BreakTrans: uncovering the genomic architecture of gene fusions
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, tha...
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| Format: | Online |
| Language: | English |
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BioMed Central
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054677/ |
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pubmed-4054677 |
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pubmed-40546772014-06-12 BreakTrans: uncovering the genomic architecture of gene fusions 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 Software 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 BioMed Central 2013 2013-08-23 /pmc/articles/PMC4054677/ /pubmed/23972288 http://dx.doi.org/10.1186/gb-2013-14-8-r87 Text en Copyright © 2013 Chen et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
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 |
| spellingShingle |
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 BreakTrans: uncovering the genomic architecture of gene fusions |
| author_facet |
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 |
| author_sort |
Chen, Ken |
| title |
BreakTrans: uncovering the genomic architecture of gene fusions |
| title_short |
BreakTrans: uncovering the genomic architecture of gene fusions |
| title_full |
BreakTrans: uncovering the genomic architecture of gene fusions |
| title_fullStr |
BreakTrans: uncovering the genomic architecture of gene fusions |
| title_full_unstemmed |
BreakTrans: uncovering the genomic architecture of gene fusions |
| title_sort |
breaktrans: uncovering the genomic architecture of gene fusions |
| description |
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 |
| publisher |
BioMed Central |
| publishDate |
2013 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054677/ |
| _version_ |
1612100095745982464 |