Breakfusion: Targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data

Bioinformatics

Volumn 28, Issue 14, 2012, Pages 1923-1924

  Chen, Ken ^a   Wallis, John W ^b,c   Kandoth, Cyriac ^b   Kalicki veizer, Joelle M ^b   Mungall, Karen L ^d   Mungall, Andrew J ^d   Jones, Steven J ^d   Marra, Marco A ^d   Ley, Timothy J ^b,c   Mardis, Elaine R ^b,c   Wilson, Richard K ^b,c   Weinstein, John N ^a   Ding, Li ^b,c  

^a UNIVERSITY OF TEXAS MD ANDERSON CANCER CENTER   (United States)

^b WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c WASHINGTON UNIVERSITY   (United States)

^d BRITISH COLUMBIA CANCER AGENCY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; HUMAN; METHODOLOGY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; TUMOR CELL LINE;

CELL LINE, TUMOR; COMPUTATIONAL BIOLOGY; HUMANS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, RNA; SOFTWARE; TRANSCRIPTOME;

EID: 84864143346     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts272     Document Type: Article

References (14)

1. Berger, M. F. et al. (2010) Integrative analysis of the melanoma transcriptome. Genome Res, 20, 413-427.
2. Brudno, M. et al. (2003) Glocal alignment: finding rearrangements during alignment. Bioinformatics, 19 (Suppl. 1), i54-i62.
3. Chen, K. et al. (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods, 6, 677-681.
4. Edgren, H. et al. (2011) Identification of fusion genes in breast cancer by paired-end RNA-sequencing, Genome Biol., 12, R6.
5. Garber, M. et al. (2011) Computational methods for transcriptome annotation and quantification using RNA-seq. Nat. Methods, 8, 469-477.
6. Grabherr, M. G. et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat. Biotechnol., 29, 644-652.
7. Kent, W. J. (2002) BLAT - The BLAST-like alignment tool. Genome Res., 12, 656-664.
8. Kim, D. and Salzberg, S. L. (2011) TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome Biol., 12, R72.
9. Martin, J. A. and Wang, Z. (2011) Next-generation transcriptome assembly. Nat. Rev. Genet., 12, 671-682.
10. McPherson, A. et al. (2011) deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput. Biol., 7, e1001138.
11. Mills, R. E. et al. (2011) Mapping copy number variation by population-scale genome sequencing. Nature, 470, 59-65.
12. Robertson, G. et al. (2010) De novo assembly and analysis of RNA-seq data, Nat Methods, 7, 909-U962.
13. Sboner, A. et al. (2010) FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data. Genome Biol., 11.
14. 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.