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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Antigens / chemistry*
  • Antigens / immunology
  • Antigens / metabolism
  • Binding Sites
  • Databases, Protein*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Internet
  • Macaca mulatta
  • Major Histocompatibility Complex / genetics
  • Major Histocompatibility Complex / immunology
  • Mice
  • Models, Molecular
  • Molecular Sequence Annotation*
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Protein Structure, Secondary
  • Receptors, Antigen, T-Cell / chemistry*
  • Receptors, Antigen, T-Cell / immunology
  • Receptors, Antigen, T-Cell / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Single-Cell Analysis
  • Software*
  • T-Lymphocytes / cytology
  • T-Lymphocytes / immunology

Substances

  • Antigens
  • Receptors, Antigen, T-Cell