Abstract 4668: A next generation sequencing assay to detect the fusion products of ALK, ROS1 and RET with any fusion partner genes and hotspot mutations in FFPE samples

Targeted drugs have been widely used in the treatment of lung cancer, especially for non small cell lung cancer (NSCLC) patients. NCCN guideline lists multiple drugs which are particularly effective in the subgroup of patients with specific gene mutation variants, including the fusion transcripts of ALK, ROS1 and RET, and the mutations of EGFR, KRAS, BRAF and HER2. Multiple techniques have been developed to detect fusion transcripts in tumor samples, such as FISH, IHC and PCR assays. FISH is the most accurate method for fusion detection currently. The split probe FISH assay, which does not require the pre-knowledge of what is the fusion partner with ALK for example, can detect unknown ALK fusion products as well. However, it fails to identify which gene is fused with ALK (or other oncogene) in the chimera products, therefore is not informative for the mechanism or drug resistance study. In addition, due to the limitation on the fluoresce dye, it is quite difficult to multiplex fusion FISH probes for different genes into one assay. We describe here a next generation sequencing assay to detect a panel of fusion transcripts and mutations in one single assay. Our single assay can detect the fusion products of ALK, ROS1 and RET with any known or unknown fusion partners, together with the hotspot mutations in EGFR, KRAS, BRAF and HER2. Our assay can identify not only the exact sequence of the unknown fusion partners, but also any mutations within the full coding regions of ALK, ROS1 and RET. This information is critical for the resistance mechanism study and the next generation inhibitor drug development, since about half of the ALK inhibitor resistance was caused by the mutations in ALK gene itself. We have identified a novel ALK fusion gene with a never-reported fusion partner in a lung cancer patient. The xenograft model derived from this patient responds to crizotinib well in the in vivo study (published on Journal of Thoracic Oncology). We have demonstrated that our assay can reliably detect both the novel fusion and the well known EML4-ALK fusion from only 1-2 5um FFPE slides of the lung tumor tissues, together with other possible fusions and mutations as well. Note: This abstract was not presented at the meeting. Citation Format: Qiang Xu, Guan Wang, Bo Li, Maoxiang Qian, Douglas Fang, Lele Sun, Yundi Chen, Hongye Sun. A next generation sequencing assay to detect the fusion products of ALK, ROS1 and RET with any fusion partner genes and hotspot mutations in FFPE samples. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4668. doi:10.1158/1538-7445.AM2014-4668