Abstract 1238P
Background
Identifying driver genes is crucial to make clinical decision for patients with non-small cell lung cancer (NSCLC). Except short turnaround time, higher success rate, it is still debating that PCR may cause false negative result due to its limited coverage. This study directly compared the performance of AmoyDx 11-gene PCR and NGS in the detection of known driver gene mutations in Chinese NSCLC patients.
Methods
FFPE samples from a total of 765 Chinese NSCLC patients were collected. The test performance of AmoyDx 11-gene PCR (EGFR, KRAS, ALK, HER2, ROS1, MET, BRAF, NTRK1/ 2/3, and RET) and NGS were compared.
Results
The overall percent agreement (OPA), positive percent agreement (PPA), and negative percent agreement (NPA) between AmoyDx 11-gene PCR and NGS were 98.8%, 99.3%, and 97.1%, respectively (Table). The PPA between the two assays were the same (100.0%) in common drivers (EGFR/KRAS/ALK) and rare drivers, the OPA and NPA were higher in rare drivers (99.5% vs. 99.9% and 98.8% vs. 99.8%) in AmoyDx 11-gene PCR. For rare drivers, concordance between PCR and NGS were shown in HER2 (OPA: 99.7%, PPA: 95.1% and NPA: 100.0%), ROS1 (OPA: 99.9%, PPA: 100.0% and NPA: 99.9%), MET (OPA:99.9%, PPA:96.4% and NPA:100.0%), BRAF and RET (OPA: 100.0%, PPA: 100.0% and NPA: 100.0%), respectively. Most of interestingly, for EGFR exon 20 insertion (EGFR ex20ins), a good concordance rate of 99.6% (PPA: 100.0% and NPA: 99.6%) was achieved. Table: 1238P
Comparison of AmoyDx 11-gene PCR and NGS for detecting known driver genes in NSCLC patients
| NGS (mutant) | NGS (wild) | OPA | PPA | NPA | ||
| Total drivers | PCR (mutant) | 591 | 5 | 98.8% | 99.3% | 97.1% |
| PCR (wild) | 4 | 165 | ||||
| Common drivers | PCR (mutant) | 425 | 4 | 99.5% | 100.0% | 98.8% |
| PCR (wild) | 0 | 336 | ||||
| Rare drivers | PCR (mutant) | 156 | 1 | 99.9% | 100.0% | 99.8% |
| PCR (wild) | 0 | 608 | ||||
| EGFR exon20ins | PCR (mutant) | 24 | 3 | 99.6% | 100.0% | 99.6% |
| PCR (wild) | 0 | 738 | ||||
| HER2 | PCR (mutant) | 39 | 0 | 99.7% | 95.1% | 100.0% |
| PCR (wild) | 2 | 724 | ||||
| ROS1 | PCR (mutant) | 19 | 1 | 99.9% | 100.0% | 99.9% |
| PCR (wild) | 0 | 745 | ||||
| BRAF | PCR (mutant) | 19 | 0 | 100.0% | 100.0% | 100.0% |
| PCR (wild) | 0 | 746 | ||||
| RET | PCR (mutant) | 25 | 0 | 100.0% | 100.0% | 100.0% |
| PCR (wild) | 0 | 740 | ||||
| MET | PCR (mutant) | 27 | 0 | 99.9% | 96.4% | 100.0% |
| PCR (wild) | 1 | 737 |
Conclusions
AmoyDx 11-gene PCR displayed high concordance to NGS in detecting driver mutations of NSCLC, especially rare drivers (EGFR ex20ins), suggesting it is an excellent choice in clinical practice.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Has not received any funding.
Disclosure
M. Li, F. Gai, C. Zhu: Financial Interests, Personal, Full or part-time Employment: Amoy Diagnostics. All other authors have declared no conflicts of interest.
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