Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23-gene panel with utility for non-invasive diagnosis and risk stratification

Douglas Ward, Naheema Gordon, Rebecca Boucher, Sarah Pirrie, Laura Baxter, Sascha Ott, Lee Silcock, Celina Whalley, Joanne Stockton, Andrew Beggs, Mike Griffiths, Ben Abbotts, Hanieh Ijakipour, Fathimath Latheef, Robbie Robinson, Andrew White, Nicholas James, Maurice Zeegers, KK Cheng, Rik Bryan

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Objectives: To develop a focused panel of somatic mutations (SMs) present in the majority of urothelial bladder cancers (UBCs), to investigate the diagnostic and prognostic utility of this panel, and to compare the identification of SMs in urinary cell-pellet (cp)DNA and cell-free (cf)DNA as part of the development of a non-invasive clinical assay. Patients and Methods: A panel of SMs was validated by targeted deep-sequencing of tumour DNA from 956 patients with UBC. In addition, amplicon and capture-based targeted sequencing measured mutant allele frequencies (MAFs) of SMs in 314 urine cpDNAs and 153 urine cfDNAs. The association of SMs with grade, stage, and clinical outcomes was investigated by univariate and multivariate Cox models. Concordance between SMs detected in tumour tissue and cpDNA and cfDNA was assessed. Results: The panel comprised SMs in 23 genes: TERT (promoter), FGFR3, PIK3CA, TP53, ERCC2, RHOB, ERBB2, HRAS, RXRA, ELF3, CDKN1A, KRAS, KDM6A, AKT1, FBXW7, ERBB3, SF3B1, CTNNB1, BRAF, C3orf70, CREBBP, CDKN2A, and NRAS; 93.5–98.3% of UBCs of all grades and stages harboured ≥1 SM (mean: 2.5 SMs/tumour). RAS mutations were associated with better overall survival (P = 0.04). Mutations in RXRA, RHOB and TERT (promoter) were associated with shorter time to recurrence (P < 0.05). MAFs in urinary cfDNA and cpDNA were highly correlated; using a capture-based approach, >94% of tumour SMs were detected in both cpDNA and cfDNA. Conclusions: SMs are reliably detected in urinary cpDNA and cfDNA. The technical capability to identify very low MAFs is essential to reliably detect UBC, regardless of the use of cpDNA or cfDNA. This 23-gene panel shows promise for the non-invasive diagnosis and risk stratification of UBC.

Original languageEnglish
Pages (from-to)532-544
Number of pages13
JournalBJU international
Issue number3
Early online date11 May 2019
Publication statusPublished - Sept 2019

Bibliographical note

© 2019 The Authors BJU International published by John Wiley & Sons Ltd on behalf of BJU International.


  • DNA
  • Bladder cancer
  • detection
  • diagnosis
  • mutations
  • prognosis
  • urine


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