Detecting T cell receptors involved in immune responses from single repertoire snapshots

Abstract

Hypervariable T cell receptors (TCRs) play a key role in adaptive immunity, recognizing a vast diversity of pathogen-derived antigens.Our ability to extract clinically relevant information from large high-throughput sequencing of TCR repertoires (RepSeq) data is limited, because little is known about TCR-disease associations.We present Antigen-specific Lymphocyte Identification by Clustering of Expanded sequences (ALICE), a statistical approach that identifies TCR sequences actively involved in current immune responses from a single RepSeq sample and apply it to repertoires of patients with a variety of disorders -patients with autoimmune disease (ankylosing spondylitis [AS]), under cancer immunotherapy, or subject to an acute infection (live yellow fever [YF] vaccine).We validate the method with independent assays.ALICE requires no longitudinal data collection nor large cohorts, and it is directly applicable to most RepSeq datasets.Its results facilitate the identification of TCR variants associated with diseases and conditions, which can be used for diagnostics and rational vaccine design.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 40

1. 1.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

2. 2.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

3. 3.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

4. 4.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

5. 5.
   A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures · 2014

   No notice
6. 6.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

7. 7.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

8. 8.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

9. 9.

   This reference’s wording can’t be shown under the paper’s licence.

   Not in our library

10. 10.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

11. 11.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

12. 12.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

13. 13.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

14. 14.
    VDJtools: Unifying Post-analysis of T Cell Receptor Repertoires · 2015

    No notice
15. 15.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

16. 16.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

17. 17.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

18. 18.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

19. 19.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

20. 20.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

21. 21.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

22. 22.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

23. 23.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

24. 24.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

25. 25.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

26. 26.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

27. 27.
    T cell receptor repertoires of mice and humans are clustered in similarity networks around conserved public CDR3 sequences · 2017

    No notice
28. 28.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

29. 29.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

30. 30.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

31. 31.
    Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance · 2018

    No notice
32. 32.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

33. 33.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

34. 34.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

35. 35.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

36. 36.
    A novel source of arterial valve cells linked to bicuspid aortic valve without raphe in mice · 2018

    No notice
37. 37.
    OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs · 2019

    No notice
38. 38.
    Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity · 2018

    No notice
39. 39.
    High-throughput immune repertoire analysis with IGoR · 2018

    No notice
40. 40.

    This reference’s wording can’t be shown under the paper’s licence.

    Not in our library

Cited by papers we hold 6

• The clonal structure and dynamics of the human T cell response to an organic chemical hapten · 2021
  Not checked
• TCR meta-clonotypes for biomarker discovery with tcrdist3 enabled identification of public, HLA-restricted clusters of SARS-CoV-2 TCRs · 2021
  No notice
• Longitudinal high-throughput TCR repertoire profiling reveals the dynamics of T-cell memory formation after mild COVID-19 infection · 2021
  No notice
• GIANA allows computationally-efficient TCR clustering and multi-disease repertoire classification by isometric transformation · 2021
  Corrected
• VDJdb in 2019: database extension, new analysis infrastructure and a T-cell receptor motif compendium · 2019
  No notice
• Detection of Enriched T Cell Epitope Specificity in Full T Cell Receptor Sequence Repertoires · 2019
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.