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

Bioinformatics. 2017 Feb 15;33(4):555-557. doi: 10.1093/bioinformatics/btw674.


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 .


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Antigens, Neoplasm / analysis*
  • Antigens, Neoplasm / genetics
  • Gene Fusion*
  • Genomics / methods*
  • Humans
  • Male
  • Prostatic Neoplasms / genetics*
  • Prostatic Neoplasms / metabolism
  • Sequence Analysis, DNA / methods
  • Software*


  • Antigens, Neoplasm