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

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