Abstract CN02-02: Comprehensive detection of structural alterations in the circulation of cancer patients
Authors: Sausen Mark 
Published: May 2016

Cancer is a genetic disease resulting from the accumulation of genetic alterations which initiate and promote uncontrolled cellular growth and invasion. These genetic alterations are the targets of approved therapies that preferentially inhibit tumor cells while limiting damage to normal cells. Liquid biopsies of circulating tumor DNA (ctDNA) offer a considerable advantage for analyses of cancer patients as they allow for the detection of alterations in multiple metastatic lesions throughout the course of therapy. However, the detection of tumor specific genomic alterations in ctDNA has largely centered on point mutations. The identification of tumor-derived structural changes including gene fusions and amplifications has been 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 many clinical responses to targeted therapies have been those directed at gene products from amplified loci, as well as those involved in activating translocations, we developed digital genomic approaches to detect such changes in a highly specific manner. These include amplification of the MET and ERBB2 tyrosine kinases as well as translocation of the ALK and ROS1 tyrosine kinases.

Development of the METDetect assay to capture and sequence the genomic regions corresponding to the MET gene, including coding and non-coding loci as well as control regions yielded an average of 33Gb of sequence data at a coverage of 3,125-fold per analyzed base when applied to 205 plasma samples from a variety of cancer patients, including gastric, lung and others. Analytical validation analyses showed that amplification-associated rearrangements resulting from focal amplification of the MET gene were readily detected to a level of 0.10% mutant DNA molecules while these were not present in tumors or cell-free DNA without such alterations. MET amplification was also evaluated in the tissue of patients with MET amplification through either FISH or next-generation sequence approaches, and ranged from 2.2-fold to 30-fold. A concordance of &gt;90% was achieved when MET amplification in plasma DNA was compared to MET amplification status in matched tumor tissue. No MET amplification associated rearrangements or amplified copy number results were observed in plasma samples from 19 patients whose tumors did not harbor MET amplification. Extension of these noninvasive approaches to clinically actionable 63 gene and 9 gene panels demonstrated that ERBB2 amplification, as well as ALK and ROS1 translocation were detectable with a lower limit of detection of 0.20% and 0.10% in the plasma of patients with breast and lung cancers, respectively. Taken together, these data indicate that structural alterations, including amplifications and translocations, can be readily identified using noninvasive approaches in the circulation of cancer patients.

Citation Format: Mark Sausen. Comprehensive detection of structural alterations in the circulation of cancer patients. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr CN02-02.