PMID- 32511325
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20240216
DP  - 2020 Jun 29
TI  - Prioritization of SARS-CoV-2 epitopes using a pan-HLA and global population 
      inference approach.
LID - 2020.03.30.016931 [pii]
LID - 10.1101/2020.03.30.016931 [doi]
AB  - SARS-CoV-2 T cell response assessment and vaccine development may benefit from an 
      approach that considers the global landscape of the human leukocyte antigen (HLA) 
      proteins. We predicted the binding affinity between 9-mer and 15-mer peptides 
      from the SARS-CoV-2 peptidome for 9,360 class I and 8,445 class II HLA alleles, 
      respectively. We identified 368,145 unique combinations of peptide-HLA complexes 
      (pMHCs) with a predicted binding affinity less than 500nM, and observed 
      significant overlap between class I and II predicted pMHCs. Using simulated 
      populations derived from worldwide HLA frequency data, we identified sets of 
      epitopes predicted in at least 90% of the population in 57 countries. We also 
      developed a method to prioritize pMHCs for specific populations. Collectively, 
      this public dataset and accessible user interface (Shiny app: 
      https://rstudio-connect.parkerici.org/content/13/) can be used to explore the 
      SARS-CoV-2 epitope landscape in the context of diverse HLA types across global 
      populations.
FAU - Campbell, Katie M
AU  - Campbell KM
AD  - Department of Medicine, Division of Hematology-Oncology, University of 
      California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
AD  - These authors contributed equally to this work.
AD  - Senior author.
AD  - Lead Contact.
FAU - Steiner, Gabriela
AU  - Steiner G
AD  - Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA.
AD  - These authors contributed equally to this work.
FAU - Wells, Daniel K
AU  - Wells DK
AD  - Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA.
FAU - Ribas, Antoni
AU  - Ribas A
AD  - Department of Medicine, Division of Hematology-Oncology, University of 
      California, Los Angeles (UCLA), Los Angeles, CA, 90095, USA.
AD  - Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA.
AD  - Department Surgery, Division of Surgical Oncology, University of California, Los 
      Angeles, Los Angeles, CA, USA.
AD  - Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
FAU - Kalbasi, Anusha
AU  - Kalbasi A
AD  - Department Surgery, Division of Surgical Oncology, University of California, Los 
      Angeles, Los Angeles, CA, USA.
AD  - Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA.
AD  - Department of Radiation Oncology, UCLA, CA, 90095, USA.
AD  - Senior author.
LA  - eng
GR  - KL2 TR001882/TR/NCATS NIH HHS/United States
GR  - R35 CA197633/CA/NCI NIH HHS/United States
GR  - T32 CA009120/CA/NCI NIH HHS/United States
PT  - Preprint
DEP - 20200629
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
PMC - PMC7239055
OTO - NOTNLM
OT  - SARS-CoV-2
OT  - T cells
OT  - epitope prediction
OT  - public resource
COIS- Declaration of Interests K.M.C is a shareholder in Geneoscopy LLC. D.K.W. is a 
      founder, equity holder and receives consulting fees from Immunai. A.R. is 
      supported by the National Institute of Health (R35 CA197633), the Ressler Family 
      Fund, the Agilent Thought Leader Award, a Stand Up to Cancer- Bristol-Meyer 
      Squibb Catalyst Research Grant (Grant Number: SU2C-AACR-CT06-17). This research 
      grant is administered by the American Association for Cancer Research, the 
      scientific partner of SU2C. A.R. is a member researcher at the Parker Institute 
      for Cancer Immunotherapy.
EDAT- 2020/06/09 06:00
MHDA- 2020/06/09 06:01
PMCR- 2020/07/10
CRDT- 2020/06/09 06:00
PHST- 2020/06/09 06:00 [pubmed]
PHST- 2020/06/09 06:01 [medline]
PHST- 2020/06/09 06:00 [entrez]
PHST- 2020/07/10 00:00 [pmc-release]
AID - 2020.03.30.016931 [pii]
AID - 10.1101/2020.03.30.016931 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2020 Jun 29:2020.03.30.016931. doi: 
      10.1101/2020.03.30.016931.