publication . Part of book or chapter of book . 2017

sampling from t cell receptor repertoires

Ferrarini, M; Molina-Paris, C; Lythe, G;
Open Access
  • Published: 01 Jan 2017
  • Publisher: Springer International Publishing
  • Country: United Kingdom
Abstract
Modern single-cell sequencing techniques allow the unique T cell receptor (TCR) signature of each of a sample of hundreds of T cells to be read. The mathematical challenge is to extrapolate from the properties of a sample to those of the whole repertoire of an individual, made up of many millions of T cells. We consider the distribution of the number of repeats of any TCR in a sample, the mean number of cells needed to find a repeat with probability one half, and the relationship between the true distribution of clonal sizes and that experimentally observed in a sample. In the simplest hypothesis for the structure of the repertoire, the same number of cells make...
Subjects
free text keywords: Biology, Geometric distribution, Statistics, Sampling (statistics), Computational biology, Repertoire, T-cell receptor, Bernoulli distribution
Funded by
EC| QUANTI
Project
QUANTI
Quantitative T cell Immunology
  • Funder: European Commission (EC)
  • Project Code: 317040
  • Funding stream: FP7 | SP3 | PEOPLE
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22 references, page 1 of 2

1. M.K. Jenkins, H.H. Chu, J.B. McLachlan, and J.J. Moon. On the composition of the preimmune repertoire of T cells specific for peptide-major histocompatibility complex ligands. Annual Review of Immunology, 28:275-294, 2009.

2. R. Varma. TCR triggering by the pMHC complex: valency, affinity, and dynamics. Science Signaling, 1(19):pe21, 2008.

3. BENEDITA Rocha and HARALD von Boehmer. Peripheral selection of the T cell repertoire. Science, 251(4998):1225-1228, 1991.

4. I. Bains, R. Antia, R. Callard, and A.J. Yates. Quantifying the development of the peripheral naive CD4+ T-cell pool in humans. Blood, 113(22):5480, 2009.

5. Franc¸ois Van Laethem, Anastasia N Tikhonova, and Alfred Singer. MHC restriction is imposed on a diverse T cell receptor repertoire by CD4 and CD8 co-receptors during thymic selection. Trends in Immunology, 33(9):437-441, 2012.

6. RE Langman and M Cohn. The ET (elephant-tadpole) paradox necessitates the concept of a unit of B-cell function: the protecton. Molecular Immunology, 24(7):675-697, 1987.

7. Joseph N Blattman, Rustom Antia, David JD Sourdive, Xiaochi Wang, Susan M Kaech, Kaja Murali-Krishna, John D Altman, and Rafi Ahmed. Estimating the precursor frequency of naive antigen-specific CD8 T cells. Journal of Experimental Medicine, 195(5):657-664, 2002. [OpenAIRE]

8. Stanca M Ciupe, Blythe H Devlin, Mary Louise Markert, and Thomas B Kepler. Quantification of total T-cell receptor diversity by flow cytometry and spectratyping. BMC Immunology, 14(1):1-12, 2013.

9. Niclas Thomas, Katharine Best, Mattia Cinelli, Shlomit Reich-Zeliger, Hilah Gal, Eric Shifrut, Asaf Madi, Nir F riedman, John Shawe-Taylor, and Benny Chain. Tracking global changes induced in the CD4 T cell receptor repertoire by immunisation with a complex antigen using local sequence features of CDR3 protein sequence. biorxiv.org, 2014.

10. Andrew K Sewell. Why must T cells be cross-reactive? Nature Reviews Immunology, 12(9):669-677, 2012. [OpenAIRE]

11. Janko Nikolich- Zˇugich, Mark K. Slifka, and Ilhem Messaoudi. The many important facets of T-cell repertoire diversity. Nature Reviews Immunology, 4(2):123-132, 2004.

12. Veronika Zarnitsyna, Brian Evavold, Louie Schoettle, Joseph Blattman, and Rustom Antia. Estimating the diversity, completeness, and cross-reactivity of the T cell repertoire. Frontiers in Immunology, 4:485, 2013.

13. Anand Murugan, Thierry Mora, Aleksandra M Walczak, and Curtis G Callan. Statistical inference of the generation probability of T-cell receptors from sequence repertoires. Proceedings of the National Academy of Sciences, 109(40):16161-16166, 2012.

14. D. Mason. A very high level of crossreactivity is an essential feature of the T-cell receptor. Immunology Today, 19(9):395-404, 1998.

15. T.P. Arstila, A. Casrouge, V. Baron, J. Even, J. Kanellopoulos, and P. Kourilsky. A direct estimate of the human αβ T cell receptor diversity. Science, 286(5441):958, 1999. [OpenAIRE]

22 references, page 1 of 2
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