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

@entity146 @entity5 @entity2557 @entity876 @entity150 @entity8882 @entity10160
BACKGROUND: Urothelial @entity150 is a highly heterogeneous disease. @entity5 cell lines are useful tools for its study. This is a comprehensive genomic characterization of 40 urothelial @entity150 (UBC) cell lines including information on origin, mutation status of genes implicated in @entity150 ( @entity2557 , @entity10160 , @entity876 , and RAS), copy number alterations assessed using high density SNP arrays, @entity8882 ( @entity8882 ) events, and gene expression. RESULTS: Based on gene mutation patterns and genomic changes we identify lines representative of the @entity2557 -driven @entity5 pathway and of the @entity876 /RB @entity5 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 @entity5 but not previously described as affected in bladder cell lines. We also identify new evidence for frequent regions of @entity8882 , often coinciding with regions reported to be lost in @entity5 . Previously undescribed chromosome X losses found in UBC lines also point to potential @entity5 suppressor genes. Cell lines representative of the @entity2557 -driven pathway showed a lower number of @entity8882 events. CONCLUSIONS: Overall, there is a predominance of more @entity146 subtypes among the cell lines. We provide a cell line classification that establishes their relatedness to the major molecularly-defined @entity150 subtypes. The compiled information should serve as a useful reference to the @entity150 research community and should help to select cell lines appropriate for the functional analysis of @entity150 genes, for example those being identified through massive parallel sequencing.
