MOLECULAR ASSAYS FOR CHROMOSOMAL TRANSLOCATIONS IN THE DIAGNOSIS OF PEDIATRIC SOFT-TISSUE SARCOMAS

Objective.-To compare molecular assays for characteristic chromosomal translocations with standard histopathologic and cytogenetic analysis in the differential diagnosis of pediatric soft tissue sarcomas. Desig n.-Blinded comparison with histopathologic diagnosis. Setting.-Tertiar y care children's hospital. Patients.-A total of 79 soft tissue sarcom a patients with frozen tumor tissue and histopathologic slides availab le for review. Methods.-The RNA from the tumors was assayed by the rev erse transcriptase-polymerase chain reaction. These assays detect PAX3 -FKHR and PAX7-FKHR chimeric transcripts in alveolar rhabdomyosarcoma, EWS-FLI1 and EWS-ERG chimeric transcripts in Ewing's sarcoma, and EWS -WT1 chimeric transcripts in desmoplastic small round cell tumor. Main Outcome Measures.-The polymerase chain reaction findings were compare d with cytogenetic and histopathologic results. Results.-These assays detected chimeric transcripts in all cases in which translocations wer e found by standard cytogenetics as well as additional cases without c ytogenetically detectable translocations, PAX3-FKHR or PAX7-FKHR fusio ns were present in 18 of 21 alveolar rhabdomyosarcomas, two of 30 embr yonal rhabdomyosarcomas, and one of seven undifferentiated sarcomas. E WS-FLI1 or EWS-ERG fusions were detected in six of eight Ewing's sarco mas and one of seven undifferentiated sarcomas. The EWS-WT1 fusion was found in three of three desmoplastic small round cell tumors. Conclus ions.-Molecular assays for specific gene fusions provide a genetic app roach to the differential diagnosis of soft tissue sarcomas. The genet ic categories correspond closely to the standard histopathologic categ ories. The polymerase chain reaction assays for chimeric transcripts a re useful tools for the rapid and objective assessment of pediatric so ft tissue sarcomas.