AbstractBackgroundMyeloid sarcoma (MS) is a rare, extramedullary tumor consisting of myeloid blasts. Little is known about the genetic background of MS and the prognostic value of genetic abnormalities in MS. In particular, the broad variety of gene fusions that occur in MS is marginally covered by traditional testing methods due to lack of fresh tumor specimens.MethodsHere, we analyzed the clinical and genetic features of 61 MS cases. We performed RNA sequencing (RNA‐seq) on formalin‐fixed paraffin‐embedded (FFPE) or fresh samples to analyze fusion genes in 26 cases. In addition, we performed genetic abnormalities‐based risk stratification using fusion genes and gene mutations.ResultsA total of 305 fusion genes were identified in 22 cases, including the following five recurrent fusion genes:RUNX1‐RUNX1T1,CBFβ‐MYH11,ETV6‐MECOM,FUS‐ERG, andPICALM‐MLLT10. The prognosis in the adverse‐risk group was significantly worse than that in the favorable/intermediate‐risk group (median survival: 12 months vs. not reached;p= 0.0004).ConclusionThese results indicated the efficacy of RNA‐seq using FFPE‐derived RNA as a clinical routine for detecting fusion genes, which can be used as markers for risk stratification in MS.