title: A comprehensive transcriptional portrait of human cancer cell lines.
abstract: 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.
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Christiaan
authors.initials: C
authors.lastname: Klijn
authors.affiliation: 1] Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA. [2] Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Steffen
authors.initials: S
authors.lastname: Durinck
authors.affiliation: 1] Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA. [2] Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Eric W
authors.initials: EW
authors.lastname: Stawiski
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Haverty
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Zhaoshi
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Hanbin
authors.initials: H
authors.lastname: Liu
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Jeremiah
authors.initials: J
authors.lastname: Degenhardt
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Oleg
authors.initials: O
authors.lastname: Mayba
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Florian
authors.initials: F
authors.lastname: Gnad
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Jinfeng
authors.identifier: 0000000203438222
authors.initials: J
authors.lastname: Liu
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Gregoire
authors.initials: G
authors.lastname: Pau
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Jens
authors.initials: J
authors.lastname: Reeder
authors.affiliation: 1] Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA. [2] Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Kiran
authors.initials: K
authors.lastname: Mukhyala
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Suresh K
authors.initials: SK
authors.lastname: Selvaraj
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Mamie
authors.initials: M
authors.lastname: Yu
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Gregory J
authors.initials: GJ
authors.lastname: Zynda
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Brauer
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Thomas D
authors.initials: TD
authors.lastname: Wu
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Robert C
authors.initials: RC
authors.lastname: Gentleman
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Gerard
authors.identifier: 0000000250879151
authors.initials: G
authors.lastname: Manning
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Yauch
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Richard
authors.identifier: 0000000258904374
authors.initials: R
authors.lastname: Bourgon
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: David
authors.initials: D
authors.lastname: Stokoe
authors.affiliation: Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Zora
authors.initials: Z
authors.lastname: Modrusan
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Neve
authors.affiliation: Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Frederic J
authors.initials: FJ
authors.lastname: de Sauvage
authors.affiliation: Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Settleman
authors.affiliation: Department of Molecular Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Somasekar
authors.initials: S
authors.lastname: Seshagiri
authors.affiliation: Department of Bioinformatics and Computational Biology, Genentech Inc., South San Francisco, California, USA.
authors.forename: Zemin
authors.initials: Z
authors.lastname: Zhang
mesh_terms: D001483:Base Sequence; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D009154:Mutation / Q000235:genetics; D009369:Neoplasms / Q000235:genetics*; D050596:Oncogene Fusion / Q000235:genetics; D009928:Organ Specificity / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D014158:Transcription, Genetic