Prior therapy defines mutation profiles in childhood cancer at relapse.

Children with cancer develop many short- and long-term side-effects of treatment1, but the amount of DNA damage associated with chemotherapy exposure is unclear2. Here we used mutational signatures to measure this damage using whole-genome-sequenced tumours from a multi-institutional cohort for which therapy dose and total exposure were uniformly collected3-5. Chemotherapy and radiotherapy were the only exogenous mutagens in relapsed childhood tumours and were often the dominant source of DNA alteration. Compared with treatment-naive tumours, post-therapy cancers carried nearly three times the number of private signatures, and two times the total burden of somatic mutations. Further, the mutagenic effects of different chemotherapies varied. Platinum-based therapies, for which we more than doubled the number of associated signatures, led to the highest number of variants in most patients. Using therapy exposure dates to track when therapy-associated mutations become detectable, we defined a minimum threshold for platinum-associated mutations to emerge. Remarkably, more than one-third of tumours treated with platinum drugs displayed detectable platinum signatures within one year. This work provides genomic evidence for the critical mutagenic effects of chemotherapy in childhood cancer, as a specific driver of tumour evolution. These data highlight opportunities for treatment de-escalation and the future possibility of tracking resistant clones before expansion.