Related Experiment Video
Updated: May 15, 2026
Detection of Targetable Alterations in Non-small Cell Lung Cancer using Next-generation Sequencing
Published on: October 10, 2025
Exploratory Identification of Gene Copy Number Cut-Off for NGS-Based MET Amplification Assessment and Clinical
Si-Yang Maggie Liu1, Zhi Xie1, Lixu Yan2
1Guangdong Lung Cancer Institute, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, People's Republic of China.
Introduction:
MET amplification is a critical oncogenic driver and a major mechanism of acquired resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) in non-small-cell lung cancer (NSCLC). Currently, next-generation sequencing (NGS)-based assays are increasingly used in clinical practice. However, they lack a unified standard for defining MET amplification across multiple NGS platforms with a potential actionable threshold.
Methods:
This was a multiple-site joint study to optimize the cut-off value for MET amplification using tumor tissue and NGS analysis. In the training cohort, five NGS panels were used to detect MET gene copy number (GCN), and fluorescence in situ hybridization (FISH) was used as a reference. Receiver operating characteristic (ROC) curve analysis was used to identify the optimal cutoff with 100% specificity and 66.7% sensitivity. The results were validated in an independent cohort to explore the correlation between MET amplification and efficacy of MET inhibitors in patients with NSCLC.
Results:
In the training cohort (n=21), the optimal MET GCN cut-off was determined to be 6.55, yielding an area under the curve of 0.9, corresponding to an accuracy of 85.7%. MET polysomy, identified using FISH (n=2), was also detected using NGS. All five NGS panels demonstrated good concordance with FISH, with accuracies ranging from 75.0% to 85.7%. In the validation cohort (n=29), NGS analysis demonstrated a good performance, with an accuracy rate of 79.3%. Patients with MET GCN ≥ 6.55 had a significantly longer median progression free survival than those with MET GCN < 6.55 (hazard ratio = 0.42; p = 0.03).
Conclusion:
In this study, an exploratory cut-off of 6.55 for MET GCN by NGS was associated with MET amplification and longer progression-free survival in patients receiving targeted therapy. However, given the retrospective design and limited sample size, these findings should be regarded as exploratory and require validation in larger, prospective cohorts before broader clinical application.
Insights
This study optimized the threshold for MET amplification detection using next-generation sequencing (NGS) in non-small-cell lung cancer (NSCLC). A cutoff of 6.55 for MET gene copy number (GCN) by NGS correlated with improved progression-free survival in patients receiving targeted therapy.
Area of Science:
- Oncology
- Genetics
- Molecular Diagnostics
Background:
- MET amplification is a key driver in non-small-cell lung cancer (NSCLC) and a cause of resistance to EGFR-TKIs.
- Next-generation sequencing (NGS) is widely used but lacks standardized thresholds for defining MET amplification.
- Establishing a reliable cutoff is crucial for guiding targeted therapy decisions.
Purpose of the Study:
- To optimize the cutoff value for defining MET amplification using tumor tissue and NGS analysis.
- To validate the identified cutoff in an independent cohort.
- To explore the correlation between MET amplification and the efficacy of MET inhibitors in NSCLC patients.
Main Methods:
- A multi-site study utilized five NGS panels to measure MET gene copy number (GCN).
- Fluorescence in situ hybridization (FISH) served as the reference standard.
- Receiver operating characteristic (ROC) curve analysis determined the optimal cutoff value.
Main Results:
- An optimal MET GCN cutoff of 6.55 was identified in the training cohort (n=21), achieving 85.7% accuracy.
- NGS panels showed good concordance with FISH, with accuracies ranging from 75.0% to 85.7%.
- In the validation cohort (n=29), a MET GCN ≥ 6.55 was associated with significantly longer progression-free survival (HR=0.42, p=0.03).
Conclusions:
- An exploratory cutoff of 6.55 for MET GCN by NGS is associated with MET amplification and improved progression-free survival in NSCLC patients on targeted therapy.
- These findings require validation in larger, prospective studies due to the retrospective design and limited sample size.
- The established cutoff provides a potential standard for defining MET amplification in clinical practice.
