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As next-generation sequencing (NGS) of tumor cells becomes more sophisticated, it is likely to inform all aspects of cancer management, from diagnostic testing to treatment and drug discovery. In this issue, Frampton et al describe a comprehensive NGS assay applicable to clinical samples that identifies single-base substitutions, copy-number variations and focal amplifications in 287 cancer-related genes, fusion events involving 19 frequently rearranged genes and 3,549 single-nucleotide polymorphisms in other locations throughout the genomeall within a single sequencing run.