Comparison of three methods for detecting epidermal growth factor receptor mutations in plasma DNA samples of Chinese
Ling Qin1, Wei Zhong, Li Zhang
1Department of Internal Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
Background:
Epidermal growth factor receptor (EGFR) mutations can predict tumor response to tyrosine kinase inhibitors (TKIs). Detecting EGFR mutations in plasma DNA samples in patients with advanced non-small cell lung cancer is challenging and promising. We compared three methods for detecting plasma EGFR mutations, including direct DNA sequencing, denaturing high-performance liquid chromatography (DHPLC) and Scorpions Amplification Refractory Mutation System (Scorpions ARMS).
Methods:
Plasma DNA samples from 73 patients with stage IIIB to IV adenocarcinoma were analyzed for EGFR mutations in exons 19 (deletion mutation) and 21 (L858R mutation) using direct DNA sequencing, DHPLC and Scorpions ARMS. Sensitivities of the three methods were compared and the relationship between EGFR mutations and patients' survival was analyzed.
Results:
In 73 patients, we detected EGFR mutations in 5 samples (6.9%) by direct DNA sequencing, in 22 samples (30.1%) by DHPLC, and in 28 samples (38.4%) by Scorpions ARMS. EGFR mutations were found in 13 samples in exon 19 and in 9 samples in exon 21 by DHPLC, while we found mutations in 15 samples in exon 19 and in 13 samples in exon 21 by Scorpions ARMS. Among the 73 patients, there was 90.4% concordance between DHPLC and Scorpions ARMS (66/73, κ = 0.79, P = 0.07). Of the 73 patients, 46 patients were treated with gefitinib, including 18 patients with mutations and 28 patients without mutations as determined by Scorpions ARMS. The 18 patients with mutations had a significantly longer progression-free survival (PFS) time (median PFS was 21.0 months) than the 28 patients without mutations (median PFS was 7.0 months) (P = 0.022).
Conclusions:
Among the three methods for detecting EGFR mutations in plasma DNA samples of patients with advanced lung adenocarcinoma, direct gene sequencing had the lowest sensitivity, while Scorpion ARMS showed the highest mutation detecting capability. DHPLC is slightly less sensitive than Scorpion ARMS. EGFR mutations in exons 19 (deletion mutation) and 21 (L858R mutation) predict a longer PFS.
Insights
Scorpion ARMS is the most sensitive method for detecting EGFR mutations in plasma DNA, outperforming direct sequencing and DHPLC. Detecting these mutations, particularly in exons 19 and 21, predicts longer progression-free survival in lung cancer patients treated with gefitinib.
Area of Science:
- Molecular diagnostics
- Oncology
- Genetics
Background:
- Epidermal growth factor receptor (EGFR) mutations are key biomarkers for predicting response to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC).
- Detecting EGFR mutations in circulating tumor DNA (ctDNA) from plasma samples presents a minimally invasive yet challenging approach for advanced NSCLC patients.
Purpose of the Study:
- To compare the sensitivity and concordance of three distinct methods for detecting plasma EGFR mutations: direct DNA sequencing, denaturing high-performance liquid chromatography (DHPLC), and Scorpions Amplification Refractory Mutation System (Scorpions ARMS).
- To analyze the correlation between identified EGFR mutations and patient survival outcomes, specifically progression-free survival (PFS).
Main Methods:
- Plasma DNA from 73 patients with stage IIIB-IV lung adenocarcinoma was analyzed for EGFR mutations in exons 19 and 21.
- Direct DNA sequencing, DHPLC, and Scorpions ARMS were employed to detect mutations.
- Statistical analysis was performed to compare method sensitivities, concordance, and the relationship between mutations and PFS.
Main Results:
- Scorpions ARMS detected mutations in 38.4% of samples, DHPLC in 30.1%, and direct sequencing in only 6.9%.
- High concordance (90.4%) was observed between DHPLC and Scorpions ARMS.
- Patients with EGFR mutations (detected by Scorpions ARMS) treated with gefitinib exhibited significantly longer median PFS (21.0 months) compared to those without mutations (7.0 months).
Conclusions:
- Scorpions ARMS demonstrated the highest sensitivity for detecting plasma EGFR mutations, followed by DHPLC, with direct sequencing being the least sensitive.
- EGFR mutations in exons 19 and 21 are significant predictors of improved progression-free survival in advanced lung adenocarcinoma patients receiving gefitinib therapy.