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

      Shugay, Mikhail; Bagaev, Dmitriy V; Zvyagin, Ivan V; Vroomans, Renske M; Crawford, Jeremy Chase; Dolton, Garry; Komech, Ekaterina A; Sycheva, Anastasiya L; Koneva, Anna E; Egorov, Evgeniy S; Eliseev, Alexey V; Van Dyk, Ewald; Dash, Pradyot; Attaf, Meriem; Rius, Cristina; Ladell, Kristin; McLaren, James E; Matthews, Katherine K; Clemens, E Bridie; Douek, Daniel C; Luciani, Fabio; van Baarle, Debbie; Kedzierska, Katherine; Kesmir, Can; Thomas, Paul G; Price, David A; Sewell, Andrew K; Chudakov, Dmitriy M (2018-01-04)
      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.