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 researchers from Genetech describe RNA sequencing and single-nucleotide polymorphism (SNP) array analysis of 675 human cancer cell lines. They 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. The researchers combine multiple genome and transcriptome features in a pathway-based approach to enhance prediction of response to targeted therapeutics. These results provide a valuable resource for studies that use cancer cell lines.