title: BreakTrans: uncovering the genomic architecture of gene fusions.
abstract: Producing gene fusions through genomic structural rearrangements is a major mechanism for tumor evolution. Therefore, accurately detecting gene fusions and the originating rearrangements is of great importance for personalized cancer diagnosis and targeted therapy. We present a tool, BreakTrans, that systematically maps predicted gene fusions to structural rearrangements. Thus, BreakTrans not only validates both types of predictions, but also provides mechanistic interpretations. BreakTrans effectively validates known fusions and discovers novel events in a breast cancer cell line. Applying BreakTrans to 43 breast cancer samples in The Cancer Genome Atlas identifies 90 genomically validated gene fusions. BreakTrans is available at http://bioinformatics.mdanderson.org/main/BreakTrans.
authors: Ken
authors: K
authors: Chen
authors: Nicholas E
authors: NE
authors: Navin
authors: Yong
authors: Y
authors: Wang
authors: Heather K
authors: HK
authors: Schmidt
authors: John W
authors: JW
authors: Wallis
authors: Beifang
authors: B
authors: Niu
authors: Xian
authors: X
authors: Fan
authors: Hao
authors: H
authors: Zhao
authors: Michael D
authors: MD
authors: McLellan
authors: Katherine A
authors: KA
authors: Hoadley
authors: Elaine R
authors: ER
authors: Mardis
authors: Timothy J
authors: TJ
authors: Ley
authors: Charles M
authors: CM
authors: Perou
authors: Richard K
authors: RK
authors: Wilson
authors: Li
authors: L
authors: Ding
mesh_terms: D001271:Atlases as Topic; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D056905:Chromosome Breakpoints; D005260:Female; D018628:Gene Dosage; D015894:Genome, Human; D006801:Humans; D058977:Molecular Sequence Annotation; D050596:Oncogene Fusion; D015514:Oncogene Proteins, Fusion / Q000235:genetics*; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D015514:Oncogene Proteins, Fusion
references: Nat Genet. 2011 Mar;43(3):269-76
references: 21317889
references: Nature. 2012 Oct 4;490(7418):61-70
references: 23000897
references: Nat Med. 2011 Nov 20;17(12):1646-51
references: 22101766
references: Blood. 1988 Aug;72(2):567-72
references: 3165295
references: Genome Biol. 2011;12(1):R6
references: 21247443
references: Nat Methods. 2011 Jan;8(1):61-5
references: 21102452
references: Bioinformatics. 2012 Jul 15;28(14):1923-4
references: 22563071
references: Nat Rev Genet. 2011 May;12(5):363-76
references: 21358748
references: Genome Res. 2012 Feb;22(2):346-61
references: 21994251
references: Bioinformatics. 2009 Jul 15;25(14):1754-60
references: 19451168
references: Mol Cell. 2010 Dec 22;40(6):877-92
references: 21172654
references: Nature. 2009 Dec 24;462(7276):1005-10
references: 20033038
references: Nat Methods. 2009 Sep;6(9):677-81
references: 19668202
references: Nat Genet. 2007 Jan;39(1):41-51
references: 17173048
references: Nat Methods. 2011 Jun 12;8(8):652-4
references: 21666668
references: Genome Res. 2011 May;21(5):676-87
references: 21467264
references: Nature. 2010 Oct 28;467(7319):1061-73
references: 20981092
references: Genome Res. 2009 Jul;19(7):1270-8
references: 19447966
references: Genome Res. 2007 Sep;17(9):1296-303
references: 17675364
references: J Proteome Res. 2009 Dec;8(12):5451-64
references: 19817483
references: Nature. 1973 Jun 1;243(5405):290-3
references: 4126434
references: Bioinformatics. 2011 Jun 1;27(11):1481-8
references: 21478487
references: Cell. 2012 Jul 20;150(2):264-78
references: 22817890
references: Bioinformatics. 2003 Oct;19 Suppl 2:ii162-71
references: 14534186
references: Genome Res. 2012 Nov;22(11):2250-61
references: 22745232
references: Cell Signal. 2006 Feb;18(2):236-43
references: 15979845
references: Cell. 2011 Jan 7;144(1):27-40
references: 21215367
references: Nucleic Acids Res. 2011 Aug;39(15):e100
references: 21622959
references: Nature. 2011 Feb 10;470(7333):214-20
references: 21307934
references: Nature. 2011 Apr 7;472(7341):90-4
references: 21399628
references: Sci Transl Med. 2011 Nov 30;3(111):111ra121
references: 22133722
references: Oncogene. 2013 Jan 24;32(4):462-70
references: 22370640
references: Genome Biol. 2011 Aug 11;12(8):R72
references: 21835007
references: Nucleic Acids Res. 2010 Oct;38(18):e178
references: 20802226
references: Nat Rev Cancer. 2007 Apr;7(4):233-45
references: 17361217
references: Cell. 2012 Jan 20;148(1-2):59-71
references: 22265402
references: Oncogene. 2011 Mar 3;30(9):1059-71
references: 21042280
references: Nature. 2012 Jan 11;481(7382):506-10
references: 22237025
references: PLoS Comput Biol. 2011 May;7(5):e1001138
references: 21625565