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

• Published in: Genome biology Vol. 10; no. 10; p. R115
• Main Authors: Levin, Joshua Z, Berger, Michael F, Adiconis, Xian, Rogov, Peter, Melnikov, Alexandre, Fennell, Timothy, Nusbaum, Chad, Garraway, Levi A, Gnirke, Andreas
• Format: Journal Article
• Language: English
• Published: London BioMed Central 16.10.2009
• Subjects: Amino Acid Sequence; Animal Genetics and Genomics; Base Sequence; Bioinformatics; Biomedical and Life Sciences; cDNA libraries; complementary DNA; DNA, Complementary - genetics; Evolutionary Biology; Gene Expression Profiling - methods; Gene Expression Regulation, Neoplastic - genetics; genes; high-throughput nucleotide sequencing; Human Genetics; Humans; K562 Cells; Life Sciences; Method; Microbial Genetics and Genomics; Molecular Sequence Data; mutation; Mutation - genetics; neoplasms; Neoplasms - genetics; nucleic acid hybridization; oligonucleotide probes; Oncogene Proteins, Fusion - chemistry; Oncogene Proteins, Fusion - genetics; Oncogene Proteins, Fusion - metabolism; Plant Genetics and Genomics; RNA; RNA, Messenger - genetics; RNA, Messenger - metabolism; Sequence Analysis, DNA - methods; transcriptome; Chronic Myeloid Leukemia; Fusion Transcript; Additional Data File; cDNA Library; Sequence Coverage
• ISSN: 1474-760X; 1465-6906; 1474-760X; 1465-6914
• DOI: 10.1186/gb-2009-10-10-r115

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.