Recommended NGS Panel for Lung Cancer
For advanced non-squamous non-small cell lung cancer (NSCLC), a comprehensive NGS panel should include DNA sequencing for EGFR (complete exons 18-21), KRAS (including G12C), BRAF (V600E), HER2 (exon 20 insertions), MET (exon 14 skipping and amplification), PIK3CA, and TP53, combined with RNA-based NGS for fusion detection in ALK, ROS1, RET, NTRK1-3, and NRG1. 1
Essential DNA Targets (Mutations and Amplifications)
EGFR mutations require complete sequencing of exons 18-21 by NGS to identify all sensitizing mutations, not just the common exon 19 deletions and L858R mutations, as other mutations in exon 18 variably sensitize while some confer resistance. 1 Allele-specific EGFR sequencing solutions that don't provide complete coverage should be avoided. 1
KRAS G12C mutations must be included as specific inhibitors are now available for this smoking-related target. 1
BRAF V600E mutations should be tested as TKIs are available for this target. 1
HER2 exon 20 insertion mutations need coverage as promising targeted drugs and antibody-drug conjugates are in development. 1
MET alterations require dual detection capability:
- DNA-based NGS for exon 14 skipping mutations 1
- Copy number analysis for MET amplification, which is an important resistance mechanism to EGFR and ALK inhibitors 1
TP53 comutations should be assessed as they may be associated with lower efficacy of EGFR, ALK, and ROS1 TKIs. 1
Essential RNA Targets (Gene Fusions)
RNA-based NGS is strongly preferred over DNA-based methods for fusion detection as it can identify an expanding range of fusion genes and may detect additional MET exon 14 skipping cases missed by DNA sequencing. 1
The panel must include:
- ALK fusions (though positive IHC with validated assay may be used to prescribe ALK inhibitors, molecular confirmation is preferred) 1
- ROS1 fusions (IHC-positive cases must be confirmed by molecular method) 1
- RET fusions (multiple TKIs available) 1
- NTRK1-3 fusions (if NGS is the primary screening tool, IHC confirmation should be considered) 1
- NRG1 fusions (emerging target) 1
Patient Population for Testing
All patients with advanced non-squamous NSCLC should undergo comprehensive NGS testing. 1
Squamous cell carcinoma patients should NOT routinely undergo testing except in unusual cases including: 1
- Age <50 years
- Never smokers (<100 cigarettes lifetime) or former light smokers (≤15 pack-years)
- Long-time ex-smokers (quit >15 years ago)
Critical Implementation Considerations
Avoid sequential single-gene testing as it depletes scarce tissue material and misses potentially actionable targets. 1 NGS testing identifies significantly more actionable alterations—studies show 31% of adenocarcinomas wild-type by limited panels had actionable variants detected by broader NGS. 2
The panel must have adequate technical specifications:
- Sensitivity of ≥1% variant allele frequency for mutations 1
- Complete coverage of all specified exons, not just hotspots 1
- Validated bioinformatics pipelines for accurate variant calling 1
Turnaround time is critical—results must be available before first-line therapy initiation to guide treatment decisions. 1
Resistance Testing at Disease Progression
At progression on targeted therapy, repeat molecular testing is essential to identify resistance mechanisms, either through re-biopsy or cell-free DNA (cfDNA) testing. 1 While osimertinib use has decreased the importance of EGFR T790M detection, identifying MET amplification as a resistance mechanism has become increasingly important. 1
Advantages Over Limited Panels
Real-world data demonstrates that NGS testing results in only 10% potentially missed targeted therapy options compared to 40.2% with non-NGS approaches. 3 When only non-NGS testing was used, BRAF and ROS1 were tested in only 56.1% and 83.7% of cases respectively, compared to ≥92% with NGS. 3
Unsuccessful genotyping occurs in only 13.2% of NGS-tested patients versus 52.2% with non-NGS methods, making comprehensive NGS the most efficient approach. 3