title: Advanced urothelial carcinoma: next-generation sequencing reveals diverse genomic alterations and targets of therapy.
abstract: 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.
authors.affiliation: 1] Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA [2] Foundation Medicine, Cambridge, MA, USA.
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Ross
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.affiliation: Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA.
authors.forename: Rami N
authors.initials: RN
authors.lastname: Al-Rohil
authors.affiliation: Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA.
authors.forename: Tipu
authors.initials: T
authors.lastname: Nazeer
authors.affiliation: Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, NY, USA.
authors.forename: Christine E
authors.initials: CE
authors.lastname: Sheehan
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Geoff A
authors.initials: GA
authors.lastname: Otto
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: He
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Gary
authors.initials: G
authors.lastname: Palmer
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Roman
authors.initials: R
authors.lastname: Yelensky
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Doron
authors.initials: D
authors.lastname: Lipson
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Siraj
authors.initials: S
authors.lastname: Ali
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Sohail
authors.initials: S
authors.lastname: Balasubramanian
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: John A
authors.initials: JA
authors.lastname: Curran
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Lazlo
authors.initials: L
authors.lastname: Garcia
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Mahoney
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Sean R
authors.initials: SR
authors.lastname: Downing
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Hawryluk
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Vincent A
authors.initials: VA
authors.lastname: Miller
authors.affiliation: Foundation Medicine, Cambridge, MA, USA.
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D002295:Carcinoma, Transitional Cell / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D017422:Sequence Analysis, DNA; D001749:Urinary Bladder Neoplasms / Q000235:genetics*