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Incidence and distribution of UroSEEK gene panel in a multi-institutional cohort of bladder urothelial carcinoma

Abstract

Noninvasive approaches for early detection of bladder cancer are actively being investigated. We recently developed a urine- based molecular assay for the detection and surveillance of bladder neoplasms (UroSEEK). UroSEEK is designed to detect alterations in 11 genes that include most common genetic alterations in bladder cancer. In this study, we analyzed 527 cases, including 373 noninvasive and 154 invasive urothelial carcinomas of bladder from transurethral resections or cystectomies performed at four institutions (1991–2016). Two different mutational analysis assays of a representative tumor area were performed: first, a singleplex PCR assay for evaluation of the TERT promoter region (TERTSeqS) and second, a multiplex PCR assay using primers designed to amplify regions of interest of 10 (FGFR3, PIK3CA, TP53, HRAS, KRAS, ERBB2, CDKN2A, MET, MLL, and VHL) genes (UroSeqS). Overall, 92% of all bladder tumors were positive for at least one genetic alteration in the UroSEEK panel. We found TERT promoter mutations in 77% of low-grade noninvasive papillary carcinomas, with a relatively lower incidence of 65% in high-grade noninvasive papillary carcinomas and carcinomas in situ; p = 0.017. Seventy-two percent of pT1 and 63% of muscle-invasive bladder tumors harbored TERT promoter mutations with g.1295228C>T alteration being the most common in all groups. FGFR3 and PIK3CA mutations were more frequent in low-grade noninvasive papillary carcinomas compared with high-grade noninvasive papillary carcinomas and carcinomas in situ (p < 0.0001), while the opposite was true for TP53 (p < 0.0001). Significantly higher rates of TP53 and CDKN2A mutation rates (p = 0.005 and 0.035, respectively) were encountered in muscle-invasive bladder tumors compared with those of pT1 stage. The overwhelming majority of all investigated tumors showed at least one mutation among UroSEEK assay genes, confirming the comprehensive coverage of the panel and supporting its potential utility as a noninvasive urine-based assay.

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Acknowledgements

We are grateful for the generous support provided by the Johns Hopkins Greenberg Bladder Cancer Institute, Henry and Marsha Laufer, the Virginia and DK Ludwig Fund for Cancer Research, the Commonwealth Foundation, the John Templeton Foundation, and the Conrad R Hilton Foundation. All sequencing was performed at the Sol Goldman Sequencing Facility at Johns Hopkins. This work was also supported by grants from the NIH (Grants CA-77598, CA 06973, GM 07309, and ES019564).

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Conflict of interest

NP, KWK, and BV: founders of Personal Genome Diagnostics and PapGene and advisors to Sysmex-Inostics. KWK and BV also advise Eisai. BV is also an advisor to Camden Partners. These companies and others have licensed technologies from Johns Hopkins that are related to the work described in this paper. These licenses are associated with equity or royalty payments to NP, KWK, GJN, and BV. Additional patent applications on the work described in this paper may be filed by Johns Hopkins University. The terms of these arrangements are managed by the university in accordance with its conflict of interest policies. The remaining authors declare that they have no conflict of interest.

Correspondence to George J. Netto.

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