Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts
1 Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
2 Cancer Program, Broad Institute of MIT and Harvard, 5 Cambridge Center, Cambridge, MA 02142, USA
3 Sequencing Platform, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
4 Department of Medical Oncology and Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA
Genome Biology 2009, 10:R115 doi:10.1186/gb-2009-10-10-r115Published: 16 October 2009
Targeted RNA-Seq combines next-generation sequencing with capture of sequences from a relevant subset of a transcriptome. When testing by capturing sequences from a tumor cDNA library by hybridization to oligonucleotide probes specific for 467 cancer-related genes, this method showed high selectivity, improved mutation detection enabling discovery of novel chimeric transcripts, and provided RNA expression data. Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes.