T cell receptor sequence clustering and antigen specificity
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...
| Main Authors: | , , , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Elsevier
2020
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| _version_ | 1797055772217049088 |
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| author | M Vujovic KF Degn FI Marin AL Schaap-Johansen B Chain TL Andresen J Kaplinsky P Marcatili |
| author_facet | M Vujovic KF Degn FI Marin AL Schaap-Johansen B Chain TL Andresen J Kaplinsky P Marcatili |
| author_sort | M Vujovic |
| collection | OXFORD |
| description | 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. |
| first_indexed | 2024-03-06T19:14:34Z |
| format | Journal article |
| id | oxford-uuid:17e6af32-b620-45f9-98e3-f4edb5f0b2dd |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-06T19:14:34Z |
| publishDate | 2020 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | oxford-uuid:17e6af32-b620-45f9-98e3-f4edb5f0b2dd2022-03-26T10:40:21ZT cell receptor sequence clustering and antigen specificityJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:17e6af32-b620-45f9-98e3-f4edb5f0b2ddEnglishSymplectic ElementsElsevier2020M VujovicKF DegnFI MarinAL Schaap-JohansenB ChainTL AndresenJ KaplinskyP MarcatiliThere 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. |
| spellingShingle | M Vujovic KF Degn FI Marin AL Schaap-Johansen B Chain TL Andresen J Kaplinsky P Marcatili T cell receptor sequence clustering and antigen specificity |
| title | T cell receptor sequence clustering and antigen specificity |
| title_full | T cell receptor sequence clustering and antigen specificity |
| title_fullStr | T cell receptor sequence clustering and antigen specificity |
| title_full_unstemmed | T cell receptor sequence clustering and antigen specificity |
| title_short | T cell receptor sequence clustering and antigen specificity |
| title_sort | t cell receptor sequence clustering and antigen specificity |
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