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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq

View ORCID ProfileBrian J. Haas, Alex Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas G. Doak, Nathalie Pochet, Jing Sun, Catherine J. Wu, Thomas R. Gingeras, Aviv Regev
doi: https://doi.org/10.1101/120295
Brian J. Haas
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Alex Dobin
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Nicolas Stransky
3Blueprint Medicines, Cambridge, MA 02129, USA
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Bo Li
4Department of Computer Science, University of California, Berkeley 94720, USA
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Xiao Yang
5Grail, Inc., Menlo Park, CA 94025, USA
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Timothy Tickle
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Asma Bankapur
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Carrie Ganote
6National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405, USA
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Thomas G. Doak
6National Center for Genome Analysis Support, Indiana University, Bloomington, Indiana 47405, USA
7Department of Biology, University of Indiana, Bloomington, Indiana 47405, USA
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Nathalie Pochet
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
8Program in Translational Neuro Psychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
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Jing Sun
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
9Division of Medical Oncology, Dana-Farber Cancer Institute; Department of Medicine, Brigham and Women’s Hospital; Harvard Medical School, Boston, MA 02115, USA
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Catherine J. Wu
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
9Division of Medical Oncology, Dana-Farber Cancer Institute; Department of Medicine, Brigham and Women’s Hospital; Harvard Medical School, Boston, MA 02115, USA
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Thomas R. Gingeras
2Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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Aviv Regev
1Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
10Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
11Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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Abstract

Motivation Fusion genes created by genomic rearrangements can be potent drivers of tumorigenesis. However, accurate identification of functionally fusion genes from genomic sequencing requires whole genome sequencing, since exonic sequencing alone is often insufficient. Transcriptome sequencing provides a direct, highly effective alternative for capturing molecular evidence of expressed fusions in the precision medicine pipeline, but current methods tend to be inefficient or insufficiently accurate, lacking in sensitivity or predicting large numbers of false positives. Here, we describe STAR-Fusion, a method that is both fast and accurate in identifying fusion transcripts from RNA-Seq data.

Results We benchmarked STAR-Fusion’s fusion detection accuracy using both simulated and genuine Illumina paired-end RNA-Seq data, and show that it has superior performance compared to popular alternative fusion detection methods.

Availability and implementation STAR-Fusion is implemented in Perl, freely available as open source software at http://star-fusion.github.io, and supported on Linux.

Contact bhaas{at}broadinstitute.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted March 24, 2017.
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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
Brian J. Haas, Alex Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas G. Doak, Nathalie Pochet, Jing Sun, Catherine J. Wu, Thomas R. Gingeras, Aviv Regev
bioRxiv 120295; doi: https://doi.org/10.1101/120295
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STAR-Fusion: Fast and Accurate Fusion Transcript Detection from RNA-Seq
Brian J. Haas, Alex Dobin, Nicolas Stransky, Bo Li, Xiao Yang, Timothy Tickle, Asma Bankapur, Carrie Ganote, Thomas G. Doak, Nathalie Pochet, Jing Sun, Catherine J. Wu, Thomas R. Gingeras, Aviv Regev
bioRxiv 120295; doi: https://doi.org/10.1101/120295

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