RGD Reference Report - A comprehensive transcriptional portrait of human cancer cell lines. - Rat Genome Database

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A comprehensive transcriptional portrait of human cancer cell lines.

Authors: Klijn, Christiaan  Durinck, Steffen  Stawiski, Eric W  Haverty, Peter M  Jiang, Zhaoshi  Liu, Hanbin  Degenhardt, Jeremiah  Mayba, Oleg  Gnad, Florian  Liu, Jinfeng  Pau, Gregoire  Reeder, Jens  Cao, Yi  Mukhyala, Kiran  Selvaraj, Suresh K  Yu, Mamie  Zynda, Gregory J  Brauer, Matthew J  Wu, Thomas D  Gentleman, Robert C  Manning, Gerard  Yauch, Robert L  Bourgon, Richard  Stokoe, David  Modrusan, Zora  Neve, Richard M  de Sauvage, Frederic J  Settleman, Jeffrey  Seshagiri, Somasekar  Zhang, Zemin 
Citation: Klijn C, etal., Nat Biotechnol. 2015 Mar;33(3):306-12. doi: 10.1038/nbt.3080. Epub 2014 Dec 8.
RGD ID: 18183309
Pubmed: PMID:25485619   (View Abstract at PubMed)
DOI: DOI:10.1038/nbt.3080   (Journal Full-text)

Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic responses. Although substantial effort has been made to define the genomic constitution of cancer cell line panels, the transcriptome remains understudied. Here we describe RNA sequencing and single-nucleotide polymorphism (SNP) array analysis of 675 human cancer cell lines. We report comprehensive analyses of transcriptome features including gene expression, mutations, gene fusions and expression of non-human sequences. Of the 2,200 gene fusions catalogued, 1,435 consist of genes not previously found in fusions, providing many leads for further investigation. We combine multiple genome and transcriptome features in a pathway-based approach to enhance prediction of response to targeted therapeutics. Our results provide a valuable resource for studies that use cancer cell lines.

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