Comprehensive Analysis of Next-Generation Sequencing and ARMS-PCR for Detecting EGFR S768 Mutations in Chinese Non-Small Cell Lung Cancer Patients

Background: Accurate detection of mutations at the EGFR S768 site is crucial for selecting appropriate treatment regimens for patients with non-small cell lung cancer (NSCLC). This study compared Next-Generation Sequencing (NGS) and amplification refractory mutation system polymerase chain reaction (ARMS-PCR) for detecting EGFR S768 mutations in Chinese NSCLC patients. Methods: This study retrospectively analyzed 20,731 molecular pathology tests (8345 by NGS and 12,386 by ARMS-PCR). Results: The detection rate of EGFR S768 variants was significantly lower by ARMS-PCR than by NGS (0.40% vs. 1.15%, p < 0.001). The variants detected by ARMS-PCR were predominantly S768I, whereas NGS identified a broader spectrum, including S768I, S768_D770dup, S768_V769delinsIL, and S768_V769insLDS. Furthermore, the EGFR S768I mutation frequently co-occurred with other EGFR mutations, while insertion mutations at or near the EGFR S768 site rarely coexisted with other EGFR mutations (95.08% vs. 3.03%, p < 0.001). Notably, three cases with S768_V769delinsIL or V769_D770insSVV detected by NGS were identified as S768I by ARMS-PCR, which potentially affected the selection of patients’ treatment plans. The sequence variations such as c.2307_2308insAGCGTGGTG, c.2303_2305delinsTCT, and c.2303_2305delinsTTT may be the reasons for the inconsistency between ARMS-PCR and NGS, due to possible non-specific primer binding. However, this remains a hypothesis based on sequence comparison and required further experimental validation. Conclusions: Complex mutations or insertions around EGFR S768 site may cause discordant results between ARMS-PCR and NGS. NGS was recommended to confirm the EGFR S768 variants when the patient experiences rapid disease progression during treatment with EGFR S768I-directed targeted therapy.