Abstract: Background and purpose: BEAMing droplet digital PCR (ddPCR) is considered to be a highly sensitive method for gene mutation detection. We aimed to explore the difference in sensitivity between BEAMing ddPCR and super amplification refractory mutation system (Super ARMS) in detecting circulating tumor DNA (ctDNA) of epidermal growth factor receptor (EGFR) gene mutation in non-small cell lung cancer (NSCLC) patients with EGFR tyrosine kinase inhibitor (TKI) treatment, and to provide guidance on selecting methods for clinical application. Methods: Thirty-three plasma samples were collected from NSCLC patients who had received EGFR TKI treatment at Fudan University Shanghai Cancer Center from 2017 to 2018. A total of 10 artificial plasma samples were received from Department of National Pathology Quality Control Center (PQCC). Extracted circulating free DNA (cfDNA) was analyzed by ddPCR and Super ARMS. Results: The positive rates of ctDNA EGFR gene mutations of 19 del, T790M and L858R detected by ddPCR and Super ARMS in 33 NSCLC patients were 27.3% vs 27.3% (P=1.00), 42.4% vs 27.3% (P=0.23) and 27.3% vs 27.3% (P=1.00), respectively. The results of 10 PQCC samples showed that ddPCR was more accurate than Super ARMS in detecting EGFR T790M (P=0.01). The detected mutant abundance ranged from 0.04% and 0.05% to 7.66% for ddPCR and Super ARMS respectively. The average mutant abundance of 11 cases of T790M detected by ddPCR only was 0.19%, which was significantly different from that of 10 T790M positive samples detected by Super ARMS (1.73%, P=0.03). The distribution of T790M mutant abundance in the range of 0.01%-0.20%, 0.20%-1.00% and >1% was 42.9%, 14.2% and 42.9%, respectively. Conclusion: BEAMing ddPCR is more sensitive than Super ARMS in detecting lower frequency EGFR T790M gene mutation in NSCLC patients with EGFR TKI treatment.

Key words: Circulating tumor DNA, T790M, BEAMing droplet digital PCR