Related Experiment Video
Updated: Jan 1, 2026
Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
Evaluation of the Idylla system to detect the EGFRT790M mutation using extracted DNA
Claire Bocciarelli1, Justine Cohen1, Romain Pelletier2
1Assistance Publique-Hôpitaux de Paris, Department of Pathology, Centre Hospitalier Universitaire Henri-Mondor, 94010 Créteil, France.
Introduction:
During the last few years, detection of epidermal growth-factor-receptor (EGFR)-activating mutations has become a routine part of clinical practice because of their importance in choosing the optimal treatment strategy for non-small-cell lung cancers (NSCLCs). The emergence of third-generation EGFR-tyrosine-kinase inhibitors required the implementation of sensitive methods to detect the subclonal EGFRT790M mutation. Clinical implications make it essential to rapidly search for the T790M mutation, which is a real challenge for laboratories. The aim of this study was to compare performances of next-generation sequencing (NGS), one of the most frequently used molecular biology methods, and Idylla EGFR-Mutation Assay (henceforth Idylla), a fully automated real-time polymerase chain reaction (PCR) that is increasingly used in pathology laboratories, to detect the EGFRT790M mutation using DNA.
Methods:
This retrospective study used 47 DNA samples extracted from NSCLC biopsies that previous NGS identified as: 29 harboring EGFR and T790M resistance mutations, 11 EGFR-activating mutation without T790 M and 7 wild-type EGFR. EGFRT790M limit-of-detection (LOD) experiments used a commercial DNA known to harbor that mutation.
Results:
Idylla detected primary EGFR-activating mutations and the T790 M mutation in 97.5 % and 65.5 % of the cases, respectively. The results of this retrospective analysis and LOD experiments showed that the Idylla should only be used to detect EGFR mutations in samples with > 25 ng of DNA and > 10 % tumor cells.
Conclusions:
Idylla was able to rapidly detect EGFR-activating mutations but detecting subclone mutations, like T790M, with < 25 ng of good-quality DNA or < 10 % tumor cells (variant allele frequency below the assay's validated LOD) was not always reliable.
Insights
The Idylla assay rapidly detects EGFR mutations but struggles with the T790M resistance mutation in samples with low DNA or tumor cell content. Next-generation sequencing remains more reliable for detecting subclonal EGFR T790M mutations.
Area of Science:
- Molecular Biology
- Oncology
- Genetics
Background:
- Detection of epidermal growth-factor-receptor (EGFR)-activating mutations is crucial for non-small-cell lung cancer (NSCLC) treatment.
- The emergence of third-generation EGFR-tyrosine-kinase inhibitors necessitates sensitive detection of the EGFR T790M resistance mutation.
- Rapidly and accurately identifying the T790M mutation presents a significant challenge for clinical laboratories.
Purpose of the Study:
- To compare the performance of next-generation sequencing (NGS) and the Idylla EGFR-Mutation Assay for detecting the EGFR T790M mutation in NSCLC DNA samples.
- To evaluate the reliability of the Idylla assay under varying sample quality conditions.
Main Methods:
- A retrospective study analyzed 47 NSCLC DNA samples previously characterized by NGS.
- Samples included varying EGFR mutation statuses: EGFR-activating mutations with T790M, EGFR-activating mutations without T790M, and wild-type EGFR.
- Limit-of-detection (LOD) experiments were performed using commercial DNA harboring the T790M mutation.
Main Results:
- The Idylla assay detected primary EGFR-activating mutations in 97.5% of cases and the T790M mutation in 65.5% of cases.
- LOD experiments and retrospective analysis indicated that Idylla is reliable only for samples with > 25 ng of DNA and > 10% tumor cells.
- The assay showed limitations in detecting T790M mutations in samples with low DNA quantity or low tumor cell percentage.
Conclusions:
- The Idylla assay provides rapid detection of EGFR-activating mutations.
- Detecting subclonal mutations like T790M with Idylla is unreliable when DNA quality is compromised (< 25 ng) or tumor cell percentage is low (< 10%).
- Next-generation sequencing (NGS) remains a more robust method for detecting low-variant allele frequency mutations such as EGFR T790M.
