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). This evidence concerns the gene ABL1 and urinary bladder cancer.