BreakTrans: uncovering the genomic architecture of gene fusions

被引：19

作者：

Chen, Ken ^{[1
,2
]}

Navin, Nicholas E. ^{[1
,3
]}

Wang, Yong ^{[3
]}

Schmidt, Heather K. ^{[4
]}

Wallis, John W. ^{[4
]}

Niu, Beifang ^{[4
]}

Fan, Xian ^{[1
,2
]}

Zhao, Hao ^{[1
]}

McLellan, Michael D. ^{[4
]}

Hoadley, Katherine A. ^{[5
]}

Mardis, Elaine R. ^{[4
]}

Ley, Timothy J. ^{[4
,6
]}

Perou, Charles M. ^{[5
]}

Wilson, Richard K. ^{[4
]}

Ding, Li ^{[4
,6
]}

机构：

[1] Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA

[2] Rice Univ, Dept Comp Sci, Houston, TX 77251 USA

[3] Univ Texas MD Anderson Canc Ctr, Dept Genet, Houston, TX 77030 USA

[4] Washington Univ, Sch Med, Genome Inst, St Louis, MO 63108 USA

[5] Univ N Carolina, Sch Med, Dept Genet, Chapel Hill, NC 27599 USA

[6] Washington Univ, Sch Med, Dept Med, St Louis, MO 63110 USA

来源：

GENOME BIOLOGY | 2013年 / 14卷 / 08期

关键词：

BREAST-CANCER; STRUCTURAL VARIATION; RNA-SEQ; IDENTIFICATION; REARRANGEMENTS; EVOLUTION; DISCOVERY; ALGORITHM;

D O I：

10.1186/gb-2013-14-8-r87

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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

引用

页数：11

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