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INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.

ABSTRACT: While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens.We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens.INTEGRATE-Neo is implemented in C?++?and Python. Full source code and installation instructions are freely available from https://github.com/ChrisMaherLab/INTEGRATE-Neo .christophermaher@wustl.edu.Supplementary data are available at Bioinformatics online.

SUBMITTER: Zhang J 

PROVIDER: S-EPMC5408800 | biostudies-other | 2017 Feb

REPOSITORIES: biostudies-other

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INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery.

Zhang Jin J   Mardis Elaine R ER   Maher Christopher A CA  

Bioinformatics (Oxford, England) 20170201 4

<h4>Motivation</h4>While high-throughput sequencing (HTS) has been used successfully to discover tumor-specific mutant peptides (neoantigens) from somatic missense mutations, the field currently lacks a method for identifying which gene fusions may generate neoantigens.<h4>Results</h4>We demonstrate the application of our gene fusion neoantigen discovery pipeline, called INTEGRATE-Neo, by identifying gene fusions in prostate cancers that may produce neoantigens.<h4>Availability and implementatio  ...[more]