MuPeXI: prediction of neo-epitopes from tumor sequencing data

Anne-Mette Bjerregaard, Morten Nielsen, Sine Reker Hadrup, Zoltan Imre Szallasi, Aron Charles Eklund

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI .
Original languageEnglish
JournalCancer Immunology, Immunotherapy
Volume66
Issue number9
Pages (from-to)1123–1130
ISSN0340-7004
DOIs
Publication statusPublished - 2017

Keywords

  • Immunotherapy
  • Mutation
  • Neo-antigens
  • Neo-epitopes
  • Prediction
  • Sequencing

Cite this

@article{1174a2a51e5c45ef8f775747e56f290e,
title = "MuPeXI: prediction of neo-epitopes from tumor sequencing data",
abstract = "Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI .",
keywords = "Immunotherapy, Mutation, Neo-antigens, Neo-epitopes, Prediction, Sequencing",
author = "Anne-Mette Bjerregaard and Morten Nielsen and Hadrup, {Sine Reker} and Szallasi, {Zoltan Imre} and Eklund, {Aron Charles}",
year = "2017",
doi = "10.1007/s00262-017-2001-3",
language = "English",
volume = "66",
pages = "1123–1130",
journal = "Cancer Immunology, Immunotherapy",
issn = "0340-7004",
publisher = "Springer",
number = "9",

}

MuPeXI: prediction of neo-epitopes from tumor sequencing data. / Bjerregaard, Anne-Mette; Nielsen, Morten; Hadrup, Sine Reker; Szallasi, Zoltan Imre; Eklund, Aron Charles.

In: Cancer Immunology, Immunotherapy, Vol. 66, No. 9, 2017, p. 1123–1130.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - MuPeXI: prediction of neo-epitopes from tumor sequencing data

AU - Bjerregaard, Anne-Mette

AU - Nielsen, Morten

AU - Hadrup, Sine Reker

AU - Szallasi, Zoltan Imre

AU - Eklund, Aron Charles

PY - 2017

Y1 - 2017

N2 - Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI .

AB - Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI .

KW - Immunotherapy

KW - Mutation

KW - Neo-antigens

KW - Neo-epitopes

KW - Prediction

KW - Sequencing

U2 - 10.1007/s00262-017-2001-3

DO - 10.1007/s00262-017-2001-3

M3 - Journal article

VL - 66

SP - 1123

EP - 1130

JO - Cancer Immunology, Immunotherapy

JF - Cancer Immunology, Immunotherapy

SN - 0340-7004

IS - 9

ER -