Allele-specific PCR method for identification of EGFR mutations in non-small cell lung cancer: formalin-fixed...

The study of epidermal growth factor receptor (EGFR) gene mutations in lung adenocarcinoma patients has a special clinical significance in the selection of patients for tyrosine-kinase inhibitor therapy. The aim of this study was to identify patients with EGFR mutations using allele-specific polymerase chain reaction (PCR), from formalin-fixed paraffin-embedded (FFPE) tissue and fresh tissue (FT).

We performed a retrospective study using 13 cases of FFPE lung adenocarcinoma, and a prospective study using seven fresh samples of lung carcinomas (FT), collected by intraoperative dissection of the tumors. Using the DNA extracted from the FFPE tissue and FT, we attempted to identify deletions of exon 19 and point mutations of exon 21, according to the allele-specific PCR method described by Dahse et al. (2008).

In all seven cases of FT (three adenocarcinomas, three squamous carcinomas, one large-cell carcinoma), we identified the wild type allele and the internal control in case of exon 19, and the wild type allele for exon 21, but not the mutated alleles. Considering that no standard method for formalin fixation and paraffin embedding has been implemented at the Laboratory of Pathology, the DNA extracted from these samples became fragmented and damaged, which compromised the results of PCR testing aimed at the detection of EGFR mutations.

The presented method can be implemented at our laboratory to identify these mutations from fresh tissue collected during surgical resection. Additionally, standardization of formalin fixation and paraffin embedding of surgical samples is required, in order the enable subsequent processing using molecular biology methods.