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@article{1636697,
author = {Pogorelyy, M.V. and Minervina, A.A. and Shugay, Mikhail and Chudakov, Dmitriy and Lebedev, Y.B. and Mora, T. and Walczak, A.M.},
article_location = {USA},
article_number = {6},
doi = {http://dx.doi.org/10.1371/journal.pbio.3000314},
keywords = {ANKYLOSING-SPONDYLITIS; REACTIVE ARTHRITIS; SELECTION; DRIVEN; BLOOD},
language = {eng},
issn = {1544-9173},
journal = {PLoS Biology},
title = {Detecting T cell receptors involved in immune responses from single repertoire snapshots},
url = {https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000314},
volume = {17},
year = {2019}
}
TY - JOUR
ID - 1636697
AU - Pogorelyy, M.V. - Minervina, A.A. - Shugay, Mikhail - Chudakov, Dmitriy - Lebedev, Y.B. - Mora, T. - Walczak, A.M.
PY - 2019
TI - Detecting T cell receptors involved in immune responses from single repertoire snapshots
JF - PLoS Biology
VL - 17
IS - 6
SP - 1-13
EP - 1-13
PB - PUBLIC LIBRARY SCIENCE
SN - 15449173
KW - ANKYLOSING-SPONDYLITIS
KW - REACTIVE ARTHRITIS
KW - SELECTION
KW - DRIVEN
KW - BLOOD
UR - https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000314
L2 - https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3000314
N2 - 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.
ER -
POGORELYY, M.V., A.A. MINERVINA, Mikhail SHUGAY, Dmitriy CHUDAKOV, Y.B. LEBEDEV, T. MORA and A.M. WALCZAK. Detecting T cell receptors involved in immune responses from single repertoire snapshots. \textit{PLoS Biology}. USA: PUBLIC LIBRARY SCIENCE, 2019, vol.~17, No~6, p.~1-13. ISSN~1544-9173. Available from: https://dx.doi.org/10.1371/journal.pbio.3000314.
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