A comprehensive transcriptional portrait of human cancer cell lines

• Published in: Nature biotechnology 2015-03, Vol.33 (3), p.306-312
• Main 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
• Format: Article
• Language: English
• Subjects: 13/89; 38; 45/22; 45/90; 45/91; 631/114/2785; 631/67/69; 631/67/70; 692/699/67/69; Agriculture; Base Sequence; Bioinformatics; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Cancer; Cancer cells; Cell Line, Tumor; Cell lines; Cells; Cluster Analysis; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Genetic aspects; Genetic research; Genetic transcription; Health aspects; Humans; Life Sciences; Mutation; Mutation - genetics; Neoplasms - genetics; Oncogene Fusion - genetics; Oncology, Experimental; Organ Specificity - genetics; Polymorphism, Single Nucleotide - genetics; resource; Transcription, Genetic; Tumors
• ISSN: 1087-0156; 1546-1696
• DOI: 10.1038/nbt.3080

A comprehensive analysis of RNA sequencing and single-nucleotide polymorphism (SNP) array data provides new insights into the biology of 675 human cancer cell lines 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.