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BreakTrans: uncovering the genomic architecture of gene fusions.

Authors
  • Chen, Ken
  • Navin, Nicholas E
  • Wang, Yong
  • Schmidt, Heather K
  • Wallis, John W
  • Niu, Beifang
  • Fan, Xian
  • Zhao, Hao
  • McLellan, Michael D
  • Hoadley, Katherine A
  • Mardis, Elaine R
  • Ley, Timothy J
  • Perou, Charles M
  • Wilson, Richard K
  • Ding, Li
Type
Published Article
Publication Date
Jan 01, 2013
Volume
14
Issue
8
Identifiers
DOI: 10.1186/gb-2013-14-8-r87
PMID: 23972288
Source
Medline
License
Unknown

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.

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