Dataset Information

The UBC-40 Urothelial Bladder Cancer Cell Line Index [copy number variation]

ABSTRACT: This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression. Based on gene mutation patterns and genomic changes we identify lines representative of the FGFR3-driven tumor pathway and of the TP53/RB tumor suppressor-driven pathway. High-density array copy number analysis identified significant focal gains (1q32, 5p13.1-12, 7q11, and 7q33) and losses (i.e. 6p22.1) in regions altered in tumors but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of UPD, often coinciding with regions reported to be lost in tumors. Previously undescribed chromosome X losses found in UBC lines also point to potential tumor suppressor genes. Cell lines representative of the FGFR3-driven pathway showed a lower number of UPD events. Overall, there is a predominance of more aggressive tumor subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined bladder tumor subtypes. The compiled information should serve as a useful reference to the bladder cancer research community and should help to select cell lines appropriate for the functional analysis of bladder cancer genes, for example those being identified through massive parallel sequencing. Copy Number Variations were assessed in 45 bladder cell lines, included in the UBC-40 Urothelial Bladder Cell Line Index, with Human1M-Duov3 DNA Analysis BeadChip platform

OTHER RELATED OMICS DATASETS IN: PRJNA271340PRJNA270624PRJNA271339

ORGANISM(S): Homo sapiens

SUBMITTER: Alfredo Carrato Marinela Méndez-Pertuz Enrique Carrillo-de-Santa-Pau Daniel Rico Francisco X Real Stephen Chanock Wolfgang A Schulz Herbert Auer Gonzalo Gómez Enrique Carrillo de Santa Pau Julie Earl Alfonso Valencia H B Grossman David G Pisano Luis A Pérez-Jurado Benjamín Rodríguez-Santiago Dan Theodorescu

PROVIDER: E-GEOD-64572 | ArrayExpress | 2015-06-19

SECONDARY ACCESSION(S): GSE64572PRJNA271340

REPOSITORIES: GEO, ArrayExpress

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Dataset's files

Source:

			Action	DRS
	E-GEOD-64572.additional.1.zip	Other
	E-GEOD-64572.additional.2.zip	Other
	E-GEOD-64572.idf.txt	Idf
	E-GEOD-64572.raw.1.zip	Raw
	E-GEOD-64572.raw.2.zip	Raw

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Publications

The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies.

Earl Julie J Rico Daniel D Carrillo-de-Santa-Pau Enrique E Rodríguez-Santiago Benjamín B Méndez-Pertuz Marinela M Auer Herbert H Gómez Gonzalo G Grossman Herbert Barton HB Pisano David G DG Schulz Wolfgang A WA Pérez-Jurado Luis A LA Carrato Alfredo A Theodorescu Dan D Chanock Stephen S Valencia Alfonso A Real Francisco X FX

BMC genomics 20150522

<h4>Background</h4>Urothelial bladder cancer is a highly heterogeneous disease. Cancer cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial bladder carcinoma (UBC) cell lines including information on origin, mutation status of genes implicated in bladder cancer (FGFR3, PIK3CA, TP53, and RAS), copy number alterations assessed using high density SNP arrays, uniparental disomy (UPD) events, and gene expression.<h4>Results</h4>Based on gene mut ...[more]

PMID: 25997541

Similar Datasets

Project description:Recent studies showed the clinical utility of next-generation sequencing of urinary cell-free DNA (cfDNA) from patients with urothelial bladder cancer (UBC). In this study, we aimed to develop urinary cfDNA analysis by droplet digital PCR (ddPCR) as a high-throughput and rapid assay for UBC detection and prognosis. We analyzed urinary cfDNA of 202 samples from 2 cohorts. Test cohort was designed for investigating clinical utility of urinary cfDNA, and was composed of 74 samples from patients with UBC, and 52 samples of benign hematuria patients. Validation cohort was designed for validation and assessment of clinical utility comparing urinary cfDNA with UroVysion (Abbott, Illinois, USA), and was composed of 40 samples from patients with UBC, and 36 prospectively collected samples from patients under surveillance after surgery for urothelial carcinoma. We performed ddPCR analysis of hotspot gene mutations (TERT promoter and FGFR3). In the test cohort, the sensitivity of urinary cfDNA diagnosis was 68.9% (51/74) and the specificity was 100% in patients with UBC. The sensitivity increased to 85.9% when used in conjunction with urine cytology. In addition, patients with high TERT C228T allele frequency (?14%) had significantly worse prognosis in bladder tumor recurrence than patients with low TERT C228T allele frequency or negative TERT C228T (p = 0.0322). In the validation cohort, the sensitivity of urinary cfDNA was 57.5% (23/40) and the specificity was 100% in UBC patients. The sensitivity of the combination of urine cytology with our hotspot analysis (77.5%) was higher than that of urine cytology with UroVysion (68.9%). In the post-surgical surveillance group, patients positive for the TERT C228T mutation had significantly worse prognosis for bladder tumor recurrence than mutation negative patients (p < 0.001). In conclusion, ddPCR analysis of urinary cfDNA is a simple and promising assay for the clinical setting, surpassing UroVysion for detection and prognosis determination in UBC.