings, therapeutic costs, and therapeutic effectiveness) of parallel next generation sequencing (NGS)–based versus sequential single-gene–based testing strategies routinely used in patients with metastasized non–small-cell lung cancer in the Netherlands. METHODS A diagnostic microsimulation model was developed to simulate 100,000 patients with prevalence of genetic aberrations, extracted from real-world data from the Dutch Pathology Registry. These simulated patients were modeled to undergo different testing strategies composed of multiple tests with different test characteristics including single-gene and panel tests, test accuracy, the probability of an unsuccessful test, and TAT. Diagnostic outcomes were linked to a previously developed treatment model, to predict average long-term survival, quality-adjusted life-years (QALYs), costs, and cost-effectiveness of parallel versus sequential testing. RESULTS NGS-based parallel testing for all actionable genetic aberrations is on average €266 cheaper than single-gene–based sequential testing, and detects additional relevant targetable genetic aberrations in 20.5% of the cases, given a TAT of maximally 2 weeks. Therapeutic costs increased by €8,358, and 0.12 QALYs were gained, leading to an incremental cost-effectiveness ratio of €69,614/QALY for parallel versus sequential testing. CONCLUSION NGS-based parallel testing is diagnostically superior over single-gene–based sequential testing, as it is cheaper and more effective than sequential testing. Parallel testing remains cost-effective with an incremental cost-effectiveness ratio of 69,614 €/QALY upon inclusion of therapeutic costs and long-term outcomes.
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Affiliation(s)
- Henri B Wolff
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
| | - Elisabeth M P Steeghs
- Department of Pathology, Radboudumc, Nijmegen, the Netherlands.,Department of Pathology, Antoni van Leeuwenhoek Hospital, the Netherlands Cancer Institute, Amsterdam, the Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, the Netherlands
| | - Zakile A Mfumbilwa
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Eddy M Adang
- Department of Epidemiology, Biostatistics and HTA, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Stefan M Willems
- Department of Pathology and Medical Biology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.,PALGA Foundation, Houten, the Netherlands
| | | | - Ed Schuuring
- Department of Pathology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboudumc, Nijmegen, the Netherlands.,Department of Human Genetics, and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bastiaan B J Tops
- Princess Máxima Center for Pediatric Oncology, Bilthoven, the Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Biostatistics, Amsterdam University Medical Center, VU Amsterdam, Amsterdam, the Netherlands
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13
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Depoilly T, Garinet S, van Kempen LC, Schuuring E, Clavé S, Bellosillo B, Ercolani C, Buglioni S, Siemanowski J, Merkelbach-Bruse S, Tischler V, Demes MC, Paridaens H, Sibille C, de Montpreville VT, Rouleau E, Bartczak A, Pasieka-Lis M, Wei Teo RY, Chuah KL, Barbosa M, Quintana C, Biscuola M, Delgado-Garcia M, Vacirca D, Rappa A, Cashmore M, Smith M, Jasionowicz P, Meeney A, Desmeules P, Terris B, Mansuet-Lupo A. Multicenter Evaluation of the Idylla GeneFusion in Non-Small-Cell Lung Cancer. J Mol Diagn 2022; 24:1021-1030. [PMID: 35718095 DOI: 10.1016/j.jmoldx.2022.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/20/2022] [Accepted: 05/17/2022] [Indexed: 11/25/2022] Open
Abstract
Targeted therapy in lung cancer requires the assessment of multiple oncogenic driver alterations, including fusion genes. This retrospective study evaluated the Idylla GeneFusion prototype, an automated and ease-of-use (<2 minutes) test, with a short turnaround time (3 hours) to detect fusions involving ALK, ROS1, RET, and NTRK1/2/3 genes and MET exon 14 skipping. This multicenter study (18 centers) included 313 tissue samples from lung cancer patients with 97 ALK, 44 ROS1, 20 RET, and 5 NTRKs fusions, 32 MET exon 14 skipping, and 115 wild-type samples, previously identified with reference methods (RNA-based next generation sequencing/fluorescence in situ hybridization/quantitative PCR). Valid results were obtained for 306 cases (98%), overall concordance between Idylla and the reference methods was 89% (273/306); overall sensitivity and specificity were 85% (165/193) and 96% (108/113), respectively. Discordances were observed in 28 samples, where Idylla did not detect the alteration identified by the reference methods; and 5 samples where Idylla identified an alteration not detected by the reference methods. All of the ALK-, ROS1-, and RET-specific fusions and MET exon 14 skipping identified by Idylla GeneFusion were confirmed by reference method. To conclude, Idylla GeneFusion is a clinically valuable test that does not require a specific infrastructure, allowing a rapid result. The absence of alteration or the detection of expression imbalance only requires additional testing by orthogonal methods.
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Affiliation(s)
- Thomas Depoilly
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Simon Garinet
- Department of Biochemistry, Unit of Pharmacogenetics and Molecular Oncology, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Léon C van Kempen
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Ed Schuuring
- Department of Pathology, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Sergi Clavé
- Department of Pathology, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Cristiana Ercolani
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Pathology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Janna Siemanowski
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- Faculty of Medicine and University Hospital Cologne, Institute of Pathology, University of Cologne, Cologne, Germany
| | - Verena Tischler
- Institute of Pathology, University Hospital Bonn, Bonn, Germany
| | | | | | | | | | - Etienne Rouleau
- Service de Génétique des Tumeurs, Gustave Roussy Cancer Campus Grand Paris, Villejuif, France
| | - Artur Bartczak
- Department of Pathomorphology, Public Specialist Hospital of Lung Diseases in Zakopane, Zakopane, Poland
| | - Monika Pasieka-Lis
- Department of Pathomorphology, Public Specialist Hospital of Lung Diseases in Zakopane, Zakopane, Poland
| | - Ryan Yee Wei Teo
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Khoon Leong Chuah
- Department of Pathology, Tan Tock Seng Hospital, Novena, Republic of Singapore
| | - Marta Barbosa
- Serviço de Anatomia Patológica, Hospital do Espírito Santo de Évora, Évora, Portugal
| | - Carlos Quintana
- Serviço de Anatomia Patológica, Hospital do Espírito Santo de Évora, Évora, Portugal
| | - Michele Biscuola
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Mercedes Delgado-Garcia
- Department of Pathology, Molecular Pathology Laboratory, Hospital Universitario Virgen del Rocío-IBIS, Seville, Spain
| | - Davide Vacirca
- Division of Pathology and Laboratory Medicine, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Alessandra Rappa
- Division of Pathology and Laboratory Medicine, European Institute of Oncology (IEO), IRCCS, Milan, Italy
| | - Matthew Cashmore
- Black Country Pathology Services, New Cross Hospital, The Royal Wolverhampton NHS Trust, Wolverhampton, United Kingdom
| | - Matthew Smith
- Pathology Department, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Piotr Jasionowicz
- Pathology Department, Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham NHS Foundation Trust, Birmingham, United Kingdom
| | - Adam Meeney
- Sheffield Teaching Hospitals NHS Foundation Trust, Pathology Laboratory, Royal Hallamshire Hospital, Sheffield, United Kingdom
| | - Patrice Desmeules
- Departement d'Anatomopathologie et Cytologie, Institut Universitaire de Cardiologie et de Pneumologie de Québec (IUCPQ), Québec, Québec, Canada
| | - Benoit Terris
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France
| | - Audrey Mansuet-Lupo
- Department of Pathology, Cochin Hospital, Assistance Publique-Hôpitaux de Paris, Université Paris Cité, Paris, France.
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Chakravarty D, Johnson A, Sklar J, Lindeman NI, Moore K, Ganesan S, Lovly CM, Perlmutter J, Gray SW, Hwang J, Lieu C, André F, Azad N, Borad M, Tafe L, Messersmith H, Robson M, Meric-Bernstam F. Somatic Genomic Testing in Patients With Metastatic or Advanced Cancer: ASCO Provisional Clinical Opinion. J Clin Oncol 2022; 40:1231-1258. [PMID: 35175857 DOI: 10.1200/jco.21.02767] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE An ASCO provisional clinical opinion offers timely clinical direction to ASCO's membership following publication or presentation of potentially practice-changing data from major studies. This provisional clinical opinion addresses the appropriate use of tumor genomic testing in patients with metastatic or advanced solid tumors. CLINICAL CONTEXT An increasing number of therapies are approved to treat cancers harboring specific genomic biomarkers. However, there is a lack of clarity as to when tumor genomic sequencing should be ordered, what type of assays should be performed, and how to interpret the results for treatment selection. PROVISIONAL CLINICAL OPINION Patients with metastatic or advanced cancer should undergo genomic sequencing in a certified laboratory if the presence of one or more specific genomic alterations has regulatory approval as biomarkers to guide the use of or exclusion from certain treatments for their disease. Multigene panel-based assays should be used if more than one biomarker-linked therapy is approved for the patient's disease. Site-agnostic approvals for any cancer with a high tumor mutation burden, mismatch repair deficiency, or neurotrophic tyrosine receptor kinase (NTRK) fusions provide a rationale for genomic testing for all solid tumors. Multigene testing may also assist in treatment selection by identifying additional targets when there are few or no genotype-based therapy approvals for the patient's disease. For treatment planning, the clinician should consider the functional impact of the targeted alteration and expected efficacy of genomic biomarker-linked options relative to other approved or investigational treatments.Additional information is available at www.asco.org/assays-and-predictive-markers-guidelines.
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Affiliation(s)
| | | | | | - Neal I Lindeman
- Brigham and Womens' Hospital, Harvard Medical School, Boston, MA
| | | | | | | | | | | | | | | | - Fabrice André
- PRISM, Precision Medicine Center, Institut Gustave Roussy, Villejuif, France
| | | | | | - Laura Tafe
- Dartmouth-Hitchcock Medical Center and The Geisel School of Medicine at Dartmouth, Darmouth, NH
| | | | - Mark Robson
- Memorial Sloan Kettering Cancer Center, New York City, NY
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15
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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] [What about the content of this article? (0)] [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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16
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Xiang C, Guo L, Zhao R, Teng H, Wang Y, Xiong L, Han Y. Identification and Validation of Noncanonical RET Fusions in Non-Small-Cell Lung Cancer through DNA and RNA Sequencing. J Mol Diagn 2022; 24:374-385. [PMID: 35063667 DOI: 10.1016/j.jmoldx.2021.12.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 11/14/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022] Open
Abstract
RET fusion has emerged as a targetable driver in non-small-cell lung cancer. A comparative analysis on RET fusions at DNA [DNA sequencing (DNA-seq)] and RNA [RNA sequencing (RNA-seq)] levels was performed in this study. Archived tumor samples from 54 non-small-cell lung cancer patients with DNA-level noncanonical RET fusions were selected for RNA-seq. RNA-seq identified RET fusion transcripts in 41 of 44 samples passing quality control. In the subset of cases harboring RET 3'-end fusions and predicted to produce in-frame proteins (group A; n = 33), RNA-seq identified the same 3'-end fusions in 32 (96.9%). A total of 26 of 32 also had a reciprocal RET 5'-end fusion detected by DNA-seq that was not transcribed. In the subset with DNA-level out-of-frame RET fusions (group B; n = 9), RNA-seq identified in-frame RET fusion transcripts in 8 cases (88.9%). In the subset only identified with a RET 5'-end fusion by DNA-seq (group C; n = 2), RNA-seq detected the corresponding 3'-end fusion in one case. The discordant DNA- and RNA-level fusions observed in group B may be mediated by complex genomic rearrangement events and transcriptional or post-transcriptional processes. In conclusion, DNA-seq demonstrates a high concordance of 96.9% on detecting in-frame RET fusion, but shows a low concordance on detecting out-of-frame RET fusion and RET 5'-end fusion compared with RNA-seq.
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Affiliation(s)
- Chan Xiang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Haohua Teng
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yulu Wang
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Liwen Xiong
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
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17
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Ambrosini-Spaltro A, Farnedi A, Calistri D, Rengucci C, Prisinzano G, Chiadini E, Capelli L, Angeli D, Bennati C, Valli M, De Luca G, Caruso D, Ulivi P, Rossi G. The role of next-generation sequencing in detecting gene FUSIONS with KNOWN and UNKNOWN partners: A single-center experience with methodologies' integration. Hum Pathol 2022; 123:20-30. [PMID: 35181377 DOI: 10.1016/j.humpath.2022.02.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/22/2022]
Abstract
AIMS Next-generation sequencing (NGS) is becoming a new gold standard for determining molecular predictive biomarkers. This study aimed to evaluate the reliability of NGS in detecting gene fusions, focusing on comparing gene fusions with known and unknown partners. METHODS We collected all gene fusions from a consecutive case series using an amplicon-based DNA/RNA NGS platform and subdivided them into two groups: gene fusions with known partners and gene fusions with unknown partners. Gene fusions involving ALK, ROS1 and RET were also examined by immunohistochemistry (IHC) and/or fluorescent in situ hybridization (FISH). RESULTS Overall, 1174 malignancies underwent NGS analysis. NGS detected gene fusions in 67 cases (5.7%), further subdivided into 43 (64.2%) with known partners and 24 (35.8%) with unknown partners. Gene fusions were predominantly found in non-small cell lung carcinomas (52/67, 77.6%). Gene fusions with known partners frequently involved ALK (20/43, 46.5%) and MET (9/43, 20.9%), while gene fusions with unknown partners mostly involved RET (18/24, 75.0%). FISH/IHC confirmed rearrangement status in most (89.3%) of the gene fusions with known partners, but in only one (4.8%) of the gene fusions with unknown partners, with a significant difference (p<0.001). In 17 patients undergoing targeted therapy, the log-rank test revealed that the overall survival was higher in the known partner group than in the unknown partner group (p=0.002). CONCLUSIONS NGS is a reliable method for detecting gene fusions with known partners, but it is less accurate in identifying gene fusions with unknown partners, for which further analyses (such as FISH) are required.
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Affiliation(s)
| | - Anna Farnedi
- Pathology Unit, Morgagni-Pierantoni Hospital, Forlì, AUSL Romagna, Italy
| | - Daniele Calistri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Claudia Rengucci
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanna Prisinzano
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Elisa Chiadini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Laura Capelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Chiara Bennati
- Oncology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Mirca Valli
- Pathology Unit, Infermi Hospital, Rimini, AUSL Romagna, Italy
| | | | - Dora Caruso
- Pathology Unit, Santa Maria Delle Croci Hospital, Ravenna, AUSL Romagna, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per Lo Studio Dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giulio Rossi
- Pathology Unit, Department of Oncology, Fondazione Poliambulanza, Brescia, Italy
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18
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Reale ML, Bertaglia V, Listì A, Novello S, Passiglia F. Molecular Testing and Treatment Strategies in RET-Rearranged NSCLC Patients: Stay on Target to Look Forward. JMP 2022; 3:24-37. [DOI: 10.3390/jmp3010003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RET alterations are recognized as key oncogenic drivers in different cancer types, including non-small cell lung cancer (NSCLC). Multikinase inhibitors (MKIs) with anti-RET activities resulted in variable efficacy with significant toxicities because of low target specificity. Selective RET kinase inhibitors, such as pralsetinib and selepercatinib, demonstrated high efficacy and favorable tolerability in advanced RET-rearranged NSCLC patients, leading to their introduction in the clinical setting. Among the different approaches available for the identification of RET rearrangements, next-generation sequencing (NGS) assays present substantial advantages in terms of turnaround time and diagnostic accuracy, even if potentially limited by accessibility issues. The recent advent of novel effective targeted therapies raises several questions regarding the emergence of resistance mechanisms and the potential ways to prevent/overcome them. In this review, we discuss molecular testing and treatment strategies to manage RET fusion positive NSCLC patients with a focus on resistance mechanisms and future perspectives in this rapidly evolving scenario.
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19
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Kazdal D, Hofman V, Christopoulos P, Ilié M, Stenzinger A, Hofman P. Fusion-positive non-small cell lung carcinoma: Biological principles, clinical practice, and diagnostic implications. Genes Chromosomes Cancer 2022; 61:244-260. [PMID: 34997651 DOI: 10.1002/gcc.23022] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/26/2021] [Accepted: 12/27/2021] [Indexed: 12/11/2022] Open
Abstract
Based on superior efficacy and tolerability, targeted therapy is currently preferred over chemotherapy and/or immunotherapy for actionable gene fusions that occur in late-stage non-small cell lung carcinoma (NSCLC). Consequently, current clinical practice guidelines mandate testing for ALK, ROS1, NTRK, and RET gene fusions in all patients with newly diagnosed advanced non-squamous NSCLC (NS-NSCLC). Gene fusions can be detected using different approaches, but today RNA next-generation sequencing (NGS) or combined DNA/RNA NGS is the method of choice. The discovery of other gene fusions (involving, eg, NRG1, NUT, FGFR1, FGFR2, MET, BRAF, EGFR, SMARC fusions) and their partners has increased progressively in recent years, leading to the development of new and promising therapies and mandating the development and implementation of comprehensive detection methods. The purpose of this review is to focus on recent data concerning the main gene fusions identified in NSCLC, followed by the discussion of major challenges in this domain.
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Affiliation(s)
- Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Petros Christopoulos
- Translational Lung Research Center (TLRC) Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,Thoraxklinik and National Center for Tumor Diseases, Heidelberg University Hospital, Heidelberg, Germany
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Center for Lung Research (DZL), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Pasteur Hospital, Université Côte d'Azur, FHU OncoAge, Nice, France.,Centre Antoine Lacassagne Cancer Center, Université Côte d'Azur, CNRS, INSERM, IRCAN, FHU OncoAge, Nice, France.,Hospital-Integrated Biobank BB-0033-00025, Université Côte d'Azur, CHU Nice, FHU OncoAge, Nice, France
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20
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Aydemirli MD, Snel M, van Wezel T, Ruano D, Obbink CMH, van den Hout WB, Schepers A, Morreau H. Yield and costs of molecular diagnostics on thyroid cytology slides in the Netherlands, adapting the Bethesda classification. Endocrinol Diabetes Metab 2021; 4:e00293. [PMID: 34505415 PMCID: PMC8502216 DOI: 10.1002/edm2.293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/10/2021] [Accepted: 07/16/2021] [Indexed: 12/29/2022]
Abstract
Objective To evaluate our institutional experience with molecular diagnostics (MD) on thyroid cytology smears, evaluate the costs and describe MD guided clinical management of indeterminate Bethesda III/V thyroid nodules. Methods We performed a retrospective review of 164 Bethesda III or V thyroid cytopathology reports subjected to MD from 2013 to 2020, that altered Bethesda classification or management. MD consisted of mutation and gene fusion analysis by next‐generation sequencing (NGS) of morphologically analysed and selected cytological slides. Findings were modelled to nationwide data on Bethesda incidences from ‘the Dutch Pathology Registry’ PALGA, and costs were estimated. Results 82 of 164 cases received an upgrade in Bethesda class. Twenty cases changed from Bethesda III to IV/V, 62 from Bethesda III or V to VI, and 72 remained unaltered. We estimate net savings with implementing MD, by preventing 454 repeat cytology and 326 (diagnostic) hemithyroidectomies, to be at least 2 million Euro annually in the Netherlands. Per Bethesda III and V patient, net savings would be about 100 Euro and 4100 Euro, respectively. Conclusion NGS‐based MD on nucleic acids extracted directly from cytology slides is a feasible and cost saving tool for personalized management in indeterminate Bethesda III/V thyroid cytology. Based on the interpretation of our retrospective data, we assume that this approach results in less disease burden for the patient, reduced surgical interventions and complication risks, reduced sick leave, among others. Further evaluation of structural implementation of the presented approach in routine thyroid Bethesda III/V cytology in a prospective setting is warranted.
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Affiliation(s)
- Mehtap Derya Aydemirli
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Medical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Marieke Snel
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Wilbert B van den Hout
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Abbey Schepers
- Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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21
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Radonic T, Geurts-Giele WRR, Dubbink HJ. Response Letter. J Thorac Oncol 2021; 16:e56. [PMID: 34154793 DOI: 10.1016/j.jtho.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/17/2021] [Indexed: 11/23/2022]
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22
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Piton N, Marguet F, Guisier F, Lamy A, Sabourin JC. [RNAseq in routine oncology]. Ann Pathol 2021:S0242-6498(21)00136-X. [PMID: 34376297 DOI: 10.1016/j.annpat.2021.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/30/2021] [Accepted: 06/07/2021] [Indexed: 11/21/2022]
Abstract
High throughput RNA sequencing, also know as RNAseq, can easily be performed on the gold-standard technique of formalin-fixed paraffin-embedded tissue, which has long been successfully used in routine practice by pathologists. For this reason, RNAseq has been fully adopted in a very short period of time in most French molecular platforms of cancer genotyping, generating "high throughput" data, both qualitative (mutations, fusions) and quantitative (gene expression profiles). This technique opens new perspectives in oncology practice: from a diagnostic point of view (some gene fusions are specific of some diagnoses, some transcriptomic signatures suggest some types of cancer), but also from a prognostic point of view (gene expression profile of an aggressive tumor, or conversely of an indolent one), and above all from a predictive point of view, guiding the choice of potential targeted therapies (example of ALK, ROS1 or NTRK translocations). This technical approach has many advantages, first and foremost it detects, at one go, a plethora of molecular alterations which were previously analyzed sequentially using heterogenous assays (immunohistochemistry, DNA genotyping, fluorescent in situ hybridization, etc.). However, it also presents several drawbacks which may easily be overcome if certain pre-analytic parameters are correctly controlled, mainly aiming at the preservation of the quality of nucleic acids. In any event, the widespread use of RNAseq has had a profound impact on the algorithms of tumor tissue processing, shaping a new, holistic era in oncology.
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23
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Uguen A. Each RET Break-Apart Fluorescence In Situ Hybridization Probe Requires Proper Interpretation Criteria. J Thorac Oncol 2021; 16:e55. [PMID: 34154792 DOI: 10.1016/j.jtho.2021.03.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 10/21/2022]
Affiliation(s)
- Arnaud Uguen
- Lymphocytes B and Auto-Immunity, UMR 1227, CHRU Brest, INSERM, Brest University, Brest, France.
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