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

ABSTRACT

Motivation 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. Results: 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. Availability and Implementation INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from https//github.com/ChrisMaherLab/INTEGRATE-Neo . Contact christophermaher@wustl.edu. Supplementary information Supplementary data are available at Bioinformatics online.