Transcriptomics,Multiomics

Dataset Information

2

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

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


<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]

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