Total DNA input is a crucial determinant of the sensitivity of plasma cell-free DNA EGFR mutation detection using droplet digital PCR

Abstract

// Yu Zhang 1,* , Yan Xu 1,* , Wei Zhong 1,* , Jing Zhao 1 , Minjiang Chen 1 , Li Zhang 1 , Longyun Li 1 and Mengzhao Wang 1 1 Department of Respiratory Medicine, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China * These authors have contributed equally to this study Correspondence to: Mengzhao Wang, email: // Keywords : plasma cell-free DNA; droplet digital PCR; DNA concentration; epidermal growth factor receptor; advanced non-small cell lung cancer Received : May 26, 2016 Accepted : December 16, 2016 Published : December 30, 2016 Abstract We evaluated the use of droplet digital PCR (ddPCR) to detect plasma cell-free DNA (cfDNA) epidermal growth factor receptor (EGFR) mutations in advanced non-small cell lung cancer (NSCLC) patients. Compared with tumor-tissue-based detection, the sensitivity of ddPCR for detecting plasma cfDNA tyrosine kinase inhibitor (TKI)-sensitizing EGFR mutations was 61.3%, the specificity was 96.7%, and the consistency rate was 81.4% ( κ =0.605, 95% confidence interval: 0.501-0.706, p <0.0001). The sensitivity declined from 82.6% to 46.7% with decreasing cfDNA inputs ( p =0.028). The plasma cfDNA concentration correlated with gender (males vs. females =11.69 ng/mL vs. 9.508 ng/mL; p =0.044), EGFR mutation status (tumor-tissue EGFR mutation-positive (EGFR M+) vs. EGFR mutation-negative (EGFR M-) = 9.61 ng/mL vs. 12.82 ng/mL; p =0.049) and specimen collection time (≤2 years vs. >2 years=13.83 ng/mL vs. 6.575 ng/mL; p <0.001), and was greater in tumor-tissue EGFR M+ / plasma EGFR M+ patients than in tumor-tissue EGFR M+/plasma EGFR M- patients (11.61 vs. 7.73 ng/mL, respectively; p =0.003). Thus total cfDNA input crucially influences the sensitivity of plasma cfDNA EGFR mutation testing with ddPCR. Such analysis could be an effective supplemental test for advanced NSCLC patients.