title: Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.
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.
authors.affiliation: Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA. jlevin@broadinstitute.org
authors.forename: Joshua Z
authors.initials: JZ
authors.lastname: Levin
authors.forename: Michael F
authors.initials: MF
authors.lastname: Berger
authors.forename: Xian
authors.initials: X
authors.lastname: Adiconis
authors.forename: Peter
authors.initials: P
authors.lastname: Rogov
authors.forename: Alexandre
authors.initials: A
authors.lastname: Melnikov
authors.forename: Timothy
authors.initials: T
authors.lastname: Fennell
authors.forename: Chad
authors.initials: C
authors.lastname: Nusbaum
authors.forename: Levi A
authors.initials: LA
authors.lastname: Garraway
authors.forename: Andreas
authors.initials: A
authors.lastname: Gnirke
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics; D006801:Humans; D020014:K562 Cells; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics*; D009369:Neoplasms / Q000235:genetics*; D015514:Oncogene Proteins, Fusion / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018076:DNA, Complementary; D015514:Oncogene Proteins, Fusion; D012333:RNA, Messenger