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Genome Biol DOI:10.1186/gb-2009-10-10-r115

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

Publication TypeJournal Article
Year of Publication2009
AuthorsLevin, JZ, Berger, MF, Adiconis, X, Rogov, P, Melnikov, A, Fennell, T, Nusbaum, C, Garraway, LA, Gnirke, A
JournalGenome Biol
Date Published2009
KeywordsAmino Acid Sequence, Base Sequence, DNA, Complementary, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Humans, K562 Cells, Molecular Sequence Data, Mutation, Neoplasms, Oncogene Proteins, Fusion, RNA, Messenger, Sequence Analysis, DNA

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.


Alternate JournalGenome Biol.
PubMed ID19835606
PubMed Central IDPMC2784330
Grant ListDP2OD002750 / OD / NIH HHS / United States
HG03067-05 / HG / NHGRI NIH HHS / United States