PMID- 34484239
OWN - NLM
STAT- MEDLINE
DCOM- 20210915
LR  - 20240403
IS  - 1664-3224 (Electronic)
IS  - 1664-3224 (Linking)
VI  - 12
DP  - 2021
TI  - PopCover-2.0. Improved Selection of Peptide Sets With Optimal HLA and Pathogen 
      Diversity Coverage.
PG  - 728936
LID - 10.3389/fimmu.2021.728936 [doi]
LID - 728936
AB  - The use of minimal peptide sets offers an appealing alternative for design of 
      vaccines and T cell diagnostics compared to conventional whole protein 
      approaches. T cell immunogenicity towards peptides is contingent on binding to 
      human leukocyte antigen (HLA) molecules of the given individual. HLA is highly 
      polymorphic, and each variant typically presents a different repertoire of 
      peptides. This polymorphism combined with pathogen diversity challenges the 
      rational selection of peptide sets with broad immunogenic potential and 
      population coverage. Here we propose PopCover-2.0, a simple yet highly effective 
      method, for resolving this challenge. The method takes as input a set of 
      (predicted) CD8 and/or CD4 T cell epitopes with associated HLA restriction and 
      pathogen strain annotation together with information on HLA allele frequencies, 
      and identifies peptide sets with optimal pathogen and HLA (class I and II) 
      coverage. PopCover-2.0 was benchmarked on historic data in the context of HIV and 
      SARS-CoV-2. Further, the immunogenicity of the selected SARS-CoV-2 peptides was 
      confirmed by experimentally validating the peptide pools for T cell responses in 
      a panel of SARS-CoV-2 infected individuals. In summary, PopCover-2.0 is an 
      effective method for rational selection of peptide subsets with broad HLA and 
      pathogen coverage. The tool is available at 
      https://services.healthtech.dtu.dk/service.php?PopCover-2.0.
CI  - Copyright (c) 2021 Nilsson, Grifoni, Tarke, Sette and Nielsen.
FAU - Nilsson, Jonas Birkelund
AU  - Nilsson JB
AD  - Department of Health Technology, Section for Bioinformatics, Technical University 
      of Denmark, Lyngby, Denmark.
FAU - Grifoni, Alba
AU  - Grifoni A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology, La Jolla, CA, United States.
FAU - Tarke, Alison
AU  - Tarke A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology, La Jolla, CA, United States.
AD  - Department of Internal Medicine, University of Genoa, Genoa, Italy.
AD  - Department of Experimental Medicine, University of Genoa, Genoa, Italy.
FAU - Sette, Alessandro
AU  - Sette A
AD  - Center for Infectious Disease and Vaccine Research, La Jolla Institute for 
      Immunology, La Jolla, CA, United States.
FAU - Nielsen, Morten
AU  - Nielsen M
AD  - Department of Health Technology, Section for Bioinformatics, Technical University 
      of Denmark, Lyngby, Denmark.
LA  - eng
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20210817
PL  - Switzerland
TA  - Front Immunol
JT  - Frontiers in immunology
JID - 101560960
RN  - 0 (Epitopes, T-Lymphocyte)
RN  - 0 (HLA Antigens)
RN  - 0 (Peptides)
SB  - IM
MH  - Alleles
MH  - Allergy and Immunology
MH  - CD4-Positive T-Lymphocytes/immunology
MH  - CD8-Positive T-Lymphocytes/immunology
MH  - COVID-19/immunology/prevention & control
MH  - Epitopes, T-Lymphocyte/*immunology
MH  - Genotype
MH  - HLA Antigens/classification/*genetics/*immunology
MH  - Humans
MH  - Immunogenicity, Vaccine
MH  - Immunologic Techniques
MH  - Peptides/classification/*immunology
MH  - SARS-CoV-2/immunology
PMC - PMC8416060
OTO - NOTNLM
OT  - HLA
OT  - HLA class I
OT  - HLA class II
OT  - allelic coverage
OT  - epitope selection
OT  - pathogen coverage
OT  - rational epitope selection
OT  - vaccine design
COIS- The authors declare that the research was conducted in the absence of any 
      commercial or financial relationships that could be construed as a potential 
      conflict of interest.
EDAT- 2021/09/07 06:00
MHDA- 2021/09/16 06:00
PMCR- 2021/08/17
CRDT- 2021/09/06 05:55
PHST- 2021/06/22 00:00 [received]
PHST- 2021/07/30 00:00 [accepted]
PHST- 2021/09/06 05:55 [entrez]
PHST- 2021/09/07 06:00 [pubmed]
PHST- 2021/09/16 06:00 [medline]
PHST- 2021/08/17 00:00 [pmc-release]
AID - 10.3389/fimmu.2021.728936 [doi]
PST - epublish
SO  - Front Immunol. 2021 Aug 17;12:728936. doi: 10.3389/fimmu.2021.728936. eCollection 
      2021.