Vujovic, M;
Degn, KF;
Marin, FI;
Schaap-Johansen, A-L;
Chain, B;
Andresen, TL;
Kaplinsky, J;
(2020)
T cell receptor sequence clustering and antigen specificity.
Computational and Structural Biotechnology Journal
, 18
pp. 2166-2173.
10.1016/j.csbj.2020.06.041.
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Abstract
There has been increasing interest in the role of T cells and their involvement in cancer, autoimmune and infectious diseases. However, the nature of T cell receptor (TCR) epitope recognition at a repertoire level is not yet fully understood. Due to technological advances a plethora of TCR sequences from a variety of disease and treatment settings has become readily available. Current efforts in TCR specificity analysis focus on identifying characteristics in immune repertoires which can explain or predict disease outcome or progression, or can be used to monitor the efficacy of disease therapy. In this context, clustering of TCRs by sequence to reflect biological similarity, and especially to reflect antigen specificity have become of paramount importance. We review the main TCR sequence clustering methods and the different similarity measures they use, and discuss their performance and possible improvement. We aim to provide guidance for non-specialists who wish to use TCR repertoire sequencing for disease tracking, patient stratification or therapy prediction, and to provide a starting point for those aiming to develop novel techniques for TCR annotation through clustering.
| Type: | Article |
|---|---|
| Title: | T cell receptor sequence clustering and antigen specificity |
| Location: | Netherlands |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.csbj.2020.06.041 |
| Publisher version: | https://doi.org/10.1016/j.csbj.2020.06.041 |
| Language: | English |
| Additional information: | This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Clustering, Epitope specificity, T cell receptor (TCR), T cell receptor distance, T cell receptor similarity, T cell repertoire |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10111033 |
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