Method for identification of condition-associated public antigen receptor sequences

Abstract
Data availability
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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.

Data availability

The following previously published data sets were used

1. Emerson RO
2. DeWitt WS
3. Vignali M
4. Gravley J
5. Hu JK
6. Osborne EJ
7. Desmarais C
8. Klinger M
9. Carlson CS
10. Hansen JA
11. Rieder M
12. Robins HS
(2017) Immunosequencing identifies signatures of cytomegalovirus exposure history and HLA-mediated effects on the T cell repertoire
10.21417/B7001Z.

https://clients.adaptivebiotech.com/immuneaccess
1. Seay HR
2. Yusko E
3. Rothweiler SJ
4. Zhang L
5. Posgai AL
6. Campbell-Thompson M
7. Vignali M
8. Emerson RO
9. Kaddis JS
10. Ko D
11. Nakayama M
12. Smith MJ
13. Cambier JC
14. Pugliese A
15. Atkinson MA
16. Robins HS
17. Brusko TM
(2016) Tissue distribution and clonal diversity of the T and B cell repertoire in type 1 diabetes
publicly available.

https://clients.adaptivebiotech.com/immuneaccess

Article and author information

Author details

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.
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.
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.

"This ORCID iD identifies the author of this article:" 0000-0003-0430-790X
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.
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.
Thierry Mora

Laboratoire de Physique Statistique, École Normale Supérieure, Paris, France

For correspondence
tmora@lps.ens.fr

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-5456-9361
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.

"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.

Copyright

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.