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

Area of Science:

• Oncology
• Molecular Diagnostics
• Non-Small Cell Lung Cancer (NSCLC) Therapeutics

Background:

• High-level MET amplification in EGFR-treatment naive NSCLC patients (2-3%) is an adverse prognostic factor.
• Current clinical trials for MET inhibitors (capmatinib, tepotinib) use varying inclusion criteria for MET amplification.
• Accurate detection of MET amplification is critical for patient stratification and treatment selection.

Purpose of the Study:

• To evaluate and compare the concordance of various methods for detecting MET amplification in NSCLC patient samples.
• To determine the reliability of different diagnostic assays across varying levels of MET amplification.

Main Methods:

• 45 NSCLC patient samples with diverse MET amplification levels were analyzed.
• Methods included MET FISH (Fluorescence In Situ Hybridization), MET IHC (Immunohistochemistry), ddPCR, NanoString nCounter, and amplicon-based sequencing.
• Concordance analysis was performed between MET FISH and other molecular assays.

Main Results:

• MET IHC demonstrated the highest concordance with MET FISH, followed by NanoString, ddPCR, and sequencing.
• Concordance was superior in high-level MET amplification cohorts compared to low- and intermediate-level cohorts.
• Extraction-based methods yielded high false-negative rates for low- and intermediate-level MET amplification.

Conclusions:

• MET FISH is currently indispensable for detecting low-, intermediate-, and high-level MET amplifications due to high false-negative rates with other methods.
• Extraction-based methods are reliable alternatives only for detecting high-level MET amplification (Gene Copy Number ≥6).
• Standardized diagnostic criteria for MET amplification are needed for effective NSCLC targeted therapy.