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AGFusion: annotate and visualize gene fusions

Charlie Murphy, Olivier Elemento
doi: https://doi.org/10.1101/080903
Charlie Murphy
1The Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA, 10021
3Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021
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Olivier Elemento
2Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York, NY, USA, 10021
3Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, 10021
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Abstract

Summary The discovery of novel gene fusions in tumor samples has rapidly accelerated with the rise of next-generation sequencing. A growing number of tools enable discovery of gene fusions from RNA-seq data. However it is likely that not all gene fusions are driving tumors. Assessing the potential functional consequences of a fusion is critical to understand their driver role. It is also challenging as gene fusions are described by chromosomal breakpoint coordinates that need to be translated into an actual amino acid fusion sequence and predicted domain architecture of the fusion proteins. Currently there are no easy-to-use tools that can automatically reconstruct and visualize fusion proteins from genomic breakpoints. To facilitate the functional interpretation of gene fusions, we developed AGFusion, available as an online web tool that can be readily used by non-computational researchers as well as a python package that can be built into computational pipelines. With minimal input from the user, AGFusion predicts the cDNA, CDS, and protein sequences of all gene fusion products based on all combinations of gene isoforms. For protein coding fusions, AGFusion can annotate and visualize the protein domain architecture. AGFusion currently supports Homo sapiens (genome builds GRCh37 and GRCh38) and Mus musculus (genome build GRCm38) and new genomes can easily be added.

Availability AGFusion python package is freely available at https://github.com/murphycj/AGFusion under the MIT license. The AGFusion web app is available at http://agfusion.info

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted October 14, 2016.
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AGFusion: annotate and visualize gene fusions
Charlie Murphy, Olivier Elemento
bioRxiv 080903; doi: https://doi.org/10.1101/080903
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AGFusion: annotate and visualize gene fusions
Charlie Murphy, Olivier Elemento
bioRxiv 080903; doi: https://doi.org/10.1101/080903

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