RNA-seq of 675 commonly used human cancer cell lines

"Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels24, the transcriptome which represents the active program of a cell remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines. The raw sequence files were submitted to the European Genome-Phenome Archive (EGA) under accession EGAS00001000610 ( https://www.ebi.ac.uk/ega/datasets/EGAD00001000725 ). Processed, human non-identifiable data, together with a README file describing the data (140625_Klijn_README.txt) are available here in E-MTAB-2706.additional.*.zip files: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/files ."