DETECTION OF GENE FUSIONS IN RHABDOMYOSARCOMA BY REVERSE TRANSCRIPTASE-POLYMERASE CHAIN-REACTION ASSAY OF ARCHIVAL SAMPLES

Alveolar rhabdomyosarcoma is a pediatric soft-tissue tumor that is oft en difficult to distinguish from other small round-cell tumors. The PA X3-FKHR and PAX7-FKHR gene fusions that result from chromosomal transl ocations in this tumor provide potential molecular diagnostic markers. To apply these molecular markers to commonly available archival mater ial, we used reverse transcriptase-polymerase chain reaction and oligo nucleotide hybridization methodology to develop an assay capable of id entifying PAX3-FKHR and PAX7-FKHR fusion transcripts in formalin-fixed , paraffin-embedded tissue. Use of a control assay for wild-type FKHR mRNA indicated that RNA was successfully isolated, reverse-transcribed , and amplified in 15 of 16 archival cases. Comparison of assay result s for the PAX3-FKHR and PAX7-FKHR fusions with standard molecular assa ys of paired frozen material revealed that all eight cases of known fu sion-positive rhabdomyosarcoma were correctly identified and distingui shed as PAX3-FKHR or PAX7-FKHR. The seven cases of known fusion-negati ve rhabdomyosarcoma showed no evidence of either product. These result s indicate that we have developed a molecular assay that accurately id entifies the fusion transcripts characteristic of alveolar rhabdomyosa rcoma in archival samples. This assay will be useful for diagnosis and for retrospective clinicopathologic correlative studies.