1. Computational and Systems Biology
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Method for identification of condition-associated public antigen receptor sequences

  1. Mikhail V Pogorelyy
  2. Anastasia A Minervina
  3. Dmitriy M Chudakov
  4. Ilgar Z Mamedov
  5. Yuri B Lebedev  Is a corresponding author
  6. Thierry Mora  Is a corresponding author
  7. Aleksandra M Walczak  Is a corresponding author
  1. Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Russian Federation
  2. École Normale Supérieure, France
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Cite this article as: eLife 2018;7:e33050 doi: 10.7554/eLife.33050

Abstract

Diverse repertoires of hypervariable immunoglobulin receptors (TCR and BCR) recognize antigens in the adaptive immune system. The development of immunoglobulin receptor repertoire sequencing methods makes it possible to perform repertoire-wide disease association studies of antigen receptor sequences. We developed a statistical framework for associating receptors to disease from only a small cohort of patients, with no need for a control cohort. Our method successfully identifies previously validated Cytomegalovirus and type 1 diabetes responsive TCRβ sequences.

Article and author information

Author details

  1. Mikhail V Pogorelyy

    Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    No competing interests declared.
  2. Anastasia A Minervina

    Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    No competing interests declared.
  3. Dmitriy M Chudakov

    Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0430-790X
  4. Ilgar Z Mamedov

    Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
    Competing interests
    No competing interests declared.
  5. Yuri B Lebedev

    Department of Genomics of Adaptive Immunity, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
    For correspondence
    lebedev_yb@mx.ibch.ru
    Competing interests
    No competing interests declared.
  6. Thierry Mora

    Laboratoire de Physique Statistique, École Normale Supérieure, Paris, France
    For correspondence
    tmora@lps.ens.fr
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5456-9361
  7. Aleksandra M Walczak

    Laboratoire de Physique Theorique, École Normale Supérieure, Paris, France
    For correspondence
    awalczak@lpt.ens.fr
    Competing interests
    Aleksandra M Walczak, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2686-5702

Funding

Russian Science Foundation (15-15-00178)

  • Dmitriy M Chudakov
  • Ilgar Z Mamedov
  • Yuri B Lebedev

European Research Council (724208)

  • Aleksandra M Walczak

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Arup K Chakraborty, Massachusetts Institute of Technology, United States

Publication history

  1. Received: October 24, 2017
  2. Accepted: March 12, 2018
  3. Accepted Manuscript published: March 13, 2018 (version 1)
  4. Version of Record published: March 28, 2018 (version 2)

Copyright

© 2018, Pogorelyy et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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