Abstract
Liquid biopsy using cell-free DNA (cfDNA) has emerged as a minimally invasive alternative to tissue biopsy for monitoring resistance mutations in non-small cell lung cancer (NSCLC). This study presents a comparative evaluation of Next-Generation Sequencing (NGS) and Droplet Digital PCR (ddPCR) for detecting the epidermal growth factor receptor (EGFR) T790M gatekeeper mutation in plasma cfDNA. We analyzed blood samples from 114 NSCLC patients who progressed on first- or second-generation EGFR tyrosine kinase inhibitors (TKIs). Out of 114 patients, ddPCR detected the T790M mutation in 48 cases (42.1%), whereas NGS detected it in 41 cases (35.9%). Using tissue biopsy as the reference standard where available (n=62), ddPCR demonstrated a sensitivity of 81.3% and specificity of 90.0%, while NGS exhibited a sensitivity of 71.9% and specificity of 96.7%. The limit of detection (LOD) was lower for ddPCR (0.1% mutant allele fraction [MAF]) compared to NGS (0.5% MAF). However, NGS provided valuable concurrent genomic profiling, identifying additional resistance mechanisms such as MET amplification and PIK3CA mutations in 14 patients. Our findings indicate that while ddPCR is superior in sensitivity and speed for targeted T790M screening, NGS offers a broader diagnostic scope that is crucial for characterizing heterogeneous resistance profiles. A complementary testing workflow is proposed to optimize clinical decision-making.
