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BreakTrans: uncovering the genomic architecture of gene fusions

Ken Chen12*, Nicholas E Navin13, Yong Wang3, Heather K Schmidt4, John W Wallis4, Beifang Niu4, Xian Fan12, Hao Zhao1, Michael D McLellan4, Katherine A Hoadley5, Elaine R Mardis4, Timothy J Ley46, Charles M Perou5, Richard K Wilson4 and Li Ding46*

Author Affiliations

1 Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030, USA

2 Department of Computer Science, Rice University, 6100 Main St, Houston, Texas 77251, USA

3 Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030, USA

4 The Genome Institute, Washington University School of Medicine, 4444 Forest Park Ave, St Louis, MO 63108, USA

5 Department of Genetics, University of North Carolina School of Medicine, 120 Mason Farm Road, Chapel Hill, NC 27599, USA

6 Department of Medicine, Washington University School of Medicine, 660 S. Euclid Ave, St Louis, MO 63110, USA

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Genome Biology 2013, 14:R87  doi:10.1186/gb-2013-14-8-r87

Published: 23 August 2013


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 webcite