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Updated: Mar 12, 2026

Oncogenic Gene Fusion Detection Using Anchored Multiplex Polymerase Chain Reaction Followed by Next Generation Sequencing
Published on: July 5, 2019
INTEGRATE-neo: a pipeline for personalized gene fusion neoantigen discovery
Jin Zhang1,2,3, Elaine R Mardis1,3,4,5,6, Christopher A Maher1,2,3,7
1McDonnell Genome Institute.
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.
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