SAVANA detected diverse types of complex rearrangement encompassing SVs and SCNAs leading to the loss of tumor suppressor genes, such as chromothripsis events causing the inactivation of CDKN2A, NF1, TP53 or RB1 (Fig. 5d and Supplementary Figs. 26–35) or oncogene amplification across various tumor types, such as amplification of CDK4, MDM2, CCNE1 and MYC in osteosarcomas and MYC and EGFR in glioblastomas1 (Fig. 5e,f). Here, CDK4 is linked to osteosarcoma.