BreakTrans: Uncovering the genomic architecture of gene fusions

Ken Chen, Nicholas E. Navin, Yong Wang, Heather K. Schmidt, John W. Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D. McLellan, Katherine A. Hoadley, Elaine R. Mardis, Timothy J. Ley, Charles M. Perou, Richard K. Wilson, Li Ding

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12 Scopus citations

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.

Original languageEnglish
Article numberR87
JournalGenome biology
Volume14
Issue number8
DOIs
StatePublished - Aug 23 2013

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    Chen, K., Navin, N. E., Wang, Y., Schmidt, H. K., Wallis, J. W., Niu, B., Fan, X., Zhao, H., McLellan, M. D., Hoadley, K. A., Mardis, E. R., Ley, T. J., Perou, C. M., Wilson, R. K., & Ding, L. (2013). BreakTrans: Uncovering the genomic architecture of gene fusions. Genome biology, 14(8), [R87]. https://doi.org/10.1186/gb-2013-14-8-r87