10041 Background: Molecular assays for tumor markers have become an important component in diagnosing pediatric sarcomas and small round cell tumors. We developed a multiplex assay to detect 7 common translocations associated with synovial sarcoma (SYT/SSX1, SYT/SSX2), Ewing's sarcoma (EWS/FLI1, EWS/ERG), rhabdomyosarcoma (PAX3/FKHR, PAX7/FKHR), and small round cell desmoplastic tumors (SRCDT) (EWS/WT1). Methods: 27 samples were analyzed with the multiplex assay: 13 formalin-fixed paraffin-embedded tumor samples, 5 fresh frozen tumor samples, 2 commercial RNA samples (SYT/SSX1, SYT/SSX2), 3 cell line samples (EWS/FLI, EWS/ERG, PAX3/FKHR), 1 synthetic control (PAX7/FKHR), and 3 negative controls. After RNA extraction, RT-PCR was performed using the SuperScript III One-Step RT-PCR System with Platinum Taq DNA Polymerase (Invitrogen, Carlsbad, CA). 12 primers were added to a single master mix to amplify all 7 translocations and an internal control; 1 primer from each pair was fluorescently labeled. After RT-PCR, the PCR products were separated on a genetic analyzer and the translocations identified based on the size of the PCR products and their signal intensity. Samples were also analyzed by our current assay (real-time RT-PCR or standard RT-PCR/gel electrophoresis). Results: The results of our current and multiplex assays were positive for all synthetic controls, cell lines, and commercial RNA samples and were concordant for 15/18 tumor samples: 2/7 synovial sarcoma samples were positive for SYT/SSX1 and 3/7 for SYT/SSX2; 2/6 Ewing's sarcoma samples were EWS/FLI1-positive; 1/1 SRCDT sample was EWS/WT1-positive; and 4/4 rhabdomyosarcoma samples were negative. The 3 discordant samples tested negative with our current assay; the new multiplex assay detected EWS/FLI1 in 1 of these and SYT/SSX2 in 2, in agreement with the histological classification. Conclusions: This multiplex assay can detect 7 translocations commonly found in pediatric soft tissue tumors in a single-tube reaction, with increased clinical sensitivity relative to our current methods. No significant financial relationships to disclose.
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