Whole-genome sequencing of primary and relapse tumours from eight patients with relapsed acute myeloid leukaemia (AML) revealed clonal evolution patterns. The study identified two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. Chemotherapy failed to eradicate the founding clone in all cases. Relapse-specific mutations showed an increase in transversions, likely due to DNA damage from chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped by chemotherapy. The study also identified novel, recurrently mutated genes in AML, including WAC, SMC3, DIS3, DDX41 and DAXX. The analysis of eight primary tumour-relapse pairs revealed clonal heterogeneity and clonal evolution at relapse. The founding clone was identified in all cases, and some subclones were lost at relapse. The relapse clone was often derived from a subclone that had acquired mutations and survived chemotherapy. The study found that chemotherapy contributes to relapse by generating new mutations in the founding clone or its subclones, which can undergo selection and clonal expansion. The study also compared the mutational spectrum of primary tumours and relapse samples, finding that relapse-specific mutations had a higher frequency of transversions, likely due to DNA damage from chemotherapy. These findings highlight the importance of identifying disease-causing mutations in AML to develop targeted therapies that avoid cytotoxic drugs, many of which are mutagens. The study provides new insights into clonal evolution in AML and its relationship to chemotherapy. The data suggest that AML cells routinely acquire additional mutations at relapse, which may contribute to clonal selection and chemotherapy resistance. The AML genome in an individual patient is a 'moving target', and eradication of the founding clone and all of its subclones is required to achieve cures.Whole-genome sequencing of primary and relapse tumours from eight patients with relapsed acute myeloid leukaemia (AML) revealed clonal evolution patterns. The study identified two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. Chemotherapy failed to eradicate the founding clone in all cases. Relapse-specific mutations showed an increase in transversions, likely due to DNA damage from chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped by chemotherapy. The study also identified novel, recurrently mutated genes in AML, including WAC, SMC3, DIS3, DDX41 and DAXX. The analysis of eight primary tumour-relapse pairs revealed clonal heterogeneity and clonal evolution at relapse. The founding clone was identified in all cases, and some subclones were lost at relapse. The relapse clone was often derived from a subclone that had acquired mutations and survived chemotherapy. The study found that chemotherapy contributes to relapse by generating new mutations in the founding clone or its subclones, which can undergo selection and clonal expansion. The study also compared the mutational spectrum of primary tumours and relapse samples, finding that relapse-specific mutations had a higher frequency of transversions, likely due to DNA damage from chemotherapy. These findings highlight the importance of identifying disease-causing mutations in AML to develop targeted therapies that avoid cytotoxic drugs, many of which are mutagens. The study provides new insights into clonal evolution in AML and its relationship to chemotherapy. The data suggest that AML cells routinely acquire additional mutations at relapse, which may contribute to clonal selection and chemotherapy resistance. The AML genome in an individual patient is a 'moving target', and eradication of the founding clone and all of its subclones is required to achieve cures.