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

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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.

Availability and Implementation:

INTEGRATE-Neo is implemented in C ++ and Python. Full source code and installation instructions are freely available from


Supplementary information:

Supplementary data are available at Bioinformatics online.

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