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

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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

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


Dive into the research topics of 'BreakTrans: Uncovering the genomic architecture of gene fusions'. Together they form a unique fingerprint.

Cite this