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

• Authors: SHUGAY Mikhail; BAGAEV D.V.; ZVYAGIN I.V.; VROOMANS R.M.; CRAWFORD J.C.; DOLTON G.; KOMECH E.A.; SYCHEVA A.L.; KONEVA A.E.; EGOROV E.S.; ELISEEV A.V.; VAN DYK E.; DASH P.; ATTAF M.; RIUS C.; LADELL K.; MCLAREN J.E.; MATTHEWS K.K.; CLEMENS E.B.; DOUEK D.C.; LUCIANI F.; VAN BAARLE D.; KEDZIERSKA K.; KESMIR C.; THOMAS P.G.; PRICE D.A.; SEWELL A.K.; CHUDAKOV Dmitriy
• Year of publication: 2018
• Type: Article in Periodical
• Magazine / Source: Nucleic Acids Research
• MU Faculty or unit: Central European Institute of Technology
• web: http://dx.doi.org/10.1093/nar/gkx760
• Doi: https://doi.org/10.1093/nar/gkx760
• Keywords: SIV INFECTION; REPERTOIRE; TETRAMERS
• Description: 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 significant 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 specificity 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.

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• CEITEC 2020