We are analyzing https://link.springer.com/article/10.1186/s12864-015-1450-3.

Title:
The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies | BMC Genomics
Description:
Background 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. Results 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. Conclusions 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.
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Keywords {🔍}

lines, cell, cancer, ubc, number, copy, article, pubmed, bladder, table, google, scholar, gene, expression, tumor, tumors, additional, upd, file, figure, data, cas, genomic, analysis, genes, fgfr, mutations, genome, chromosome, alterations, umuc, regions, information, altered, urothelial, mutation, identified, lost, line, status, size, chr, frequency, provided, losses, probes, loh, carcinoma, central, showed,

Topics {✒️}

enrique carrillo-de-santa-pau gonzalo gómez plain view carrillo-de-santa-pau carrillo-de santa pau oncogene/tumor suppressor status global expression profiles tumor suppressor-driven pathways author information authors web-based search benjamín rodríguez-santiago fgfr3-driven pathway showed genetic/epigenetic alterations inactivate bmc genomics 16 fgfr3-driven tumor pathway article download pdf genomically unstable-high group author correspondence anticancer drug sensitivity article earl full size image marinela méndez-pertuz & francisco high-grade lines tended urothelial bladder carcinoma main oncogene involved bladder cancer subtypes papillary/luminal tumor phenotypes copy number calls open access license tumor suppressor genes copy number neutral 0 = copy number neutral urothelial cell carcinoma copy number alterations chromosome/chromosome arm gain/loss high-resolution analysis specific tumor subtypes understanding urothelial carcinoma de la salut gene copy number privacy choices/manage cookies pérez-jurado & francisco urothelial bladder tumors literature search managing bladder cancer urinary bladder cancer cell line dataset complete copy number copy number data large structural variants

Questions {❓}

P53: it has it all, but will it make it to the clinic as a marker in bladder cancer?

Schema {🗺️}

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         headline:The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies
         description: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. 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.
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            Cell line
            Genomics
            Mutation
            Oncogene
            Tumor suppressor
            Life Sciences
            general
            Microarrays
            Proteomics
            Animal Genetics and Genomics
            Microbial Genetics and Genomics
            Plant Genetics and Genomics
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      headline:The UBC-40 Urothelial Bladder Cancer cell line index: a genomic resource for functional studies
      description: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. 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.
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      dateModified:2015-05-22T00:00:00Z
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      keywords:
         Urothelial bladder cancer
         Cell line
         Genomics
         Mutation
         Oncogene
         Tumor suppressor
         Life Sciences
         general
         Microarrays
         Proteomics
         Animal Genetics and Genomics
         Microbial Genetics and Genomics
         Plant Genetics and Genomics
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            type:Person
            name:Marinela Méndez-Pertuz
            affiliation:
                  name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre)
                  address:
                     name:Epithelial Carcinogenesis Group, F BBVA Cancer Cell Biology Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
                     type:PostalAddress
                  type:Organization
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            name:Herbert Auer
            affiliation:
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                  address:
                     name:Institut de Recerca Biomèdica de Barcelona, Parc Científic de Barcelona, Barcelona, Spain
                     type:PostalAddress
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            name:Gonzalo Gómez
            affiliation:
                  name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre)
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                     name:Bioinformatics Unit, Structural Biology and Biocomputing Programme, CNIO (Spanish National Cancer Research Centre), Madrid, Spain
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