ChimeraScan: A tool for identifying chimeric transcription in sequencing data

Bioinformatics

Volumn 27, Issue 20, 2011, Pages 2903-2904

  Iyer, Matthew K ^a   Chinnaiyan, Arul M ^a   Maher, Christopher A ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE FUSION; GENETIC TRANSCRIPTION; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN; NEOPLASM; SEQUENCE ANALYSIS; TUMOR CELL LINE;

CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENE FUSION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 80054003528     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr467     Document Type: Article

References (12)

1. Hampton, O.A. et al. (2009) A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome. Genome Res., 19, 167-177.
2. Kinsella, M. et al. (2011) Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics, 27, 1068-1075.
3. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
4. Maher, C.A. et al. (2009a) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 97-101.
5. Maher, C.A. et al. (2009b) Chimeric transcript discovery by paired-end transcriptome sequencing, Proc. Natl Acad. Sci. USA, 106, 12353-12358.
6. McPherson, A. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol., 7, e1001138.
7. Palanisamy, N. et al. (2010) Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat. Med., 16, 793-798.
8. Ruan, Y. et al. (2007) Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res., 17, 828-838.
9. Steidl, C. et al. (2011) MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature, 471, 377-381.
10. Tomlins, S.A. et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 310, 644-648.
11. Volik, S. et al. (2006) Decoding the fine-scale structure of a breast cancer genome and transcriptome. Genome Res., 16, 394-404.
12. Wang, K. et al. (2010) MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178.