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Updated: Apr 3, 2026
Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Clinical Validation of Targeted Next Generation Sequencing for Colon and Lung Cancers
Nicky D'Haene1, Marie Le Mercier1, Nancy De Nève1
1Department of Pathology, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium.
Objective:
Recently, Next Generation Sequencing (NGS) has begun to supplant other technologies for gene mutation testing that is now required for targeted therapies. However, transfer of NGS technology to clinical daily practice requires validation.
Methods:
We validated the Ion Torrent AmpliSeq Colon and Lung cancer panel interrogating 1850 hotspots in 22 genes using the Ion Torrent Personal Genome Machine. First, we used commercial reference standards that carry mutations at defined allelic frequency (AF). Then, 51 colorectal adenocarcinomas (CRC) and 39 non small cell lung carcinomas (NSCLC) were retrospectively analyzed.
Results:
Sensitivity and accuracy for detecting variants at an AF >4% was 100% for commercial reference standards. Among the 90 cases, 89 (98.9%) were successfully sequenced. Among the 86 samples for which NGS and the reference test were both informative, 83 showed concordant results between NGS and the reference test; i.e. KRAS and BRAF for CRC and EGFR for NSCLC, with the 3 discordant cases each characterized by an AF <10%.
Conclusions:
Overall, the AmpliSeq colon/lung cancer panel was specific and sensitive for mutation analysis of gene panels and can be incorporated into clinical daily practice.
Insights
Next Generation Sequencing (NGS) gene mutation testing is crucial for targeted therapies. The AmpliSeq colon/lung cancer panel demonstrates high sensitivity and specificity, making it suitable for clinical use.
Area of Science:
- Oncology
- Genetics
- Molecular Diagnostics
Background:
- Next Generation Sequencing (NGS) is increasingly used for gene mutation testing, essential for guiding targeted cancer therapies.
- Clinical integration of NGS requires rigorous validation to ensure accuracy and reliability.
Purpose of the Study:
- To validate the Ion Torrent AmpliSeq Colon and Lung cancer panel for clinical application.
- To assess the sensitivity and specificity of the panel in detecting gene mutations relevant to colorectal and lung cancers.
Main Methods:
- Validation using commercial reference standards with known allelic frequencies (AF).
- Retrospective analysis of 51 colorectal adenocarcinomas (CRC) and 39 non-small cell lung carcinomas (NSCLC) using the Ion Torrent Personal Genome Machine.
- Interrogation of 1850 hotspots across 22 cancer-related genes.
Main Results:
- 100% sensitivity and accuracy for variants with AF >4% in reference standards.
- Successful sequencing achieved in 98.9% of 90 clinical samples.
- High concordance (83/86) between NGS panel results and reference tests for key genes (KRAS, BRAF, EGFR), with discordant cases having low AF (<10%).
Conclusions:
- The AmpliSeq colon/lung cancer panel is a specific and sensitive tool for mutation analysis.
- The panel's performance supports its incorporation into routine clinical practice for cancer gene mutation testing.
