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PMID: 19835606 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

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

Genome biology ·Vol. 10 ·No. 10 ·2009-00-00 ·Pages R115

Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A

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.

MeSH Terms
Amino Acid Sequence Base Sequence DNA, Complementary/genetics Gene Expression Profiling/methods Gene Expression Regulation, Neoplastic/genetics Humans K562 Cells Molecular Sequence Data Mutation/genetics Neoplasms/genetics Oncogene Proteins, Fusion/chemistry,genetics,metabolism RNA, Messenger/genetics,metabolism Sequence Analysis, DNA/methods
Chemicals
DNA, Complementary Oncogene Proteins, Fusion RNA, Messenger
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Levin Joshua Z
Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA. jlevin@broadinstitute.org
Berger Michael F
Adiconis Xian
Rogov Peter
Melnikov Alexandre
Fennell Timothy
Nusbaum Chad
Garraway Levi A
Gnirke Andreas
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2009-10-10-r115
Email
jlevin@broadinstitute.org
Published
2009-00-00
Epub
2009-00-16
Pages
R115
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2784330
Subset
IM
Grants
NIH HHS · DP2OD002750 · United States
NHGRI NIH HHS · HG03067-05 · United States
External Links
PubMed source DOI: 10.1186/gb-2009-10-10-r115 PMC Full Text View journal details
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