PMID- 37293077
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20231204
DP  - 2023 May 26
TI  - Neural Network Models for Sequence-Based TCR and HLA Association Prediction.
LID - 2023.05.25.542327 [pii]
LID - 10.1101/2023.05.25.542327 [doi]
AB  - T cells rely on their T cell receptors (TCRs) to recognize foreign antigens 
      presented by human leukocyte antigen (HLA) proteins. TCRs contain a record of an 
      individual's past immune activities, and some TCRs are observed only in 
      individuals with certain HLA alleles. As a result, characterising TCRs requires a 
      thorough understanding of TCR-HLA associations. To this end, we propose a neural 
      network method named Deep learning Prediction of TCR-HLA association (DePTH) to 
      predict TCR-HLA associations based on their amino acid sequences. We show that 
      the DePTH can be used to quantify the functional similarities of HLA alleles, and 
      that these HLA similarities are associated with the survival outcomes of cancer 
      patients who received immune checkpoint blockade treatment.
FAU - Liu, Si
AU  - Liu S
AD  - Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA.
FAU - Bradley, Philip
AU  - Bradley P
AD  - Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA.
AD  - Herbold Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, 
      USA.
AD  - Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA.
FAU - Sun, Wei
AU  - Sun W
AD  - Public Health Science Division, Fred Hutchinson Cancer Center, Seattle, USA.
AD  - Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, USA.
AD  - Department of Biostatistics, University of Washington, Seattle, USA.
AD  - Department of Biostatistics, University of North Carolina, Chapel Hill, USA.
LA  - eng
GR  - R56 AI169192/AI/NIAID NIH HHS/United States
PT  - Preprint
DEP - 20230526
PL  - United States
TA  - bioRxiv
JT  - bioRxiv : the preprint server for biology
JID - 101680187
UIN - PLoS Comput Biol. 2023 Nov 20;19(11):e1011664. PMID: 37983288
PMC - PMC10245990
OTO - NOTNLM
OT  - T cell receptor
OT  - amino acid sequence
OT  - human leukocyte antigen
OT  - immune checkpoint blockade
OT  - neural network
COIS- Competing interests The authors declare that they have no competing interests.
EDAT- 2023/06/09 06:42
MHDA- 2023/06/09 06:43
PMCR- 2023/06/07
CRDT- 2023/06/09 04:29
PHST- 2023/06/09 06:42 [pubmed]
PHST- 2023/06/09 06:43 [medline]
PHST- 2023/06/09 04:29 [entrez]
PHST- 2023/06/07 00:00 [pmc-release]
AID - 2023.05.25.542327 [pii]
AID - 10.1101/2023.05.25.542327 [doi]
PST - epublish
SO  - bioRxiv [Preprint]. 2023 May 26:2023.05.25.542327. doi: 
      10.1101/2023.05.25.542327.