Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript

Bioinformatics

Volumn 28, Issue 24, 2012, Pages 3232-3239

  Benelli, Matteo ^a,b   Pescucci, Chiara ^b   Marseglia, Giuseppina ^b   Severgnini, Marco ^c   Torricelli, Francesca ^a,b   Magi, Alberto ^b  

^a CAREGGI UNIVERSITY HOSPITAL   (Italy)

^b UNIVERSITY OF FLORENCE   (Italy)

^c CNR   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALGORITHM; ARTICLE; CHEMISTRY; GENE EXPRESSION PROFILING; GENE FUSION; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TUMOR CELL LINE;

ALGORITHMS; CELL LINE, TUMOR; GENE EXPRESSION PROFILING; GENE FUSION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; RNA, NEOPLASM; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA;

EID: 84870815979     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts617     Document Type: Article

References (28)

1. Berger, M. et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res., 20, 413-427.
2. Cabili, M. et al. (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev., 25, 1915-1927.
3. Edgren, H. et al. (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol., 12, R6.
4. Ge, H. et al. (2011) Fusionmap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics, 27, 1922-1928.
5. Iyer, M. et al. (2011) Chimerascan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics, 27, 2903-2904.
6. Jiang, H. and Wong, W. (2009) Statistical inferences for isoform expression in RNA-seq. Bioinformatics, 25, 1026-1032.
7. Kent, W. (2002) Blat-the blast-like alignment tool. Genome Res., 4, 656-664.
8. Kim, D. and Salzberg, S. (2011) Tophat-fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol., 12, R72.
9. Kinsella, M. et al. (2011) Sensitive gene fusion detection using ambiguously mapping RNA-seq read pairs. Bioinformatics, 27, 1068-1075.
10. Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
11. Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
12. Maher, C. et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 97-101.
13. McPherson, A. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-seq data. PLoS Comput. Biol., 7, e1001138.
14. Mitelman, F. et al. (2007) The impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer, 7, 233-245.
15. Mortazavi, A. et al. (2008) Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods, 5, 621-628.
16. Nagalakshmi, U. et al. (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science, 320, 1344-1349.
17. Pflueger, D. et al. (2011) Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing. Genome Res., 21, 56-67.
18. Picardi, E. et al. (2010) Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res., 38, 4755-4767.
19. Robertson, G. et al. (2010) De novo assembly and analysis of RNA-seq data. Nat. Methods, 7, 909-912.
20. Ruffalo, M. et al. (2011) Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics, 27, 2790-2796.
21. Sboner, A. et al. (2010) FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol., 11, R104.
22. Seal, R. et al. (2011) genenames.org: the HGNC resources in 2011. Nucleic Acids Res., 39, D514-D519.
23. Soda, M. et al. (2007) Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature, 448, 561-566.
24. Steidl, C. et al. (2011) MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature, 471, 377-381.
25. Tomlins, S. et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 310, 644-648.
26. Trapnell, C. et al. (2010) Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol., 28, 511-515.
27. Wang, K. et al. (2010) Annovar: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res., 38, e164.
28. Zhang, L. et al. (2012) RNA-seq reveals novel transcriptome of genes and their isoforms in human pulmonary microvascular endothelial cells treated with thrombin. PLoS One, 2, e31229.