BACKGROUND: Ewing's sarcoma/peripheral primitive neuroectodermal tumor 
(ES/pPNET) is often difficult to distinguish from other small round cell tumors. 
The EWS-Ets gene fusions that result from chromosomal translocations in this 
tumor provide potential molecular diagnostic markers. To apply these molecular 
markers to commonly available archival materials, we evaluated the feasibility 
of detecting EWS-Ets including EWS-Fli1 and EWS-ERG fusion transcripts in 
paraffin-embedded tissues and its diagnostic value for detecting ES/pPNET.
METHODS: Thirteen paraffin-embedded samples of ES/pPNETs were retrieved from 
archives. Thirteen cases of other tumors with small round cell features 
(including rhabdomyosarcoma, neuroblastoma, lymphoma, small cell carcinoma, and 
desmoplastic small round cell tumor) were used as negative controls. Beta-actin 
and beta2-microglobulin were used as internal controls. A nested reverse 
transcriptase-polymerase chain reaction (RT-PCR)-based assay was performed to 
detect the EWS-Fli1 and EWS-ERG fusion transcripts.
RESULTS: Beta-actin and beta2-microglobulin were detected in 10/13 and 13/13 
ES/pPNETs, respectively. EWS-Fli1 fusion transcripts were detected in 11 of 13 
(85%) ES/pPNETs. Three chimeric transcripts, all EWS-Fli1, were detected in 
ES/pPNET samples. Among 11 EWS-Fli1-positive cases, 7 cases had a type I fusion 
transcript involving fusion of EWS exon 7 with Fli1 exon 6, 2 cases had a type 
II fusion transcript involving EWS exon 7 with Fli1 exon 5, and 2 cases 
expressed fusion transcripts involving EWS exon 7 and Fli1 exon 8. Type I 
EWS-Fli1 fusion predominated over other types. Fusion types could not be 
distinguished in the remaining 2 cases. Thirteen negative controls did not show 
detectable chimeric messages. There was a significant relationship between 
EWS-Fli1 fusion transcripts and CD99 expression.
CONCLUSIONS: Molecular detection of EWS-Fli1 fusion transcripts in 
formalin-fixed paraffin-embedded material by nested RT-PCR is feasible and is 
useful for the diagnosis and differential diagnosis of ES/pPNETs.