VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
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Bagaev, Dmitriy V
Zvyagin, Ivan V
Vroomans, Renske M
Crawford, Jeremy Chase
Komech, Ekaterina A
Sycheva, Anastasiya L
Koneva, Anna E
Egorov, Evgeniy S
Eliseev, Alexey V
Van Dyk, Ewald
McLaren, James E
Matthews, Katherine K
Clemens, E Bridie
Douek, Daniel C
van Baarle, Debbie
Thomas, Paul G
Price, David A
Sewell, Andrew K
Chudakov, Dmitriy M
MetadataShow full item record
TitleVDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Published inNucleic Acids Res 2018; 46(D1):D419-27
PubliekssamenvattingThe 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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