Comparative analysis of EGFR mutations between circulating tumor DNA and tissue samples in non-small cell lung carcinoma patients using BEAMing PCR: results of a single institutional observational study

In this study we measured the human epidermal growth factor receptor (EGFR) mutations in both tissue and circulating tumor DNA (ctDNA) by using beads, emulsion, amplification and magnetics polymerase chain reaction (BEAMing PCR). Noninvasive mutation detection by assessing circulating tumor DNA (ctDNA) offers many advantages over tumor biopsy. One hundred non-small cell lung cancer (NSCLC) patients were enrolled and both preoperative plasma samples and formalin-fixed and paraffin embedded (FFPE) samples were collected for the study. EGFR mutation status was determined by BEAMing PCR in ctDNA. Real-time quantitative PCR (qPCR) data were collected from our hospital database (EMR-qPCR, Electronic Medical Records) for comparative analysis. Additionally, qPCR was also done from FFPE tissues using Diatech EGFR qPCR kit. The positive concordance rate was 98.8%, 100% and 95.5% for exon 19, 20 and 21 respectively when BEAMing data were compared with EMR-qPCR data. Additionally, when BEAMing and Diatech qPCR data were compared we obtained 90%, 100%, 96% and 98% respectively for exon 19, 20, 21 (L858R) and 21 (L861Q). For both the comparisons, the value of Cohen’s kappa agreement showed significant results. The advantage of BEAMing is its ability to identify mutated DNA sequence in the cancer cells in the background of normal cell DNA contamination. This could be useful for disease monitoring and progression.