Abstract C196: EGFR mutation detection in ctDNA isolated from NSCLC patient plasma; a cross-platform comparison of leading technologies.
Authors: Brown Helen , Brant Roz , Dearden Simon , Jenkins Suzanne , Thress Kenneth , Horvais Alain , March Ruth , Barrett J. Carl 
Published: August 2014

Emerging evidence suggests that circulating tumor DNA (ctDNA) provides an alternative diagnostic sample when surgical biopsies are inaccessible, and could enable disease diagnosis, frequent assessment of disease progression, and almost real-time monitoring of the emergence of resistance mutations. We hypothesized that novel highly sensitive technologies enable EGFR T790M mutation detection in ctDNA from patients that had previously been treated with and become resistant to EGFR-TKIs. We have used 3 technologies to assess T790M mutation detection rate. Samples comprised patients with sensitizing EGFR mutations and wild type EGFR patients who had been previously treated with EGFR TKI therapies. In approximately 50% of EGFR mutation positive cases, acquired resistance to EGFR-TKIs is mediated by an EGFR T790M mutation. Reference data for T790M mutations from tumor material was unavailable.We undertook a comprehensive cross-technology comparison of three technology platforms: ARMS based detection using the Roche cobas EGFR mutation detection kit; digital droplet PCR using the BioRad ddPCR instrument (by MolecularMD) and bead based digital PCR using the Inostics BEAMing technology for the detection of T790M mutations. In total, 135 frozen plasma samples, obtained from 2 clinical studies, were used to estimate T790M detection rates in ctDNA. Within the study group, 72 samples were taken from EGFR mutation positive patients, of which around 36 (expected range 28-44) would be expected to have T790M mutations, the remaining samples would be expected to be T790M negative. Each individual patient plasma sample was split and evaluated across multiple platforms. In addition, the suitability of 3 ctDNA preparation kits (cobas Circulating DNA Isolation kit, QIAamp Circulating Nucleic Acid kit and QIAamp DNA Mini kit) in terms of DNA yield was evaluated. The QIAamp Circulating Nucleic Acid kit and cobas Circulating DNA Isolation kit were equally effective in preparing ctDNA from plasma samples. Overall, concordance of EGFR T790M mutation status was high between all 3 methods. In addition, the false positive rate in the known EGFR mutation negative cases was low for all 3 methods. However, differences were seen in the rate of false negative results (assay sensitivity) between methods. DNA preparation kits specifically designed for use with ctDNA samples are preferable to other methods. Current technologies for the detection of T790M mutations in ctDNA, where patient tumor material is not available, still require further development to increase detection rates in these samples.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C196.

Citation Format: Helen Brown, Roz Brant, Simon Dearden, Suzanne Jenkins, Kenneth Thress, Alain Horvais, Ruth March, J. Carl Barrett. EGFR mutation detection in ctDNA isolated from NSCLC patient plasma; a cross-platform comparison of leading technologies. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C196.