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Nucleic Acids Res. 2018 Jan 4;46(D1):D419-D427. doi: 10.1093/nar/gkx760.

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

Author information

1
Pirogov Russian National Research Medical University, Moscow 117997, Russia.
2
Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.
3
Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
4
Central European Institute of Technology, Brno 60177, Czech Republic.
5
Nizhny Novgorod State Medical Academy, Nizhny Novgorod 603950, Russia.
6
Theoretical Biology and Bioinformatics, Science Faculty, Utrecht University, Utrecht 3512 JE, The Netherlands.
7
Department of Immunology, St. Jude's Children's Research Hospital, Memphis, TN 38105, USA.
8
Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.
9
Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville VIC 3010, Australia.
10
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
11
Viral Immunology Systems Program, Kirby Institute, School of Medical Sciences, University of New South Wales, Kensington NSW 2052, Australia.
12
Center for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven 3720 BA, The Netherlands.
13
Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK.

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.

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