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Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Comparison between Three Different Techniques for the Detection of EGFR Mutations in Liquid Biopsies of Patients with
Milena Casula1, Marina Pisano1, Panagiotis Paliogiannis2
1Unit of Cancer Genetics, Institute of Genetic Biomedical Research (IRGB), National Research Council (CNR), 07100 Sassari, Italy.
Abstract:
Oncogenic mutations in the EGFR gene are targets of tyrosine kinase inhibitors (TKIs) in lung adenocarcinoma (LC) patients, and their search is mandatory to make decisions on treatment strategies. Liquid biopsy of circulating tumour DNA (ctDNA) is increasingly used to detect EGFR mutations, including main activating alterations (exon 19 deletions and exon 21 L858R mutation) and T790M mutation, which is the most common mechanism of acquired resistance to first- and second-generation TKIs. In this study, we prospectively compared three different techniques for EGFR mutation detection in liquid biopsies of such patients. Fifty-four ctDNA samples from 48 consecutive advanced LC patients treated with TKIs were tested for relevant EGFR mutations with Therascreen® EGFR Plasma RGQ-PCR Kit (Qiagen). Samples were subsequently tested with two different technologies, with the aim to compare the EGFR detection rates: real-time PCR based Idylla™ ctEGFR mutation assay (Biocartis) and next-generation sequencing (NGS) system with Ion AmpliSeq Cancer Hotspot panel (ThermoFisher). A high concordance rate for main druggable EGFR alterations was observed with the two real-time PCR-based assays, ranging from 100% for T790M mutation to 94% for L858R variant and 85% for exon 19 deletions. Conversely, lower concordance rates were found between real-time PCR approaches and the NGS method (L858R: 88%; exon19-dels: 74%; T790M: 37.5%). Our results evidenced an equivalent detection ability between PCR-based techniques for circulating EGFR mutations. The NGS assay allowed detection of a wider range of EGFR mutations but showed a poor ability to detect T790M.
Insights
Two real-time PCR methods show high concordance for detecting EGFR mutations in lung cancer liquid biopsies. Next-generation sequencing detected more mutations but struggled with T790M resistance markers.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- Epidermal Growth Factor Receptor (EGFR) mutations drive lung adenocarcinoma (LC) and are targets for tyrosine kinase inhibitors (TKIs).
- Liquid biopsy using circulating tumor DNA (ctDNA) is crucial for detecting EGFR mutations (e.g., exon 19 deletions, L858R, T790M) to guide LC treatment.
- T790M is a key resistance mechanism against first- and second-generation TKIs.
Purpose of the Study:
- To prospectively compare the diagnostic performance of three distinct techniques for EGFR mutation detection in ctDNA from advanced LC patients.
- To evaluate the concordance rates between two real-time PCR assays and a next-generation sequencing (NGS) method.
Main Methods:
- Fifty-four ctDNA samples from 48 advanced LC patients were analyzed.
- EGFR mutations were detected using Therascreen® EGFR Plasma RGQ-PCR Kit (Qiagen).
- Samples were further tested with the Idylla™ ctEGFR mutation assay (Biocartis) and an Ion AmpliSeq Cancer Hotspot panel (ThermoFisher) NGS system.
Main Results:
- High concordance was observed between the two real-time PCR assays for main EGFR alterations (T790M: 100%, L858R: 94%, exon 19 deletions: 85%).
- Lower concordance rates were found between PCR-based methods and NGS (L858R: 88%, exon 19 deletions: 74%, T790M: 37.5%).
- NGS identified a broader spectrum of EGFR mutations but demonstrated poor sensitivity for the T790M mutation.
Conclusions:
- PCR-based techniques exhibit equivalent detection capabilities for common circulating EGFR mutations in lung cancer.
- NGS offers broader mutation detection but has limitations in identifying specific resistance mutations like T790M.
- The choice of method depends on the specific EGFR mutations of clinical interest, particularly for resistance monitoring.
