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

2017; Oxford University Press; Volume: 46; Issue: D1 Linguagem: Inglês

10.1093/nar/gkx760

1362-4962

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

Single-cell and spatial transcriptomics

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.