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Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts

Joshua Z Levin1*, Michael F Berger2, Xian Adiconis1, Peter Rogov1, Alexandre Melnikov1, Timothy Fennell3, Chad Nusbaum1, Levi A Garraway24 and Andreas Gnirke1

Author affiliations

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

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Citation and License

Genome Biology 2009, 10:R115  doi:10.1186/gb-2009-10-10-r115

Published: 16 October 2009

Abstract

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.