AbstractBackgroundAlveolar Rhabdomyosarcomas (RMA) are characterized by chromosomal translocations, fusing the PAX3 or PAX7 gene with FKHR in about 85%. Previous studies have suggested that the fusion type is associated with prognosis. In order to investigate the predictive value of the PAX–FKHR fusion status on disease outcome of patients with RMA treated in the CWS trials we performed a retrospective analysis.ProcedureBetween 1986 and 2004, out of 446 patients with RMA treated in four consecutive CWS trials, tumor samples from 126 patients were available for RT‐PCR analysis. Survival depending on fusion status in context with known clinical risk‐factors was analyzed.ResultsOut of 126 samples, 121 had adequate quality for PAX–FKHR fusion status analysis. PAX–FKHR fusions were detected in 101 samples: 60% PAX3–FKHR and 24% PAX7–FKHR fusions, 17% were fusion‐negative. There was no significant difference in survival between patients with PAX3–FKHR versus PAX7–FKHR positive tumors. The fusion transcript negative cohort showed a more favorable outcome than the fusion transcript positive cohort among patients with metastatic disease. From the established clinical risk‐factors none was associated with a significantly higher risk of failure or death in a multivariate analysis.ConclusionsPAX–FKHR fusion type was not a significant predictor for survival in our analysis. More extensive molecular analyses are needed to identify features with prognostic relevance and useful therapeutic impact. Pediatr Blood Cancer 2011; 57: 406–414. © 2011 Wiley‐Liss, Inc.