Evaluation of digital PCR for detecting low-level EGFR mutations in advanced lung adenocarcinoma patients: a cross-platform comparison study

Jincui Gu,Yanbin Zhou,Lei Li,Guanhua Rao,Bing Liu,Shaoli Li,Wanchun Zang,Yang Yu,Lixia Huang

doi:10.18632/oncotarget.18866

Abstract

Emerging evidence has indicated that circulating tumor DNA (ctDNA) from plasma could be used to analyze EGFR mutation status for NSCLC patients; however, due to the low level of ctDNA in plasma, highly sensitive approaches are required to detect low frequency mutations. In addition, the cutoff for the mutation abundance that can be detected in tumor tissue but cannot be detected in matched ctDNA is still unknown. To assess a highly sensitive method, we evaluated the use of digital PCR in the detection of EGFR mutations in tumor tissue from 47 advanced lung adenocarcinoma patients through comparison with NGS and ARMS. We determined the degree of concordance between tumor tissue DNA and paired ctDNA and analyzed the mutation abundance relationship between them. Digital PCR and Proton had a high sensitivity (96.00% vs. 100%) compared with that of ARMS in the detection of mutations in tumor tissue. Digital PCR outperformed Proton in identifying more low abundance mutations. The ctDNA detection rate of digital PCR was 87.50% in paired tumor tissue with a mutation abundance above 5% and 7.59% in paired tumor tissue with a mutation abundance below 5%. When the DNA mutation abundance of tumor tissue was above 3.81%, it could identify mutations in paired ctDNA with a high sensitivity. Digital PCR will help identify alternative methods for detecting low abundance mutations in tumor tissue DNA and plasma ctDNA.

Highlights

epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (EGFR EGFR tyrosine kinase inhibitors (TKIs)) therapies have shown to be of great benefit to nonsmall cell lung cancer (NSCLC) patients harboring EGFR activating mutations, such as L858R and exon 19 deletions [1, 2]
We have demonstrated that digital polymerase chain reaction (PCR) is a low detection limit method for detecting low abundance mutations in tumor tissue and circulating tumor DNA (ctDNA) based on the following results: (1) digital PCR had a higher detection rate of EGFR mutations than amplification refractory mutation system (ARMS) PCR or Proton, (2) digital PCR outperformed Proton in the detection of low abundance mutations, and (3) ctDNA mutations detected by digital PCR had a high rate of concordance with tumor tissue mutations detected by ARMS PCR
We have shown that the use of digital PCR can achieve a high sensitivity for identifying mutations in ctDNA when the mutation abundance in paired tumor tissue DNA is above 3.81%

Summary

Introduction

EGFR tyrosine kinase inhibitor (EGFR TKI) therapies have shown to be of great benefit to nonsmall cell lung cancer (NSCLC) patients harboring EGFR activating mutations, such as L858R and exon 19 deletions [1, 2]. Since the third generation EGFI-TKI AZD9291 (Osimertinib) is highly effective in NSCLC patients with EGFR T790M mutation and has been approved by the US FDA [6, 7, 8], it is recommended that tumor tissue biopsy results be obtained to assess EGFR mutation status so that those patients can receive the appropriate treatment. Tumor biopsy is usually used as the gold standard for detecting gene mutation. It might not supply a sufficient amount of tumor tissue for mutation analysis, and invasive intervention may be risky and discomforting for patients, especially in those who need www.impactjournals.com/oncotarget Number (%). A highly sensitive method with a low detection limit is required to provide precise and valuable mutation information for clinical decision-making [17]

Methods

Results

Conclusion