Genomic rearrangements are a defining feature of cancer, and can lead to gene fusions and chimeric transcripts with respective fusion proteins that have oncogenic properties. The fusion transcripts can have diagnostic, prognostic and therapeutic implications. However, the fusion partners and the exact breakpoints vary from patient to patient and from cancer type to another. This can result in significant sequence variation, and together with the large number of potential genes able to participate in fusion events makes reliable detection of fusion events challenging for many traditional methods. The TRAC (Transcript Analysis with aid of Affinity Capture) method solves a number of these issues by a combination of specific capture and detection probes. By capturing all known 5’ fusion partners and detecting potential 3’ partners for a given cancer type, only a very limited set of positive signals are detected from an individual sample, enabling high-level of multiplexing. In practice, dozens of different fusion events can be detected per sample by using an easily modifiable pool of capture/detection probes. This effectively enables detection of all known fusion types in sarcomas from one sample without the prerequisite of knowing the exact cancer type. TRAC is a direct hybridization based assay that enables rapid quantification of multiple mRNA targets simultaneously from large number of samples. Transcript levels can be measured directly from cell or tissue lysates without the need for RNA extraction, cDNA conversion or PCR-amplification. The TRAC protocol is straightforward and enables sample analysis in a high-throughput format with little hands-on time. In this analysis, TRAC was used to detect the fusion transcripts COL1A1-PDGFB, FUS-DDIT3, and SS18-SSX1/2 from three types of sarcoma tissue biopsies. All fusion types were detected for the respective targets. In addition, twenty Ewing sarcoma cell lines were analyzed for the EWSR1-FLI1 fusion, identifying 12 cell lines positive for the chimeric transcript. Sarcoma tissue lysate was found applicable for direct TRAC analysis. These results demonstrate that the TRAC Fusion Transcript Assay is functional and capable of discriminating sarcomas based on fusion transcript expression. The assay is easy to set up and it can be run using standard laboratory equipment with little hands-on time.

Citation Format: Laura Mattinen, Jari Rautio, Jani Salmivaara, jussi Halleen, Marko Sirkiä. Gene fusion detection in sarcoma using TRAC technology. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3629.