Advanced urothelial carcinoma: next-generation sequencing reveals diverse genomic alterations and targets of therapy.


Journal Article

Although urothelial carcinoma (UC) of the urinary bladder generally portends a favorable prognosis, metastatic tumors often follow an aggressive clinical course. DNA was extracted from 40 μm of formalin-fixed, paraffin-embedded (FFPE) sections from 35 stage IV UCs that had relapsed and progressed after primary surgery and conventional chemotherapy. Next-generation sequencing (NGS) was performed on hybridization-captured, adaptor ligation-based libraries for 3320 exons of 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer to at an average sequencing depth of 1164 × and evaluated for all classes of genomic alterations (GAs). Actionable GAs were defined as those impacting the selection of targeted anticancer therapies on the market or in registered clinical trials. A total of 139 GAs were identified, with an average of 4.0 GAs per tumor (range 0-10), of which 78 (56%) were considered actionable, with an average of 2.2 per tumor (range 0-7). Twenty-nine (83%) cases harbored at least one actionable GA including: PIK3CA (9 cases; 26%); CDKN2A/B (8 cases; 23%); CCND1 (5 cases; 14%); FGFR1 (5 cases; 14%); CCND3 (4 cases; 11%); FGFR3 (4 cases; 11%); MCL1 (4 cases; 11%); MDM2 (4 cases; 11%); EGFR (2 cases, 6%); ERBB2 (HER2/neu) (2 cases, 6%); NF1 (2 cases, 6%) and TSC1 (2 cases, 6%). Notable additional alterations included TP53 (19 cases, 54%) and RB1 (6 cases; 17%). Genes involved in chromatin modification were altered by nonsense mutation, splice site mutation or frameshift indel in a mutually exclusive manner in nearly half of all cases including KDM6A (10 cases; 29%) and ARID1A (7 cases; 20%). Comprehensive NGS of 35 UCs of the bladder revealed a diverse spectrum of actionable GAs in 83% of cases, which has the potential to inform treatment decisions for patients with relapsed and metastatic disease.

Full Text

Duke Authors

Cited Authors

  • Ross, JS; Wang, K; Al-Rohil, RN; Nazeer, T; Sheehan, CE; Otto, GA; He, J; Palmer, G; Yelensky, R; Lipson, D; Ali, S; Balasubramanian, S; Curran, JA; Garcia, L; Mahoney, K; Downing, SR; Hawryluk, M; Miller, VA; Stephens, PJ

Published Date

  • February 2014

Published In

Volume / Issue

  • 27 / 2

Start / End Page

  • 271 - 280

PubMed ID

  • 23887298

Pubmed Central ID

  • 23887298

Electronic International Standard Serial Number (EISSN)

  • 1530-0285

Digital Object Identifier (DOI)

  • 10.1038/modpathol.2013.135


  • eng

Conference Location

  • United States