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Annals of Clinical & Laboratory Science 32:219-224 (2002)
© 2002 Association of Clinical Scientists

TaqMan Junction Probes and the Reverse Transcriptase Polymerase Chain Reaction: Detection of Alveolar Rhabdomyosarcoma, Synovial Sarcoma, and Desmoplastic Small Round Cell Tumor

Thomas J. Cummings, Nicholas M. Brown and Timothy T. Stenzel
Department of Pathology, Duke University Medical Center, Durham, North Carolina

Address correspondence to: Thomas J. Cummings, M.D., Duke University Medical Center, Department of Pathology, Box 3712, Durham, NC, USA 27710; tel 919 684 6592; fax 919 681 7634; e-mail: cummi008{at}mc.duke.edu.

The reverse transcriptase polymerase chain reaction (RT-PCR) provides a technique to diagnose a group of sarcomas and small round cell tumors that contain specific chromosomal translocations and chimeric gene fusion products. We adapted real-time qualitative RT-PCR to utilize dual-labeled, fluorogenic, TaqMan probes, which hybridize to targets that overlap the junction of the chimeric gene fusions in alveolar rhabdomyosarcoma (ARMS), synovial sarcoma (SS), and desmoplastic small round cell tumor (DSRCT). Assays were confirmed on cell lines and tissue samples; appropriate negative amplification assays were obtained when each tumor-specific probe and primer set was used on different neoplasms and cell lines that were not expected to harbor the specific translocations and chimeric gene fusions. Although our cases are few, we speculate that as more molecular variants of ARMS, SS, and DSRCT are discovered, clinical correlations based on precise molecular features will be required and fusion site specificity will be assured by the use of junction-based TaqMan probes.

Keywords: RT-PCR, TaqMan junction probes, chromosomal translocations, chimeric gene fusion products






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