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

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    Authors
    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
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    Type
    Article
    Language
    en
    
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    Title
    VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
    Published in
    Nucleic Acids Res 2018; 46(D1):D419-27
    Publiekssamenvatting
    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.
    DOI
    10.1093/nar/gkx760
    PMID
    28977646
    URI
    http://hdl.handle.net/10029/621387
    ae974a485f413a2113503eed53cd6c53
    10.1093/nar/gkx760
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