PMID- 36346610
OWN - NLM
STAT- MEDLINE
DCOM- 20221110
LR  - 20221114
IS  - 1940-6029 (Electronic)
IS  - 1064-3745 (Linking)
VI  - 2552
DP  - 2023
TI  - A Computational Pipeline for Predicting Cancer Neoepitopes.
PG  - 475-488
LID - 10.1007/978-1-0716-2609-2_27 [doi]
AB  - Mutant Peptide eXtractor and Informer (MuPeXI), by Bjerregaard et al. (Cancer 
      Immunol Immunother CII 66:1123-1130, 2017), is a program which identifies 
      tumor-specific peptides and assesses their potential to be neoepitopes. MuPeXI 
      takes as input a VCF file and a list of human leukocyte antigen (HLA) types and 
      optionally a gene expression profile to assess a peptide's potential to be a 
      neoepitope. MuPeXI can be downloaded and run both locally and on a web server. 
      Here, we describe a pipeline for processing the input data so that it can be used 
      for MuPeXI and how to run MuPeXI both locally and as a web server.
CI  - (c) 2023. Springer Science+Business Media, LLC, part of Springer Nature.
FAU - Schaap-Johansen, Anna-Lisa
AU  - Schaap-Johansen AL
AD  - Department of Health Technology, Technical University of Denmark, OrstedsPlads, 
      Lyngby, Denmark.
FAU - Marcatili, Paolo
AU  - Marcatili P
AD  - Department of Health Technology, Technical University of Denmark, OrstedsPlads, 
      Lyngby, Denmark. pamar@dtu.dk.
LA  - eng
PT  - Journal Article
PL  - United States
TA  - Methods Mol Biol
JT  - Methods in molecular biology (Clifton, N.J.)
JID - 9214969
RN  - 0 (Antigens, Neoplasm)
RN  - 0 (Peptides)
SB  - IM
MH  - Humans
MH  - *Neoplasms/genetics
MH  - Antigens, Neoplasm/genetics
MH  - Peptides/metabolism
MH  - Immunotherapy
OTO - NOTNLM
OT  - Immunotherapy
OT  - Mutation
OT  - Neoantigens
OT  - Neoepitopes
OT  - Prediction
OT  - Sequencing
OT  - Variant calling
EDAT- 2022/11/09 06:00
MHDA- 2022/11/11 06:00
CRDT- 2022/11/08 11:19
PHST- 2022/11/08 11:19 [entrez]
PHST- 2022/11/09 06:00 [pubmed]
PHST- 2022/11/11 06:00 [medline]
AID - 10.1007/978-1-0716-2609-2_27 [doi]
PST - ppublish
SO  - Methods Mol Biol. 2023;2552:475-488. doi: 10.1007/978-1-0716-2609-2_27.