Abstract 5246: Noninvasive detection of MET gene amplification in the circulation of cancer patients

Abstract

Abstract The detection of tumor specific genomic alterations in circulating tumor DNA (ctDNA) has largely centered on point mutations. The identification of tumor-derived structural changes including rearrangements and amplifications has been more challenging. Approaches that analyze allelic imbalance are often not sufficiently specific to accurately define such events for solid tumor malignancies that shed low levels of DNA. Since some of the most robust clinical responses to targeted therapies have been those directed at gene products from amplified loci, we developed a method to detect such changes in a highly specific manner. One of the most attractive therapeutic targets in oncology is currently the MET/HGF pathway, which is activated as a result of gene amplification of the MET tyrosine kinase receptor. This pathway can be activated de novo or as a mechanism of acquired resistance to EGFR inhibition in a variety of cancers. We have developed an assay, termed METDetect, to capture and sequence the genomic regions corresponding to the MET gene, including coding and non-coding loci as well as control regions. Sequencing of these regions resulted an average of 33Gb of sequence data at a coverage of 3,125-fold per analyzed base. Validation analyses showed that amplification associated rearrangements resulting from focal amplification of the MET gene were readily detected to a level of 0.25% mutant DNA molecules while these were not present in tumors or ctDNA without such alterations. We applied METDetect to 205 plasma samples from patients with gastric, lung and esophageal cancer. MET amplification was also evaluated through either FISH or next-generation sequence approaches, and ranged from 2.2-fold to 30-fold in the tissue of patients with MET amplification. A concordance of >90% was achieved when MET amplification in plasma DNA was compared to MET amplification status in matched tumor tissue. We detected between 1 and 86 rearrangements associated with MET amplification in the plasma and calculated the global MET copy number to be 1.0-10.0 fold (average 2.2-fold) for each amplified case. Finally, no MET amplification associated rearrangements or amplified copy number results were noted in plasma samples from 19 patients whose tumors did not harbor MET amplification. METDetect is a noninvasive, ctDNA-based assay with high precision and accuracy for the detection of MET amplification in patients with cancer. Citation Format: Mark Sausen, Samuel V. Angiuoli, Bryan Chesnick, Kevin Galens, Siân Jones, Maura Kadan, Lisa Kann, Karli Lytle, Derek Murphy, Monica Nesselbush, Sonya Parpart-Li, David Riley, Manish Shukla, Theresa Zhang, Victor E. Velculescu, Luis A. Diaz. Noninvasive detection of MET gene amplification in the circulation of cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5246. doi:10.1158/1538-7445.AM2015-5246