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

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

    Research output: Contribution to journalArticlepeer-review

    182 Citations (Scopus)

    Abstract

    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.

    Original languageEnglish
    Pages (from-to)D419-D427
    JournalNucleic Acids Research
    Volume46
    Issue numberD1
    DOIs
    Publication statusPublished - 1 Jan 2018

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