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Tay TKY, Tan GS, Lee SH, Sam XX, Lim TH, Ng JWK, Tan DSW, Lim TKH. Comparison of an amplicon-based large panel next generation sequencing (NGS) assay with conventional testing methods for MET and HER2 amplification in lung and breast cancers. Pathology 2024; 56:325-333. [PMID: 38195375 DOI: 10.1016/j.pathol.2023.10.011] [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: 03/02/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 01/11/2024]
Abstract
The frequency of MET and HER2 amplification being detected by next generation sequencing (NGS) is increasing due to NGS being increasingly adopted for molecular profiling of cancers. However, the accuracy of NGS in detecting these gene amplifications remains uncertain due to conflicting reports in the scientific literature. We studied the accuracy of an amplicon-based large panel NGS assay in detecting MET and HER2 amplification in lung and breast cancers, respectively, by comparing it against conventional testing methods. Amongst 48 lung cancers, four of five cancers that were MET amplified on fluorescence in situ hybridisation (FISH) were classified as amplified on NGS while 42 of the remaining 43 non-amplified cancers were classified as non-amplified on NGS, giving a sensitivity of 80%, specificity of 97.7% and overall concordance of 95.8%. Of the 46 breast cancers tested, only six of the nine cancers that were HER2-positive on immunohistochemistry (IHC)/FISH were HER2-positive on NGS, while all the remaining HER2-negative cases were negative on NGS, giving a sensitivity of 66.7%, specificity of 100% and overall concordance of 93.5%. All the false-negative cases had low level gene amplification (MET:CEP7 or HER2:CEP17 FISH ratio of <3). The low sensitivity for HER2 amplification may be confounded by the small sample size and disproportionate number of cases with low level amplification. In summary, the NGS assay has good concordance with conventional testing methods but may be less sensitive in detecting low level gene amplification.
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Affiliation(s)
- Timothy Kwang Yong Tay
- Department of Anatomical Pathology, Singapore General Hospital, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore.
| | - Gek San Tan
- Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Say Hwee Lee
- Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Xin Xiu Sam
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Tse Hui Lim
- Department of Molecular Pathology, Singapore General Hospital, Singapore
| | - Jeremy Wee Kiat Ng
- Department of Molecular Pathology, Singapore General Hospital, Singapore
| | | | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore; Department of Molecular Pathology, Singapore General Hospital, Singapore
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Ahn MJ, Mendoza MJL, Pavlakis N, Kato T, Soo RA, Kim DW, Liam CK, Hsia TC, Lee CK, Reungwetwattana T, Geater S, Chan OSH, Prasongsook N, Solomon BJ, Nguyen TTH, Kozuki T, Yang JCH, Wu YL, Mok TSK, Tan DSW, Yatabe Y. Asian Thoracic Oncology Research Group (ATORG) Expert Consensus Statement on MET Alterations in NSCLC: Diagnostic and Therapeutic Considerations. Clin Lung Cancer 2022; 23:670-685. [PMID: 36151006 DOI: 10.1016/j.cllc.2022.07.012] [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] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/29/2022] [Indexed: 01/27/2023]
Abstract
Non-small cell lung cancer (NSCLC) is a heterogeneous disease, with many oncogenic driver mutations, including de novo mutations in the Mesenchymal Epithelial Transition (MET) gene (specifically in Exon 14 [ex14]), that lead to tumourigenesis. Acquired alterations in the MET gene, specifically MET amplification is also associated with the development of epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI) resistance in patients with EGFR-mutant NSCLC. Although MET has become an actionable biomarker with the availability of MET-specific inhibitors in selected countries, there is differential accessibility to diagnostic platforms and targeted therapies across countries in Asia-Pacific (APAC). The Asian Thoracic Oncology Research Group (ATORG), an interdisciplinary group of experts from Australia, Hong Kong, Japan, Korea, Mainland China, Malaysia, the Philippines, Singapore, Taiwan, Thailand and Vietnam, discussed testing for MET alterations and considerations for using MET-specific inhibitors at a consensus meeting in January 2022, and in subsequent offline consultation. Consensus recommendations are provided by the ATORG group to address the unmet need for standardised approaches to diagnosing MET alterations in NSCLC and for using these therapies. MET inhibitors may be considered for first-line or second or subsequent lines of treatment for patients with advanced and metastatic NSCLC harbouring MET ex14 skipping mutations; MET ex14 testing is preferred within multi-gene panels for detecting targetable driver mutations in NSCLC. For patients with EGFR-mutant NSCLC and MET amplification leading to EGFR TKI resistance, enrolment in combination trials of EGFR TKIs and MET inhibitors is encouraged.
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Affiliation(s)
- Myung-Ju Ahn
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Nick Pavlakis
- Department of Medical Oncology, Royal North Shore Hospital, University of Sydney, Sydney, NSW, Australia
| | - Terufumi Kato
- Department of Thoracic Oncology, Kanagawa Cancer Center, Yokohama, Japan
| | - Ross A Soo
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Singapore
| | - Dong-Wan Kim
- Department of Internal Medicine, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Chong Kin Liam
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Te-Chun Hsia
- Department of Respiratory Therapy, China Medical University, Taichung, Taiwan; Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Chee Khoon Lee
- National Health and Medical Research Council Clinical Trials Centre, The University of Sydney, Sydney, NSW, Australia
| | - Thanyanan Reungwetwattana
- Division of Medical Oncology, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Sarayut Geater
- Division of Internal Medicine, Faculty of Medicine, Songklanagarind Hospital, Prince of Songkla University, Songkhla, Thailand
| | - Oscar Siu Hong Chan
- Department of Clinical Oncology, Hong Kong Integrated Oncology Centre, Hong Kong SAR, China
| | - Naiyarat Prasongsook
- Division of Medical Oncology, Department of Medicine, Phramongkutklao Hospital, Bangkok, Thailand
| | - Benjamin J Solomon
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Toshiyuki Kozuki
- Department of Thoracic Oncology and Medicine, National Hospital Organization Shikoku Cancer Center, Matsuyama, Ehime, Japan
| | - James Chih-Hsin Yang
- Department of Medical Oncology, National Taiwan University Cancer Center and National Taiwan University Hospital, Taipei, Taiwan
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Tony Shu Kam Mok
- Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
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Schmitt C, Schulz AA, Winkelmann R, Smith K, Wild PJ, Demes M. Comparison of MET gene amplification analysis by next-generation sequencing and fluorescence in situ hybridization. Oncotarget 2021; 12:2273-2282. [PMID: 34733418 PMCID: PMC8555686 DOI: 10.18632/oncotarget.28092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 06/11/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
MET gene alterations are known to be involved in acquired resistance to epidermal growth factor receptor inhibition. MET amplifications present a potential therapeutic target in non-small cell lung cancer. Although next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) are conventionally used to assess MET amplifications, there are currently no clinically defined cut-off values for NGS, with FISH still being the gold standard. A collective of 20 formalin-fixed paraffin-embedded lung cancer tissue samples (mean age 64 years) were selected based on increased MET gene copy number (CNV) status or the presence of mutations detected by NGS (GeneReader, QIAGEN) and were further assessed by FISH (MET/CEN7, Zytomed). Of these, 17 tumor samples were MET-amplified and one patient was found to have a MET rearrangement by NGS, while two samples had no MET gene alteration. In contrast to the NGS result, FISH analysis showed only one highly amplified sample and 19 negative samples. The single highly amplified case detected by FISH was also positive by NGS with a fold change (FC) of 3.18 and a mean copy number (CNMV 10−100%) of 20.5. Therefore, for the assessment of MET amplifications using the QIAGEN NGS workflow, we suggest detecting amplified cases with an FC value of ≥ 3.0 and a CNMV 10−100% value of ≥ 20.0 by FISH. In summary, NGS allows for DNA- and RNA-based analysis of specific MET gene amplifications, point mutations or rearrangements.
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Affiliation(s)
- Christina Schmitt
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Anna-Alice Schulz
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Ria Winkelmann
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Kevin Smith
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany
| | - Peter J Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.,Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main 60590, Germany.,Frankfurt Institute for Advanced Studies (FIAS), Frankfurt am Main 60438, Germany
| | - Melanie Demes
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main 60590, Germany.,Wildlab, University Hospital Frankfurt MVZ GmbH, Frankfurt am Main 60590, Germany
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Schubart C, Stöhr R, Tögel L, Fuchs F, Sirbu H, Seitz G, Seggewiss-Bernhardt R, Leistner R, Sterlacci W, Vieth M, Seidl C, Mugler M, Kapp M, Hohenforst-Schmidt W, Hartmann A, Haller F, Erber R. MET Amplification in Non-Small Cell Lung Cancer (NSCLC)-A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting. Cancers (Basel) 2021; 13:5023. [PMID: 34638507 DOI: 10.3390/cancers13195023] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 08/12/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Lung cancer has a high incidence and affects both men and women. Targeted therapy options directed at certain mutant proteins, and which avoid systemic chemotherapy are already available and emerging. The gene mesenchymal epithelial transition (MET), encoding a receptor tyrosine kinase protein, is amplified in a subpopulation of lung cancer patients. The aim of our consecutive study was to assess whether next-generation sequencing (NGS) is a reliable method for the detection of MET gene copy number. Our study confirmed that NGS is able to detect cases harboring a high-level MET gene amplification but is unreliable and fails to detect the various levels of MET gene amplification. Therefore, NGS cannot replace the gold standard method of fluorescence in situ hybridization for the detection of MET gene copy number. Abstract In non-small cell lung cancer (NSCLC), approximately 1–3% of cases harbor an increased gene copy number (GCN) of the MET gene. This alteration can be due to de novo amplification of the MET gene or can represent a secondary resistance mechanism in response to targeted therapies. To date, the gold standard method to evaluate the GCN of MET is fluorescence in situ hybridization (FISH). However, next-generation sequencing (NGS) is becoming more relevant to optimize therapy by revealing the mutational profile of each NSCLC. Using evaluable n = 205 NSCLC cases of a consecutive cohort, this study addressed the question of whether an amplicon based NGS assay can completely replace the FISH method regarding the classification of MET GCN status. Out of the 205 evaluable cases, only n = 9 cases (43.7%) of n = 16 high-level MET amplified cases assessed by FISH were classified as amplified by NGS. Cases harboring a MET GCN > 10 showed the best concordance when comparing FISH versus NGS (80%). This study confirms that an amplicon-based NGS assessment of the MET GCN detects high-level MET amplified cases harboring a MET GCN > 10 but fails to detect the various facets of MET gene amplification in the context of a therapy-induced resistance mechanism.
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