Publication details

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
Citation
Web	http://dx.doi.org/10.1093/nar/gkx760
Doi	http://dx.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.
Related projects:	CEITEC 2020