@article{4c2c9cbeb521461cb85c9ee33901e7b7,
title = "BreakTrans: Uncovering the genomic architecture of gene fusions",
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.",
author = "Ken Chen and Navin, {Nicholas E.} and Yong Wang and Schmidt, {Heather K.} and Wallis, {John W.} and Beifang Niu and Xian Fan and Hao Zhao and McLellan, {Michael D.} and Hoadley, {Katherine A.} and Mardis, {Elaine R.} and Ley, {Timothy J.} and Perou, {Charles M.} and Wilson, {Richard K.} and Li Ding",
note = "Funding Information: We thank Andrew Mcpherson for helping set up nFuse-0.1.4 and Tenghui Chen for assistance in fusion analysis. Nick Navin is a Nadia{\textquoteright}s Gift Foundation Damon Runyon-Rachleff Innovator (DRR-25-13). This work was supported in part by the National Cancer Institute (NCI) grant R01-CA172652-01 to KC, R21CA174397-01 and R01CA169244-01 to NN, National Human Genome Research Institute (NHGRI) grant U01-HG006517 and U54-HG003079, and the National Cancer Institute Cancer Center Support Grant P30-CA016672 and U24-CA143848. The results published here are in part based upon data generated by TCGA established by the NCI and NHGRI. Information about TCGA and the investigators and institutions who constitute the TCGA research network can be found at [43].",
year = "2013",
month = aug,
day = "23",
doi = "10.1186/gb-2013-14-8-r87",
language = "English (US)",
volume = "14",
journal = "Genome biology",
issn = "1474-7596",
publisher = "BioMed Central",
number = "8",
}