Methods for comparing the diversity of samples of the T cell receptor repertoire.
Analysis of T cell receptor (TCR) data has become a crucial element in many studies aimed at better understanding the evolution of the T cell repertoire and the role of TCR diversity in immune responses. In this paper we focus on comparing the diversity between samples of the TCR repertoire. We discuss some of the limitations and potential problems inherent in some of the more popular approaches to comparing samples of the TCR repertoire and we suggest alternate methods that both avoid these problems and enrich the analysis of TCR data. Examples from published studies of the CD8(+) T cell responses to the influenza A virus D(b)NP(366) and D(b)PA(224) epitopes in mice are used to demonstrate the implementation of these methods. One example involves a comparison between the central and effector memory T cell subsets, defined on the basis of CD62L expression, and the other examines changes in the TCR repertoire over time.
Venturi
Vanessa
V
Department of Haematology, Prince of Wales Hospital and, Centre for Vascular Research, University of New South Wales, Kensington NSW 2052, Australia. v.venturi@unsw.edu.au
Kedzierska
Katherine
K
Turner
Stephen J
SJ
Doherty
Peter C
PC
Davenport
Miles P
MP
D000818:Animals; D000940:Antigenic Variation; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology; D022801:Complementarity Determining Regions / Q000032:analysis; D003627:Data Interpretation, Statistical; D007156:Immunologic Memory; D009980:Influenza A virus / Q000276:immunology; D019041:L-Selectin / Q000032:analysis; D051379:Mice; D008810:Mice, Inbred C57BL; D015233:Models, Statistical; D009976:Orthomyxoviridae Infections / Q000276:immunology / Q000821:virology; D010446:Peptide Fragments / Q000276:immunology; D011948:Receptors, Antigen, T-Cell / Q000032:analysis*; D012107:Research Design; D018401:Sample Size; D016176:T-Lymphocyte Subsets / Q000276:immunology*; D013997:Time Factors; D014758:Viral Core Proteins / Q000276:immunology
D022801:Complementarity Determining Regions; D010446:Peptide Fragments; D011948:Receptors, Antigen, T-Cell; D014758:Viral Core Proteins; C102366:nucleoprotein (366-374), influenza virus; D019041:L-Selectin