For patients in the second cohort without pathognomonic fusion transcript detected, novel fusion transcripts were identified by RNA Exome sequencing, with a median sequencing detection sensitivity of 0.39 fusion supporting reads per million uniquely mapped reads, and validated using the RT-qPCR workflow, including COPS3-TOM1L2, NCOA1-DTNB, WWTR1-LINC01986, PLAA-MOB3B, AP1B1-CHEK2 and BRD4-LEUTX in ARMS patients. Here, PLAA is linked to alveolar rhabdomyosarcoma.