An empirical permutation test identified known oncogenic fusions enriched in specific cancer types that are consistent with their pathognomonic nature, such as ABL1 fusions in chronic myeloid leukemia (false discovery rate (FDR) <1%, n = 9), EWSR1-FLI1 fusions in Ewing’s sarcoma (FDR <1%, n = 24) and FGFR3 fusions in bladder cancer (FDR <1%, n = 3) (Supplementary Fig. 1b). The gene discussed is FGFR3; the disease is urinary bladder carcinoma.