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Updated: May 27, 2026
Ultra-Fast Amplicon-Based Next-Generation Sequencing in Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Implementing multiplexed genotyping of non-small-cell lung cancers into routine clinical practice
L V Sequist1, R S Heist1, A T Shaw1
1Massachusetts General Hospital Cancer Center, Boston; Harvard Medical School, Boston.
Background:
Personalizing non-small-cell lung cancer (NSCLC) therapy toward oncogene addicted pathway inhibition is effective. Hence, the ability to determine a more comprehensive genotype for each case is becoming essential to optimal cancer care.
Methods:
We developed a multiplexed PCR-based assay (SNaPshot) to simultaneously identify >50 mutations in several key NSCLC genes. SNaPshot and FISH for ALK translocations were integrated into routine practice as Clinical Laboratory Improvement Amendments-certified tests. Here, we present analyses of the first 589 patients referred for genotyping.
Results:
Pathologic prescreening identified 552 (95%) tumors with sufficient tissue for SNaPshot; 51% had ≥1 mutation identified, most commonly in KRAS (24%), EGFR (13%), PIK3CA (4%) and translocations involving ALK (5%). Unanticipated mutations were observed at lower frequencies in IDH and β-catenin. We observed several associations between genotypes and clinical characteristics, including increased PIK3CA mutations in squamous cell cancers. Genotyping distinguished multiple primary cancers from metastatic disease and steered 78 (22%) of the 353 patients with advanced disease toward a genotype-directed targeted therapy.
Conclusions:
Broad genotyping can be efficiently incorporated into an NSCLC clinic and has great utility in influencing treatment decisions and directing patients toward relevant clinical trials. As more targeted therapies are developed, such multiplexed molecular testing will become a standard part of practice.
Insights
Comprehensive genotyping for non-small-cell lung cancer (NSCLC) efficiently identifies actionable mutations. This molecular testing guides targeted therapy and clinical trial enrollment, improving patient care.
Area of Science:
- Oncology
- Molecular Diagnostics
- Genetics
Background:
- Personalized therapy for non-small-cell lung cancer (NSCLC) relies on targeting oncogene-addicted pathways.
- Comprehensive genetic profiling is crucial for optimizing NSCLC treatment strategies.
Purpose of the Study:
- To evaluate the utility of a multiplexed PCR-based assay for comprehensive genotyping in NSCLC.
- To assess the impact of broad molecular testing on clinical decision-making and targeted therapy selection.
Main Methods:
- Development and implementation of a SNaPshot assay for simultaneous detection of >50 mutations in key NSCLC genes.
- Integration of SNaPshot and FISH for ALK translocations into routine clinical practice.
- Analysis of genotyping results from the first 589 NSCLC patients.
Main Results:
- Pathologic prescreening confirmed tissue adequacy in 95% of cases.
- Over 51% of patients harbored at least one actionable mutation, with KRAS, EGFR, PIK3CA, and ALK translocations being most frequent.
- Genotyping identified associations between mutations and clinical characteristics, and guided targeted therapy for 22% of advanced NSCLC patients.
Conclusions:
- Broad genotyping assays can be efficiently integrated into NSCLC clinical practice.
- Multiplexed molecular testing significantly influences treatment decisions and directs patients to appropriate therapies and clinical trials.
- As targeted therapies advance, comprehensive genotyping will become a standard component of NSCLC care.
