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Front. Immunol. | doi: 10.3389/fimmu.2018.02688

Epitope specific antibodies and T cell receptors in the Immune Epitope Database.

 Swapnil Mahajan1,  Randi Vita1, Deborah Shackelford1, Jerome Lane1,  Veronique Schulten1, Laura Zarebski1, Martin C. Jespersen2, Paolo Marcatili2,  Morten Nielsen2, 3,  Alessandro Sette1 and  Bjoern Peters1*
  • 1La Jolla Institute for Allergy and Immunology (LJI), United States
  • 2Department of Bio and Health Informatics, Technical University of Denmark, Denmark
  • 3Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Argentina

The Immune Epitope Database (IEDB) is a free public resource which catalogs experiments characterizing immune epitopes. To accommodate data from next generation repertoire sequencing experiments, we recently updated how we capture and query epitope specific antibodies and T cell receptors. Specifically, we are now storing partial receptor sequences sufficient to determine CDRs and VDJ gene usage which are commonly identified by repertoire sequencing. For previously captured full length receptor sequencing data, we have calculated the corresponding CDR sequences and gene usage information using IMGT numbering and VDJ gene nomenclature format. To integrate information from receptors defined at different levels of resolution, we grouped receptors based on their host species, receptor type and CDR3 sequence. As of August 2018, we have catalogued sequence information for more than 22,510 receptors in 18,292 receptor groups, shown to bind to more than 2,241 distinct epitopes. These data are accessible as full exports and through a new dedicated query interface. The later combines the new ability to search by receptor characteristics with previously existing capability to search by epitope characteristics such as the infectious agent the epitope is derived from, or the kind of immune response involved in its recognition. We expect that this comprehensive capture of epitope specific immune receptor information will provide new insights into receptor-epitope interactions, and facilitate the development of novel tools that help in the analysis of receptor repertoire data.

Keywords: epitope, antibody, TCR - T cell receptor, AIRR, IEDB, Repertoire sequencing, CDRs, complementary determining regions

Received: 04 Sep 2018; Accepted: 31 Oct 2018.

Edited by:

Victor Greiff, University of Oslo, Norway

Reviewed by:

Andreas Lossius, University of Oslo, Norway
Pieter Meysman, University of Antwerp, Belgium  

Copyright: © 2018 Mahajan, Vita, Shackelford, Lane, Schulten, Zarebski, Jespersen, Marcatili, Nielsen, Sette and Peters. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Prof. Bjoern Peters, La Jolla Institute for Allergy and Immunology (LJI), La Jolla, United States,