Background: Rhabdomyosarcoma (RMS), an uncommon soft tissue sarcoma, is subdivided according to its histopathology into 2 major subtypes; embryonal rhabdomyosarcoma (ERMS) and alveolar rhabdomyosarcoma (ARMS). In certain circumstances, distinguishing between the two subtypes is difficult. Recently, molecular pathology has discovered a potentially new adjunctive diagnostic tool for ARMS; the detection of fusion transcripts PAX/FKHR.

Objective: To study PAX3/FKHR and PAX7/FKHR fusion in RMS, and secondarily to look for any correlation between the fusion gene detection and the histopathological findings.

Methods: The sample set consisted of 6 ERMS and 5 ARMS. Detection of the fusion gene used reverse transcription polymerase chain reaction (RT-PCR). Positive results were confirmed by nucleotide sequencing.

Results: PAX3/FKHR fusion was detected in 3 of 5 ARMS frozen tissue samples. RT-PCR gave a negative result when formalin-fixed paraffin-embedded tissue was used as a template. None of the ERMS gave positive results. Two ARMS that were fusion-gene negative stained negative for desmin, contained no anaplastic histology, presented no rhabdomyoblast differentiation, but both cases had clear evidence of cystic component and electron microscopic evidence suggesting ARMS. The fusion-negative patients seemed to have a better clinical outcome. All ARMS and ERMS showed negative results of PAX7/FKHR.

Conclusion: Laboratory detection of PAX3/FKHR fusion gene in ARMS was successfully performed. The test should be useful in differentiating ARMS from ERMS, especially in cases without typical alveolar cystic portion.