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BioMed Central, Genome Biology, 8(14), p. R87

DOI: 10.1186/gb-2013-14-8-r87

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BreakTrans: uncovering the genomic architecture of gene fusions

Journal article published in 2013 by Ken Chen, Nicholas E. Navin, Yong Wang ORCID, Heather K. Schmidt, John W. Wallis, Beifang Niu, Xian Fan, Hao Zhao, Michael D. McLellan, Katherine A. Hoadley ORCID, Elaine R. Mardis, Timothy J. Ley, Charles M. Perou, Richard K. Wilson, Li Ding
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

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