A sensitive method for detection of EGFR gene mutations in plasma

Abstract

18027 Background: Somatic mutations in the tyrosine kinase (TK) domain of the EGFR gene are associated with clinical response to TK inhibitors in patients with non-small cell lung cancer. An assay that detects such mutations in the plasma would provide a noninvasive technique to assess suitability for TK inhibitor therapy. Here we describe: 1) the development of a sensitive assay to detect the E746-A750 deletion in the TK domain of EGFR in plasma; and 2) optimization of the method for plasma DNA extraction. Methods: Our assay uses Mse I to specifically digest wild-type (WT) genomic DNA (gDNA) to reduce non-specific amplification. After digestion, samples are PCR- amplified using 1 unlabeled primer and 1 FAM-labeled primer spanning the E746-A750 deletion region and fluorescence detected with an automated analyzer. Serial dilution studies were conducted using H1650 gDNA (del E746-A750 cell line) diluted in WT gDNA after Mse I digestion. To assess detection of the deletion in plasma, 3–4 mL whole blood was spiked with 1–37 ng H1650 gDNA; gDNA from the separated plasma was then extracted (silica column/2-propanol precipitation), digested with Mse I, and amplified as above. Several extraction methods were evaluated using pooled plasma samples and PBS spiked with 10–350 ng gDNA: silica column, magnetic bead, phenol:chloroform, and 2-propanol precipitation. Results: Digestion of the WT EGFR allele followed by deletion-specific fluorescent PCR allowed detection of caof ca. 1 copy of the del E746-A750 EGFR gene (10 pg gDNA) diluted to 0.001%. Furthermore, del E746-A750 was successfully detected in 1/5 the final DNA volume (5 μl) in all spiked blood samples. Magnetic bead-based DNA extraction yielded the highest percent recovery of gDNA from PBS (69% recovery of the 10-ng sample). Phenol:chloroform extraction gave the highest yield with pooled plasma samples. Conclusions: The combination of an optimized DNA extraction method, clearing the plasma DNA sample of amplifiable WT DNA by restriction digestion, and mutation-specific fluorescent PCR provides a highly sensitive assay for detection of somatic mutations in plasma. No significant financial relationships to disclose.