Chromosomal translocations generating unique chimeric genes are highly 
characteristic of specific sarcomas, and their use as diagnostic markers has 
been suggested. From a diagnostic pathologic point of view, detection of such 
cytogenetic or molecular aberrations applicable to routinely processed archival 
tissue specimens is considered a powerful tool for tumor diagnosis. To assess 
the feasibility and reliability of the molecular detection of the transcript 
originating from the chimeric gene in paraffin-embedded tumor specimens, we 
performed a nested reverse transcription-polymerase chain reaction 
(RT-PCR)-based assay to detect the EWS-FLI1 chimeric message in a series of 
Ewing family tumors. Of 24 paraffin-embedded tumor specimens from 23 cases 
analyzed, the chimeric message was detectable in 20 (83%) specimens from 20 
cases (87%) by this nested RT-PCR assay, whereas none of 7 small round cell 
tumors not from this family (3 alveolar rhabdomyosarcomas, 2 neuroblastomas, 2 
malignant lymphomas) showed detectable chimeric messages. In the sequence 
analysis of the PCR products, the amplified chimeric messages contained the 
junctions between exon 7 of the EWS gene and any one of exons 5, 6 and 8 of the 
FLI1 gene. The detection process was usually completed within 3 days, except for 
the subseqent sequence analysis. Our results endorse the use of this molecular 
assay as an ancillary technique in the diagnosis of Ewing family tumors using 
paraffin-embedded material.