VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Research paper by
Mikhail M Shugay, Dmitriy V DV Bagaev, Ivan V IV Zvyagin, Renske M RM Vroomans, Jeremy Chase JC Crawford, Garry G Dolton, Ekaterina A EA Komech, Anastasiya L AL Sycheva, Anna E AE Koneva, Evgeniy S ES Egorov, Alexey V AV Eliseev, Ewald E Van Dyk, Pradyot P Dash, Meriem M Attaf, Cristina C Rius, Kristin K Ladell, James E JE McLaren, Katherine K KK Matthews, E Bridie EB Clemens, Daniel C DC Douek, Fabio F Luciani, Debbie D van Baarle, Katherine K Kedzierska, Can C Kesmir, Paul G PG Thomas, David A DA Price, Andrew K AK Sewell, Dmitriy M DM Chudakov
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.