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For: Heydt C, Becher AK, Wagener-Ryczek S, Ball M, Schultheis AM, Schallenberg S, Rüsseler V, Büttner R, Merkelbach-Bruse S. Comparison of in situ and extraction-based methods for the detection of MET amplifications in solid tumors. Comput Struct Biotechnol J 2019;17:1339-1347. [PMID: 31762957 PMCID: PMC6861603 DOI: 10.1016/j.csbj.2019.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 01/22/2023] Open

For:	Heydt C, Becher AK, Wagener-Ryczek S, Ball M, Schultheis AM, Schallenberg S, Rüsseler V, Büttner R, Merkelbach-Bruse S. Comparison of in situ and extraction-based methods for the detection of MET amplifications in solid tumors. Comput Struct Biotechnol J 2019;17:1339-1347. [PMID: 31762957 PMCID: PMC6861603 DOI: 10.1016/j.csbj.2019.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/05/2019] [Accepted: 09/07/2019] [Indexed: 01/22/2023] Open

Number

Cited by Other Article(s)

Shek RCM, Li PSN, Leung SCM, Chu HT, Hioe F, Tang VWL, Lui YH, Lam LRS, Ng JHY, Wong RTS, Yau MCY, Lam JYW, Siu GKH. A Novel Digital PCR Assay for Accurate Detection and Differentiation of Focal and Non-Focal Subtypes of Mesenchymal-Epithelial Transition (MET) Gene Amplification in Lung Cancer. Cancers (Basel) 2025;17:811. [PMID: 40075658 PMCID: PMC11898889 DOI: 10.3390/cancers17050811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 02/20/2025] [Accepted: 02/25/2025] [Indexed: 03/14/2025] Open

Xiao X, Xu R, Lu J, Xin B, Wang C, Zhu K, Zhang H, Chen X. The potential role of next-generation sequencing in identifying MET amplification and disclosing resistance mechanisms in NSCLC patients with osimertinib resistance. Front Oncol 2024;14:1470827. [PMID: 39497720 PMCID: PMC11532092 DOI: 10.3389/fonc.2024.1470827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 10/07/2024] [Indexed: 11/07/2024] Open

Abstract

Purposes

Osimertinib, one of the third-generation EGFR-tyrosine kinase inhibitors (TKIs) designed to target EGFR T790M mutation, significantly improves the prognosis of lung cancer. However, drug resistance still happens and MET amplification is responsible for one of the main causes. Fluorescence in situ hybridization (FISH) is the gold standard for MET amplification detection, but fundamentally limited by observer subjectivity. Herein, we assessed the value of next-generation sequencing (NGS) method in MET amplification detection in non-small cell lung cancer (NSCLC), as well as revealed the mutation profiling of NSCLC patients with osimertinib resistance to provide some valuable clues to the mechanisms of resistance.

Methods

A total of 317 cancer tissue samples from 317 NSCLC patients at time of progression following osimertinib were submitted to NGS and only 96 tissues were tested by FISH simultaneously. With FISH results as gold standard, enumeration algorithm was applied to establish the optimal model for identifying MET amplification using gene copy number (GCN) data.

Results

The optimal model for identifying MET amplification was constructed based on the GCN of MET, BRAF, CDK6 and CYP3A4, which achieved a 74.0% overall agreement with FISH and performed well in identifying MET amplification except polysomy with a sensitivity of 85.7% and a specificity of 93.9%. The inconsistency between NGS and FISH occurred mainly in polysomy subtype, while MET GCN ≥ 5 could be reliably recognized by NGS. Moreover, the most frequently mutated genes in NSCLC patients with osimertinib resistance were EGFR (59.94%), followed by TP53 (43.85%), NRG1 (9.46%), PIK3CA (6.31%), and ATM (5.36%). The known resistance mechanisms, including MET amplification, EGFR (C797S, L718Q/R), TP53, CDK4, CDK6, CDKN2A, BRAF, KRAS, NRAS and PIK3CA mutations were also disclosed in our cohort.

Conclusions

NGS assay can achieve a high concordance with FISH in MET amplification detection and has advantages in portraying various genetic alterations, which is of worthy in clinical promotion.

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Grebnev PA, Meshkov IO, Ershov PV, Makhotenko AV, Azarian VB, Erokhina MV, Galeta AA, Zakubanskiy AV, Shingalieva OS, Tregubova AV, Asaturova AV, Yudin VS, Yudin SM, Makarov VV, Keskinov AA, Makarova AS, Snigir EA, Skvortsova VI. Benchmarking of Approaches for Gene Copy-Number Variation Analysis and Its Utility for Genetic Aberration Detection in High-Grade Serous Ovarian Carcinomas. Cancers (Basel) 2024;16:3252. [PMID: 39409874 PMCID: PMC11475927 DOI: 10.3390/cancers16193252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/20/2024] [Accepted: 09/21/2024] [Indexed: 10/20/2024] Open

Affiliation(s)

Pavel Alekseevich Grebnev Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ivan Olegovich Meshkov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Pavel Viktorovich Ershov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Antonida Viktorovna Makhotenko Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentina Bogdanovna Azarian Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Marina Vyacheslavovna Erokhina Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anastasiya Aleksandrovna Galeta Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Aleksandr Vladimirovich Zakubanskiy Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Olga Sergeevna Shingalieva Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Vasilevna Tregubova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Aleksandra Vyacheslavovna Asaturova Federal State Budgetary Institution “National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov”, Ministry of Healthcare of The Russian Federation, Oparina Street, Bld. 4, 117997 Moscow, Russia; (A.V.T.); (A.V.A.)
Vladimir Sergeevich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Sergey Mihaylovich Yudin Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Valentin Vladimirovich Makarov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anton Arturovich Keskinov Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Anna Sergeevna Makarova Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Ekaterina Andreevna Snigir Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency (Centre for Strategic Planning of FMBA of Russia), Bld. 1, Pogodinskaya Street, 10, 119121 Moscow, Russia; (P.A.G.); (I.O.M.); (P.V.E.); (A.V.M.); (V.B.A.); (M.V.E.); (A.A.G.); (A.V.Z.); (O.S.S.); (V.S.Y.); (S.M.Y.); (V.V.M.); (A.S.M.)
Veronika Igorevna Skvortsova Federal Medical Biological Agency (FMBA of Russia), Volokolamskoye Shosse, 30, 123182 Moscow, Russia;

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Zheng Q, Lin X, Qi W, Yin J, Li J, Wang Y, Wang W, Li W, Liang Z. NGS and FISH for MET amplification detection in EGFR TKI resistant non-small cell lung cancer (NSCLC) patients: A prospective, multicenter study in China. Lung Cancer 2024;194:107897. [PMID: 39068705 DOI: 10.1016/j.lungcan.2024.107897] [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: 05/23/2024] [Revised: 06/30/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024]

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] [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]

Su JW, Weng CD, Lin XC, Fang MM, Xiao X, Zhang YC, Zhang XC, Su J, Xu CR, Yan HH, Chen HJ, Wu YL, Yang JJ. Plasma ddPCR for the detection of MET amplification in advanced NSCLC patients: a comparative real-world study. Ther Adv Med Oncol 2024;16:17588359241229435. [PMID: 38333112 PMCID: PMC10851729 DOI: 10.1177/17588359241229435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 01/03/2024] [Indexed: 02/10/2024] Open

Affiliation(s)

Jun-Wei Su Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Cheng-Di Weng Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Xiao-Cheng Lin Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Mei-Mei Fang Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Xiao Xiao Shanghai Yuanqi Biomedical Technology Co., Ltd, Shanghai, China
Yi-Chen Zhang Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Xu-Chao Zhang Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Jian Su Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Chong-Rui Xu Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Hong-Hong Yan Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Hua-Jun Chen Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Yi-Long Wu Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
Jin-Ji Yang Guangdong Cardiovascular Institute, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, 106 Zhongshan Er Road, Guangzhou 510080, China Guangdong Lung Cancer Institute, Guangdong Provincial People’s Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, 106 Zhongshan Er Road, Guangzhou 510080, China

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Yuan P, Xue X, Qiu T, Ying J. MET alterations detection platforms and clinical implications in solid tumors: a comprehensive review of literature. Ther Adv Med Oncol 2024;16:17588359231221910. [PMID: 38249331 PMCID: PMC10798113 DOI: 10.1177/17588359231221910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 12/04/2023] [Indexed: 01/23/2024] Open

Heydt C, Ihle MA, Merkelbach-Bruse S. Overview of Molecular Detection Technologies for MET in Lung Cancer. Cancers (Basel) 2023;15:cancers15112932. [PMID: 37296895 DOI: 10.3390/cancers15112932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open

Ihle MA, Heydt C. [Biomarker MET in tumor pathology]. PATHOLOGIE (HEIDELBERG, GERMANY) 2023;44:193-196. [PMID: 36944766 PMCID: PMC10160147 DOI: 10.1007/s00292-023-01189-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/19/2022] [Indexed: 03/23/2023]

Qin K, Hong L, Zhang J, Le X. MET Amplification as a Resistance Driver to TKI Therapies in Lung Cancer: Clinical Challenges and Opportunities. Cancers (Basel) 2023;15:612. [PMID: 36765572 PMCID: PMC9913224 DOI: 10.3390/cancers15030612] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/13/2023] [Accepted: 01/14/2023] [Indexed: 01/20/2023] Open

Oscorbin IP, Smertina MA, Pronyaeva KA, Voskoboev ME, Boyarskikh UA, Kechin AA, Demidova IA, Filipenko ML. Multiplex Droplet Digital PCR Assay for Detection of MET and HER2 Genes Amplification in Non-Small Cell Lung Cancer. Cancers (Basel) 2022;14:cancers14061458. [PMID: 35326608 PMCID: PMC8945941 DOI: 10.3390/cancers14061458] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open

Affiliation(s)

Igor P. Oscorbin Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.) Correspondence: ; Tel.: +7-9137061694
Maria A. Smertina Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
Ksenia A. Pronyaeva Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.) V. Zelman Institute for Medicine and Psychology, Novosibirsk State University, 630090 Novosibirsk, Russia
Mikhail E. Voskoboev Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.) Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
Ulyana A. Boyarskikh Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
Andrey A. Kechin Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)
Irina A. Demidova Moscow City Oncology Hospital, 143423 Stepanovskoe, Russia;
Maxim L. Filipenko Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences (ICBFM SB RAS), 630090 Novosibirsk, Russia; (M.A.S.); (K.A.P.); (M.E.V.); (U.A.B.); (A.A.K.); (M.L.F.)

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F Smit E, Dooms C, Raskin J, Nadal E, Tho LM, Le X, Mazieres J, S Hin H, Morise M, W Zhu V, Tan D, H Holmberg K, Ellers-Lenz B, Adrian S, Brutlach S, Schumacher KM, Karachaliou N, Wu YL. INSIGHT 2: a phase II study of tepotinib plus osimertinib in MET-amplified NSCLC and first-line osimertinib resistance. Future Oncol 2022;18:1039-1054. [PMID: 34918545 DOI: 10.2217/fon-2021-1406] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open

Evaluation of the TruSight Tumor 170 Assay and Its Value in Clinical Diagnostics. JOURNAL OF MOLECULAR PATHOLOGY 2022. [DOI: 10.3390/jmp3010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open

Castiglione R, Alidousty C, Holz B, Duerbaum N, Wittersheim M, Binot E, Merkelbach-Bruse S, Friedrichs N, Dettmer MS, Bosse A, Buettner R, Schultheis AM. MET-FISH Evaluation Algorithm: Proposal of a Simplified Method. JOURNAL OF CANCER SCIENCE AND CLINICAL THERAPEUTICS 2022;6:411-427. [PMID: 36713931 PMCID: PMC9878991 DOI: 10.26502/jcsct.5079180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]

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:cancers13195023. [PMID: 34638507 PMCID: PMC8508248 DOI: 10.3390/cancers13195023] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [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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Wenzel C, Herold S, Wermke M, E. Aust D, B. Baretton G. Routine Molecular Pathology Diagnostics in Precision Oncology. DEUTSCHES ARZTEBLATT INTERNATIONAL 2021;118:arztebl.m2021.0025. [PMID: 33536117 PMCID: PMC8287073 DOI: 10.3238/arztebl.m2021.0025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/01/2020] [Indexed: 11/27/2022]

Abstract

BACKGROUND

Technical advances in the field of molecular genetics permit precise genomic characterization of malignant tumors. This has not only improved our understanding of tumor biology but also paved the way for molecularly stratified treatment strategies in routine clinical practice.

METHODS

A selective search of PubMed to identify literature on molecular pathology methods, their indications, the challenges associated with molecular findings, and future developments.

RESULTS

Tumors can be characterized with the aid of immunohistochemistry, in-situ hybridization, and sequencing of DNA or RNA. The benefits of molecularly stratified tumor treatment have been demonstrated by randomized clinical trials on numerous tumor entities, e.g., non-small-cell lung cancer, colorectal cancer, and breast cancer. Therefore, initiation of specific treatment for these entities should be preceded by molecular pathology biomarker analyses, generally carried out on tumor tissue. Randomized controlled trials and non-controlled studies show that enhanced progression-free survival ensues if the pharmacological treatment is oriented on the findings of molecular pathology diagnostics. In next-generation sequencing, numerous relevant gene sequences or even whole genes can be sequenced in parallel, dispensing with complex staged diagnostics and reducing the use of biomaterials. These new methods also complement the currently relevant predictive biomarkers by permitting the investigation of genetic alterations presently of interest in the context of clinical studies. Prior to widespread routine clinical application, however, sequencing of large gene panels or whole genomes or exomes need to be even more stringently validated.

CONCLUSION

Quality-assured molecular pathology assays are universally available for the determination of currently relevant predictive biomarkers. However, the integration of extensive genomic analyses into routine molecular pathology diagnostics represents a future challenge in precision oncology.

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Jørgensen JT, Mollerup J, Yang H, Go N, Nielsen KB. MET deletion is a frequent event in gastric/gastroesophageal junction/esophageal cancer: a cross-sectional analysis of gene status and signal distribution in 1,580 patients. ANNALS OF TRANSLATIONAL MEDICINE 2021;9:225. [PMID: 33708852 PMCID: PMC7940901 DOI: 10.21037/atm-20-4081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]

Abstract

BACKGROUND

MET gene aberrations are found in several human cancers including gastric, ovarian and lung. In a large multinational cohort of patients with gastric/gastroesophageal junction/esophageal (G/GEJ/E) adenocarcinoma we assessed the MET status with respect to amplification and deletion and correlate the results with the phenotypical gene signal distribution pattern.

METHODS

Tissue specimens from 1,580 patients were analyzed using a novel fluorescence in situ hybridization (FISH) assay employing a MET/CEN-7 IQFISH Probe Mix. MET amplification and deletions were defined as a MET/CEN-7 ratio ≥2.0 and a MET/CEN-7 ratio <0.8, respectively. Furthermore, the link between the MET gene status and the phenotypical signal distribution was investigated.

RESULTS

The prevalence of MET amplification and deletions was found to be 7.2% and 8.7%, respectively. Significant differences were observed with regard to geographic regions and sex. The Asian population had the highest percentage of MET amplification (9.4%) and the lowest percentage of deletions (3.2%). MET deletions was found more frequently among males (10.1%) compared to females (5.3%) and in esophagus (17.6%) compared to the stomach (5.7%). More than 50% of the patients who harbored MET gene amplification had a heterogeneous distribution of the FISH signals. Patients with a focal signal distribution were solely to be found among the MET amplified population. MET deletion were mainly observed in the group of patients with a homogenous signal distribution.

CONCLUSIONS

The screening data from this cross-sectional study showed that MET deletion and amplification are frequent events in G/GEJ/E cancer, which are linked to different phenotypical signal distribution patterns. The role of MET deletion in relation to tumor development is not fully understood but it is likely to play a role in the oncogenic transformation of the cells.

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Campbell MR. Update on molecular companion diagnostics - a future in personalized medicine beyond Sanger sequencing. Expert Rev Mol Diagn 2020;20:637-644. [PMID: 32167388 DOI: 10.1080/14737159.2020.1743177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]