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Series GSE64572 Query DataSets for GSE64572
Status Public on Jun 19, 2015
Title The UBC-40 Urothelial Bladder Cancer Cell Line Index [copy number variation]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary 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.
Overall design 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
Contributor(s) Earl J, Rico D, Carrillo-de-Santa-Pau E, Rodríguez-Santiago B, Méndez-Pertuz M, Auer H, Gómez G, Grossman HB, Pisano DG, Schulz WA, Pérez-Jurado LA, Carrato A, Theodorescu D, Chanock S, Valencia A, Real FX
Citation(s) 25997541
Submission date Dec 30, 2014
Last update date May 06, 2016
Contact name Enrique Carrillo de Santa Pau
Organization name Spanish National Cancer Research Centre (CNIO)
Department Cancer Cell Biology Programme
Lab Epithelial Carcinogenesis group
Street address C/ Melchor Fernández Almagro, 3
City Madrid
ZIP/Postal code 28029
Country Spain
Platforms (1)
GPL6984 Illumina Human1M-Duov3 DNA Analysis BeadChip (Human1M-Duov3_B)
Samples (50)
GSM1574541 UM-UC-17_copy_number_variation_1
GSM1574542 97-1_copy_number_variation
GSM1574544 HU456_copy_number_variation
This SubSeries is part of SuperSeries:
GSE64573 The UBC-40 Urothelial Bladder Cancer Cell Line Index
BioProject PRJNA271340

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE64572_Processed_data.txt.gz 642.8 Mb (ftp)(http) TXT
GSE64572_RAW.tar 793.1 Mb (http)(custom) TAR (of IDAT)
GSE64572_Signal_intensities.txt.gz 529.4 Mb (ftp)(http) TXT
GSE64572_cell_line_calls_with_annotation.txt.gz 28.6 Mb (ftp)(http) TXT
Processed data are available on Series record

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