Bladder cancers are a leading cause of death from malignancy. Molecular markers might predict disease progression and behaviour more accurately than the available prognostic factors. Here we use whole-genome sequencing to identify somatic mutations and chromosomal changes in 14 bladder cancers of different grades and stages. As well as detecting the known bladder cancer driver mutations, we report the identification of recurrent protein-inactivating mutations in CDKN1A and FAT1. The former are not mutually exclusive with TP53 mutations or MDM2 amplification, showing that CDKN1A dysfunction is not simply an alternative mechanism for p53 pathway inactivation. We find strong positive associations between higher tumour stage/grade and greater clonal diversity, the number of somatic mutations and the burden of copy number changes. In principle, the identification of sub-clones with greater diversity and/or mutation burden within early-stage or low-grade tumours could identify lesions with a high risk of invasive progression.
Bibliographical noteFunding Information:
We are grateful to all the patients who agreed to participate in this study and to those who have provided their medical care. This work was supported by a grant from UCare to F.C.H., A.E.K., J.-B.C. and I.P.M.T., the Genomic Medicine and Surgical Innovation and Evaluation Themes of the Oxford NIHR Comprehensive Biomedical Research Centre, and core funding to the Wellcome Trust Centre for Human Genetics from the Wellcome Trust (090532/Z/09/Z). We also wish to acknowledge the support of Andrew Roth with the Pyclone analysis. We thank Dr Selina Bhattarai, Consultant Histopathologist, Leeds Teaching Hospitals NHS Trust for outlining the IHC tumour areas, and Ms Katalin Karaszi for expert sectioning of the TMA and IHC advice.