AGFusion: annotate and visualize gene fusions

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 functiona...

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Bibliographic Details
Published inbioRxiv
Main Authors Murphy, Charlie, Elemento, Olivier
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 14.10.2016
Subjects
Amino acid sequence
Breakpoints
Computer applications
Frogs
Gene fusion
Genomes
Isoforms
Next-generation sequencing
Pectin
Proteins
Ribonucleic acid
RNA
Tumors
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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.
DOI:10.1101/080903