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Guillard M, Caumont C, Marcorelles P, Merlio JP, Cappellen D, Uguen A. Performances of the Idylla GeneFusion Assay: contribution to a rapid diagnosis of targetable gene fusions in tumour samples. J Clin Pathol 2024; 77:561-567. [PMID: 37185257 DOI: 10.1136/jcp-2023-208798] [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: 01/24/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023]
Abstract
AIMS We aimed to evaluate the performances of the Idylla GeneFusion Assay (IGFA) designed to detect, in a single, rapid and fully automated assay, ALK, ROS1, RET, NTRK1, NTRK2 and NTRK3 gene fusions and MET exon 14 skipping in cancer samples. METHODS Based on a set of tumours enriched in cases with gene fusions, we applied the IGFA to tumour areas of various sizes and tumour cell contents. IGFA results were compared with those obtained with other methods (immunohistochemistry, fluorescent in situ hybridisation, DNA and RNA next-generation sequencing). RESULTS We selected 68 tumours: 49 cases with known gene fusions (8 ALK, 8 ROS1, 5 RET, 7 NTRK1, 3 NTRK2 and 6 NTRK3 ones) or MET exon 14 skipping mutations (12 cases) and 19 cases with no fusion and no MET mutation. We performed 128 IGFA tests on distinct tissue areas. The global sensitivity and specificity of the IGFA were, respectively, 62.82% and 99.2% with variations between molecular targets and tissue areas. Of note, 72.5% sensitivity and 98.79% specificity were obtained in 37 tissue areas fulfilling the manufacturer's recommendations (ie, at least 10% of tumour cells in at least 20 mm² of tissue area). The rate of non-conclusive results was higher in small samples with low percentages of tumour cells. CONCLUSIONS The IGFA could contribute to the rapid detection of targetable gene fusions and mutations, especially in context of rapidly growing cancers requiring urgent therapeutic choices.
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Affiliation(s)
- Matthieu Guillard
- Service d'Anatomie et Cytologie Pathologiques, CHRU Brest, Brest, France
| | - Charline Caumont
- Service de Biologie des Tumeurs, CHU Bordeaux, Pessac, France
- BRIC (BoRdeaux Institute of onCology), UMR1312, INSERM, Université de Bordeaux, Pessac, France
| | - Pascale Marcorelles
- Service d'Anatomie et Cytologie Pathologiques, CHRU Brest, Brest, France
- LBAI, UMR1227 INSERM, Université de Bretagne Occidentale, Brest, France
| | - Jean-Philippe Merlio
- Service de Biologie des Tumeurs, CHU Bordeaux, Pessac, France
- BRIC (BoRdeaux Institute of onCology), UMR1312, INSERM, Université de Bordeaux, Pessac, France
| | - David Cappellen
- Service de Biologie des Tumeurs, CHU Bordeaux, Pessac, France
- BRIC (BoRdeaux Institute of onCology), UMR1312, INSERM, Université de Bordeaux, Pessac, France
| | - Arnaud Uguen
- Service d'Anatomie et Cytologie Pathologiques, CHRU Brest, Brest, France
- LBAI, UMR1227 INSERM, Université de Bretagne Occidentale, Brest, France
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Wakuda K, Morita M, Sekikawa M, Morikawa N, Miura K, Doshita K, Iida Y, Kodama H, Mamesaya N, Kobayashi H, Ko R, Ono A, Kenmotsu H, Naito T, Murakami H, Muramatsu K, Kawata T, Mori K, Shimizu T, Gon Y, Takahashi T. Concordance of ALK fusion gene-rearrangement between immunohistochemistry and next-generation sequencing. Int J Clin Oncol 2024; 29:96-102. [PMID: 38183554 DOI: 10.1007/s10147-023-02451-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/24/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Although various companion diagnostic tests of ALK fusion gene-rearrangement are approved, few reports have assessed the concordance of ALK fusion gene-rearrangement in two companion diagnostic tests: next-generation sequencing (NGS) testing and immunohistochemistry (IHC). METHODS The samples evaluated for gene alterations using NGS testing between May 2019 and November 2021 were included in this study. The inclusion criteria were as follows: samples were diagnosed with non-small cell lung cancer; the results of the NGS analysis were informative; and samples had residual specimens for IHC. We performed IHC on the residual specimens and retrospectively collected sample characteristics from medical records. RESULTS A total of 185 samples were analyzed using NGS. Twenty-six samples were excluded because of failure to analyze gene alterations using NGS, no residual samples, and inadequate IHC. We analyzed 159 samples. The major histological type was adenocarcinoma (115 samples). The number of surgical and transbronchial lung biopsy specimens was 59 and 56, respectively. ALK fusion gene-rearrangement was detected in four samples using NGS, and five were detected using IHC. The sensitivity and specificity of IHC referred to by NGS were 75.0% and 98.7%, respectively. The concordance rate between IHC and NGS was 98.1%. ALK rearrangement was detected in two patients using IHC but not using NGS. In addition, ALK rearrangement was detected in one patient using NGS but not using IHC. CONCLUSION Our results suggest that IHC and NGS might be complementary tests. In patients suspected of harboring ALK fusion gene-rearrangement, it should be analyzed using another diagnostic method.
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Affiliation(s)
- Kazushige Wakuda
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan.
| | - Meiko Morita
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Motoki Sekikawa
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Noboru Morikawa
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Keita Miura
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Kosei Doshita
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Yuko Iida
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Hiroaki Kodama
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Nobuaki Mamesaya
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Haruki Kobayashi
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Ryo Ko
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Akira Ono
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Hirotsugu Kenmotsu
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Tateaki Naito
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Haruyasu Murakami
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Koji Muramatsu
- Division of Pathology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Takuya Kawata
- Division of Pathology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
| | - Keita Mori
- Department of Biostatistics, Clinical Research Support Center, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo Nagaizumi-cho Suntou-gun, Shizuoka, 411-8777, Japan
| | - Tetsuo Shimizu
- Division of Respiratory Medicine, Nihon University School of Medicine, 30-1 Ohyaguchi-Kamicho, Itabashiku, Tokyo, 173-8610, Japan
| | - Yasuhiro Gon
- Division of Respiratory Medicine, Nihon University School of Medicine, 30-1 Ohyaguchi-Kamicho, Itabashiku, Tokyo, 173-8610, Japan
| | - Toshiaki Takahashi
- Division of Thoracic Oncology, Shizuoka Cancer Center Hospital, 1007 Shimonagakubo, Nagaizumi-cho, Suntou-gun, Shizuoka, 411-8777, Japan
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Hernandez S, Conde E, Alonso M, Illarramendi A, Bote de Cabo H, Zugazagoitia J, Paz-Ares L, Lopez-Rios F. A narrative review of methods for the identification of ALK fusions in patients with non-small cell lung carcinoma. Transl Lung Cancer Res 2023; 12:1549-1562. [PMID: 37577307 PMCID: PMC10413037 DOI: 10.21037/tlcr-22-855] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/25/2023] [Indexed: 08/15/2023]
Abstract
Background and Objective This narrative review is intended to provide pragmatic knowledge of current methods for the search of anaplastic lymphoma kinase (ALK) fusions in patients with non-small cell lung carcinoma (NSCLC). This information is very timely, because a recent survey has identified that almost 50% of patients with advanced NSCLC were not candidates for targeted therapies because of biomarker testing issues. Methods PubMed was searched from January 1st, 2012 to February 28th, 2023 using the following keywords: "ALK" and "lung", including reviews and our own work. Key Content and Findings Testing rates have not reached 85% among patients' candidates to ALK inhibition. The advantages and disadvantages of the different analytical options [immunohistochemistry (IHC), fluorescence in situ hybridization (FISH), real-time polymerase chain reaction and next-generation sequencing (NGS)] are discussed. The key factor for success in ALK testing is a deep understanding of the concept of "molecular redundancy". This notion has been recommended and endorsed by all the major professional organizations in the field and can be summarized as follows: "laboratories should ensure that test results that are unexpected, discordant, equivocal, or otherwise of low confidence are confirmed or resolved using an alternative method or sample". In-depth knowledge of the different ALK testing methodologies can help clinical and molecular tumor boards implement and maintain sensible algorithms for a rapid and effective detection of predictive biomarkers in patients with NSCLC. Conclusions Multimodality testing has the potential to increase both the testing rate and the accuracy of ALK fusion identification.
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Affiliation(s)
- Susana Hernandez
- Pathology Department, Hospital Universitario 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | - Esther Conde
- Pathology Department, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, Research Institute Hospital 12 de Octubre (i+12), Ciberonc, Madrid, Spain
| | - Marta Alonso
- Pathology Department, Hospital Universitario 12 de Octubre, Research Institute Hospital 12 de Octubre (i+12), Madrid, Spain
| | | | - Helena Bote de Cabo
- Oncology Department, Hospital Universitario 12 de Octubre, H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 de Octubre (i+12)/Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Jon Zugazagoitia
- Oncology Department, Hospital Universitario 12 de Octubre, H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 de Octubre (i+12)/Spanish National Cancer Research Center (CNIO), Ciberonc, Madrid, Spain
| | - Luis Paz-Ares
- Oncology Department, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, H12O-CNIO Lung Cancer Clinical Research Unit, Research Institute Hospital 12 de Octubre (i+12)/Spanish National Cancer Research Center (CNIO), Ciberonc, Madrid, Spain
| | - Fernando Lopez-Rios
- Pathology Department, Hospital Universitario 12 de Octubre, Universidad Complutense de Madrid, Research Institute Hospital 12 de Octubre (i+12), Ciberonc, Madrid, Spain
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Zhao R, Guo L, Zhang B, Zhao J, Xiang C, Chen S, Shao J, Zhu L, Ye M, Han Y. Identification and therapeutic evaluation of ALK rearrangements in non-small-cell lung cancer. J Pathol Clin Res 2022; 8:538-549. [PMID: 35848751 PMCID: PMC9535099 DOI: 10.1002/cjp2.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 06/17/2022] [Accepted: 06/23/2022] [Indexed: 12/29/2022]
Abstract
This study aimed to present a comprehensive assessment of anaplastic lymphoma kinase (ALK) rearrangements evaluated by DNA/RNA-based next-generation sequencing (NGS) and Ventana immunohistochemistry (IHC) in patients with non-small-cell lung cancer (NSCLC) and to evaluate the therapeutic outcomes of ALK tyrosine kinase inhibitor (TKI) treatment. We investigated ALK gene fusions in 14,894 patients with NSCLC using Ventana IHC and NGS, including 12,533 cases detected via DNA-based NGS and 2,361 cases using RNA-based NGS. The overall percentage agreement (OPA), positive percentage agreement (PPA), and negative percentage agreement (NPA) were calculated when comparing the results between NGS and IHC. The therapeutic responses to ALK-TKIs were also evaluated. In total, 3.50% (439/12,533) of specimens were NGS ALK-positive (NGS-p) in the DNA-based NGS cohort and 3.63% (455/12,533) were IHC ALK-positive (IHC-p). The OPA of NGS was 99.60%, whereas its PPA and NPA were 92.75 and 99.86%, respectively. In the adenocarcinoma (ADC) subcohort, the PPA was 95.69%. In the RNA-based NGS cohort, 2.20% (52/2,361) of specimens were NGS-p and 2.63% (62/2,361) were IHC-p. The OPA of NGS was 99.49%; its PPA and NPA were 82.26 and 99.96%, respectively. Thirteen patients with discordant results received ALK-TKI treatment. In the seven NGS-p/IHC-negative (IHC-n) patients, the overall response rate (ORR) was 85.4% (6/7) and the disease control rate (DCR) was 100%. In the six NGS-negative/IHC-p patients, the ORR was 66.7% (4/6) and the DCR was 100%. In summary, a high concordance of ALK gene fusion detected via NGS and IHC was observed in this study. DNA-based NGS had a higher OPA, PPA, and PPA in the ADC subcohort, whereas RNA-based NGS had a higher NPA. Overall, the results suggest that the combination of NGS and IHC can improve the accuracy of ALK fusion detection; hence, a result determination algorithm for clinical detection of ALK gene fusion was also proposed.
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Affiliation(s)
- Ruiying Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lianying Guo
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Bo Zhang
- Department of Pulmonary, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jikai Zhao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Chan Xiang
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Shengnan Chen
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Min Ye
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghaiPR China
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