My primary research interest is the development of molecular techniques to diagnose soft tissue sarcomas and solid tumors. The reverse transcriptase polymerase chain reaction (RT-PCR) has been an instrumental technique to diagnose a group of sarcomas and small round cell tumors that appear to contain specific chromosomal translocations and chimeric gene fusion products. In our molecular diagnostics laboratory, in collaboration with Timothy Stenzel M.D., Ph.D., we adapted real-time qualitative RT-PCR to utilize dual-labeled, fluorogenic, TaqMan probes that hybridize to targets that overlap the junction of the chimeric gene fusions for the following neoplasms: Ewing's sarcoma (EWS), alveolar rhabdomyosarcoma (ARMS), synovial sarcoma (SS), and desmoplastic small round cell tumor (DSRCT). This rapid, accurate, cost-saving, and reproducible method ensures high-specificity of PCR product accumulation, thus obviating the need for post-PCR sample analysis by Southern blot, sequencing, or hybridization, and potential post-PCR product contamination. We propose that junctional probe specificity will enhance efforts to classify and correlate the precise molecular profile with the clinical behavior of these neoplasms. As more of these neoplasms are studied by molecular techniques, clinical correlation based on precise molecular features will be required and specific confirmation can be assured by use of junction-based TaqMan probes. Our design utilizes identical reaction conditions for each assay and permits multiplex analysis.
