VDJdb: a curated database of T-cell receptor sequences with known antigen specificity
By M. Shugay, D. Bagaev, I. Zvyagin, Renske M. A. Vroomans, J. Crawford, G. Dolton, E. Komech, A. L. Sycheva, Anna E. Koneva, E. Egorov and 18 more. Nucleic Acids Res., 2017
544 citations recorded by the source corpus.
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.
Subfields: Immunology, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/cfd86d8ddd03ccacd18343d091ac93745e4187d6
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In Immunology
In Molecular Biology
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Citations in the corpus
- TCRmodel: high resolution modeling of T cell receptors from sequence (2018, methodology): “By providing the community with the means to generate high resolution TCR structural models from sequence, TCRmodel complements recent public databases that provide TCR sequences (24,28), providing the means to extend the insights from these TCR sequence datasets into structural space.”
- VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium (2019, methodology): “After the first version of VDJdb (6) and a pathology-associated TCR database (McPAS-TCR (7)) were published, a commonly used iEDB database that describes immunogenic antigens was also modified to add metadata re-lated to TCR and B-cell receptor sequences (8), highlighting the overall demand for…”
- Modern Hopfield Networks and Attention for Immune Repertoire Classification (2020, background): “We envision that with (a) the increasing availability of large immunosequencing datasets (Kovaltsuk et al., 2018; Corrie et al., 2018; Christley et al., 2018; Zhang et al., 2020; Rosenfeld et al., 2018; Shugay et al., 2018), (b) further fine-tuning of ground-truth benchmarking immune receptor datase”