VDJdb: a curated database of T-cell receptor sequences with known antigen specificity

Shugay, M., Bagaev, D. V., Zvyagin, I. V., Vroomans, R. M., Crawford, J. C., Dolton, Garry M., Komech, Ekaterina A., Sycheva, Anastasiya L., Koneva, Anna E., Egorov, Evgeniy S., Eliseev, Alexey V., Van Dyk, E., Dash, P., Attaf, Meriem, Ruis, Cristina, Ladell, Kristin Ingrid ORCID: https://orcid.org/0000-0002-9856-2938, McLaren, James E. ORCID: https://orcid.org/0000-0002-7021-5934, Matthews, Katherine K., Clemens, Ella B., Douek, Daniel C., Luciani, Fabio, Van Baarle, D., Kedzierska, Katherine, Kesmir, Can, Thomas, Paul G., Price, David ORCID: https://orcid.org/0000-0001-9416-2737, Sewell, Andrew K. ORCID: https://orcid.org/0000-0003-3194-3135 and Chudakov, Dimitry M. 2018. VDJdb: a curated database of T-cell receptor sequences with known antigen specificity. Nucleic Acids Research 46 (D1) , D419-D427. 10.1093/nar/gkx760

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Abstract

The ability to decode antigen specificities encapsulated in the sequences of rearranged T-cell receptor (TCR) genes is critical for our understanding of the adaptive immune system and promises signifi- cant advances in the field of translational medicine. Recent developments in high-throughput sequencing methods (immune repertoire sequencing technology, or RepSeq) and single-cell RNA sequencing technology have allowed us to obtain huge numbers of TCR sequences from donor samples and link them to T-cell phenotypes. However, our ability to annotate these TCR sequences still lags behind, owing to the enormous diversity of the TCR repertoire and the scarcity of available data on T-cell specificities. In this paper, we present VDJdb, a database that stores and aggregates the results of published T-cell speci- ficity assays and provides a universal platform that couples antigen specificities with TCR sequences. We demonstrate that VDJdb is a versatile instrument for the annotation of TCR repertoire data, enabling a concatenated view of antigen-specific TCR sequence motifs. VDJdb can be accessed at https://vdjdb.cdr3. net and https://github.com/antigenomics/vdjdb-db.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	Oxford University Press
ISSN:	0305-1048
Date of First Compliant Deposit:	12 September 2017
Date of Acceptance:	17 August 2017
Last Modified:	09 May 2023 17:11
URI:	https://orca.cardiff.ac.uk/id/eprint/104554

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