Bellerophontes: An RNA-Seq data analysis framework for chimeric transcripts discovery based on accurate fusion model

Bioinformatics

Volumn 28, Issue 16, 2012, Pages 2114-2121

  Abate, Francesco ^a   Acquaviva, Andrea ^a   Paciello, Giulia ^a   Foti, Carmelo ^a   Ficarra, Elisa ^a   Ferrarini, Alberto ^b   Delledonne, Massimo ^b   Iacobucci, Ilaria ^c   Soverini, Simona ^c   Martinelli, Giovanni ^c   Macii, Enrico ^a  

^a POLITECNICO DI TORINO   (Italy)

^b UNIVERSITY OF VERONA   (Italy)

^c UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

RNA;

ALGORITHM; ARTICLE; BIOLOGY; CHRONIC MYELOID LEUKEMIA; COMPUTER PROGRAM; GENE FUSION; GENETICS; HUMAN; METHODOLOGY; RNA SPLICING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE FUSION; HUMANS; LEUKEMIA, MYELOGENOUS, CHRONIC, BCR-ABL POSITIVE; RNA; RNA SPLICING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE;

EID: 84865099716     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts334     Document Type: Article

References (21)

1. Ameur, A. et al. (2010) Global and unbiased detection of splice junctions from RNA-seq data. Genome Biol., 11, R34.
2. Berger, M.F. et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res., 20, 413-427.
3. Bryant, D.W. et al. (2010) Supersplat-spliced RNA-seq alignment. Bioinformatics, 26, 1500-1505.
4. Dongen, J.J. et al. (1999) Primers and protocols for standardized detection of minimal residual disease in acute lymphoblastic leukemia using immunoglobulin and T cell receptor gene rearrangements and TAL1 deletions as PCR targets: report of the BIOMED-1 CONCERTED ACTION: investigation of minimal residual disease in acute leukemias. Leukemia, 13, 110-118.
5. Edgren, H. et al. (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing. Genome Biol., 12, R6.
6. Fujita, P.A. et al. (2010) The UCSC Genome Browser database: update 2011. Nucleic Acids Res., 39, D876-D882.
7. Ge, H. et al. (2011) FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics, 27, 1922-1928.
8. Iyer, M.K. et al. (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics, 27, 2903-2904.
9. Langmead, B. et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
10. Li, H. et al. (2006) TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res., 34, D572-D580.
11. Li, Y. et al. (2011) FusionHunter: identifying fusion transcripts in cancer using pairedend RNA-seq. Bioinformatics, 27, 1708-1710.
12. Maher, C.A. et al. (2009) Transcriptome sequencing to detect gene fusions in cancer. Nature, 458, 97-101.
13. Maher, C.A. et al. (2009) Chimeric transcript discovery by paired-end transcriptome sequencing. PNAS, 106, 12353-12358.
14. McPherson, A. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol., 7, e1001138.
15. Quail, M.A. et al. (2009) Improved protocols for the illumina genome analyzer sequencing system. Curr. Prot. Human Genet., 18, 18.2.
16. Sboner, A. et al. (2010) FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol., 11, R104.
17. Soverini, S. et al. (2011) IDH2 somatic mutations in chronic myeloid leukemia patients in blast crisis. Leukemia: Off. J. Leukemia Soc. Am., 25, 178-181.
18. Steidl, C. et al. (2011) MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers. Nature, 471, 377-381.
19. Trapnell, C. et al. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25, 1105-1111.
20. 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.
21. Wang, K. et al. (2010) MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Nucleic Acids Res., 38, e178-e178.