Comparison of in situ and extraction-based methods for the detection of MET amplifications in solid tumors

Heydt, Carina; Becher, Ann-Kathrin; Wagener‐Ryczek, Svenja; Ball, Markus; Schultheis, Anne M.; Schallenberg, Simon; Rüsseler, Vanessa; Büttner, Reinhard; Merkelbach‐Bruse, Sabine

doi:10.1016/j.csbj.2019.09.003

Cited by 19 publications

(14 citation statements)

References 29 publications

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“…Various aspects of this study again emphasized that an exclusive NGS-based determination of the MET GCN cannot completely replace a FISH-based assessment of the MET gene status. Heydt et al who used custom based NGS panels from Qiagen or an Ion AmpliSeq Custom panel from Thermo Fisher already faced similar problems [ 29 ]. They convincingly showed that MET IHC had the best concordance with MET FISH when comparing n = 35 MET amplified samples (low-, intermediate- and high-level MET amplification).…”

Section: Discussionmentioning

confidence: 99%

MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

Schubart

Stöhr

Tögel

et al. 2021

Cancers

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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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Section: Discussionmentioning

confidence: 99%

MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

Schubart

Stöhr

Tögel

et al. 2021

Cancers

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“…Diverse Probensets sind kommerziell erhältlich, die den 5 ′ -Teil (telomer) und den 3 ′ -Teil (zentromer) von ROS1 erkennen, dabei variieren die Genabschnitte, die von den Sonden erfasst werden [26]. In allen bekannten Fusionsgenen ist die ROS1-Tyrosinkinase-Domäne am 3 ′ -Ende [9]. Hier existieren 2 positive ROS1-Signalkategorien (.…”

Section: Ros1unclassified

“…Abb. 2) und das "atypische" Muster mit isolierten 3 ′ -Signalen [9]. Der Grenzwert für ein positives Ergebnis liegt beim Nachweis von 15 % und mehr Tumorzellen mit "klassischem" Bruchmuster oder "atypischem" Muster [26].…”

Section: Ros1unclassified

“…Der Grenzwert für ein positives Ergebnis liegt beim Nachweis von 15 % und mehr Tumorzellen mit "klassischem" Bruchmuster oder "atypischem" Muster [26]. Das atypische Muster, das in einer großen Kohorte von ROS1translozierten LUAD in annähernd 50 % vorkommen kann, birgt die Gefahr eines falsch positiven Ergebnisses [9]. Somit sollten alle atypischen Muster mittels eines orthogonalen Verfahrens validiert werden, wobei hier sequenzierungsbasierte Tests empfehlenswert sind.…”

Section: Ros1unclassified

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Anwendungen der FISH in der Diagnostik von Lungenkarzinomen

Hieggelke

Schultheis

2020

Wien klin Mag

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ZusammenfassungDie rasante Entwicklung im Bereich der Lungenkrebstherapie wurde maßgeblich auch durch die Entdeckung molekularer Marker und der damit verbundenen Möglichkeit einer personalisierten Therapie bestimmt. Die heutige Lungenkrebsdiagnostik stellt hohe Anforderungen an den Pathologen. An kleinen Gewebeproben muss nicht nur die Diagnose gestellt, sondern müssen auch alle therapierelevanten Biomarker getestet werden. Das verlangte Mindestmaß bei fortgeschrittenem nichtkleinzelligen Lungenkarzinom („non small cell lung cancer“, NSCLC) mit Nicht-Plattenepithel-Histologie umfasst die Testung von EGFR, BRAF, ALK, ROS1 und PD-L1. Für Plattenepithelkarzinome ist bislang nur die PD-L1-IHC (Immunhistochemie, IHC) gefordert. Nach Möglichkeit sollten neuere Biomarker wie RET, MET, HER2, NTRK und KRAS integriert werden. Die Fluoreszenz-in-situ-Hybridisierung („fluorescence in situ hybridization“, FISH) ist eine gut-etablierte Methode zum Nachweis einer ALK-, ROS1- und RET-Translokation, wobei die ALK-IHC als gleichwertig anerkannt wurde. Die Relevanz der MET-FISH zum Amplifikationsnachweis im First-line-Setting ist umstritten. Nicht eindeutige Fälle sollten immer mit einem orthogonalen Verfahren validiert werden. Hierzu eignet sich bei ALK und ROS1 die IHC mit dem Vorteil schneller und kostengünstiger Testergebnisse sowie geringen Gewebeverbrauchs. Bei allen anderen Translokationen oder bei Diskrepanz zwischen IHC und FISH sollte ein sequenzierungsbasiertes Verfahren ergänzt werden. Zur Detektion der seltenen NTRK-Fusionen eignet sich bei hoher Sensitivität ein IHC-Vorscreening; die sequenzierungsbasierte Analyse ist hier bei Positivität zur Bestätigung indiziert.

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“…This discrimination seems to be important as true MET amplification is more likely to lead to oncogenic MET addiction than polysomy (20). Furthermore, in a recent comparison of MET amplifications in solid tumors by in situ and extraction-based methods, large discrepancies was found compared with extraction-based methods such as PCR and NGS (21). Another factor contributing to the variability is the differences in the cut-off selected for the individual assays, thus comparing prevalence data for MET gene amplification across different study populations can be challenging (9).…”

Section: Introductionmentioning

confidence: 99%

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

Jørgensen¹,

Mollerup²,

Yang³

et al. 2021

Ann Transl Med

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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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Comparison of in situ and extraction-based methods for the detection of MET amplifications in solid tumors

Abstract: Graphical abstract

Cited by 19 publications

References 29 publications

MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

MET Amplification in Non-Small Cell Lung Cancer (NSCLC)—A Consecutive Evaluation Using Next-Generation Sequencing (NGS) in a Real-World Setting

Anwendungen der FISH in der Diagnostik von Lungenkarzinomen

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

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