Shugay, M., Bagaev, D. V., Zvyagin, I. V., Vroomans, R. M., Crawford, J. C., Dolton, Garry M., Komech, Ekaterina A., Sycheva, Anastasiya L., Koneva, Anna E., Egorov, Evgeniy S., Eliseev, Alexey V., Van Dyk, E., Dash, P., Attaf, Meriem, Ruis, Cristina, Ladell, Kristin Ingrid  ORCID: https://orcid.org/0000-0002-9856-2938, McLaren, James E. ORCID: https://orcid.org/0000-0002-7021-5934, Matthews, Katherine K., Clemens, Ella B., Douek, Daniel C., Luciani, Fabio, Van Baarle, D., Kedzierska, Katherine, Kesmir, Can, Thomas, Paul G., Price, David ORCID: https://orcid.org/0000-0001-9416-2737, Sewell, Andrew K. ORCID: https://orcid.org/0000-0003-3194-3135 and Chudakov, Dimitry M.
2018.
VDJdb: a curated database of T-cell receptor sequences with known antigen specificity.
Nucleic Acids Research
46
(D1)
, D419-D427.
10.1093/nar/gkx760
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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 signifi- cant 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 speci- ficity 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.
| Item Type: | Article |
|---|---|
| Date Type: | Publication |
| Status: | Published |
| Schools: | Schools > Medicine |
| Publisher: | Oxford University Press |
| ISSN: | 0305-1048 |
| Date of First Compliant Deposit: | 12 September 2017 |
| Date of Acceptance: | 17 August 2017 |
| Last Modified: | 09 May 2023 17:11 |
| URI: | https://orca.cardiff.ac.uk/id/eprint/104554 |
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