vdjdb-db

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`antigen.gene` / `antigen.species` mix up for some human epitopes

1

I've just updated an analysis to use the May 2024 release and noticed that there's a few entries for anti-human TCRs that appear to have the `antigen.gene` and `antigen.species` fields...

JamieHeather

Check [stcrdab](https://opig.stats.ox.ac.uk/webapps/stcrdab-stcrpred) and [PDB](https://www.rcsb.org/search?request=%7B%22query%22%3A%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22group%22%2C%22nodes%22%3A%5B%7B%22type%22%3A%22terminal%22%2C%22service%22%3A%22full_text%22%2C%22parameters%22%3A%7B%22value%22%3A%22%5C%22t-cell%5C%22%20receptor%20tcr%22%7D%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%5D%2C%22logical_operator%22%3A%22and%22%2C%22label%22%3A%22full_text%22%7D%5D%2C%22logical_operator%22%3A%22and%22%7D%2C%22return_type%22%3A%22entry%22%2C%22request_options%22%3A%7B%22paginate%22%3A%7B%22start%22%3A0%2C%22rows%22%3A25%7D%2C%22results_content_type%22%3A%5B%22experimental%22%5D%2C%22sort%22%3A%5B%7B%22sort_by%22%3A%22score%22%2C%22direction%22%3A%22desc%22%7D%5D%2C%22scoring_strategy%22%3A%22combined%22%7D%2C%22request_info%22%3A%7B%22query_id%22%3A%22f5de3657a14b81a1670b1252242e7a17%22%7D%7D) to update [PDB_Database.txt chunk](https://github.com/antigenomics/vdjdb-db/blob/master/chunks/PDB_Database.txt) and address #360.

mikessh

Wrong HLA info for "ASNENMETM" epitope

1

Hi Thanks for all the work no VDJdb. I recently realized that one epitope (ASNENMETM) used in the Dash et al. Nature 2017 paper is annotated as restricted to H-2Kb...

dagfeller

Automatically build database then chunks are changed

LuppovDaniil

[Dolton et al. HLA A*24:02-restricted T cell receptors cross-recognize bacterial and preproinsulin peptides in type 1 diabetes. J Clin Invest. 2024 Sep ](https://www.jci.org/articles/view/164535)

LuppovDaniil

[Peng et al. Characterization of HPV6/11-reactive T-cell subsets in papillomas of patients with juvenile-onset recurrent respiratory papillomatosis and identification of HPV11 E7-specific candidate TCR clonotypes. J Virol. 2024](https://journals.asm.org/doi/abs/10.1128/jvi.00677-24)

LuppovDaniil

remove duplicated dataset: https://github.com/antigenomics/vdjdb-db/issues/351

LuppovDaniil

https://www.genenames.org/ https://www.imgt.org/IMGTrepertoire/index.php?section=LocusGenes&repertoire=nomenclatures&species=human&group=TRBV https://www.ebi.ac.uk/ipd/imgt/hla/ research geтnes nomenclature, check with mirpy genes and nomencluature tables

LuppovDaniil

[Ke-Yue Ma et al. Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature. 2024. ](https://www.nature.com/articles/s41586-024-07575-x)

LuppovDaniil

[Ke-Yue Ma et al. High-throughput and high-dimensional single-cell analysis of antigen-specific CD8+ T cells. Nat Immunol. 2021](https://pubmed.ncbi.nlm.nih.gov/34811538/)

LuppovDaniil