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Quantitative Characterization of the t Cell Receptor Repertoire of Naïve and Memory subsets Using an Integrated experimental and Computational Pipeline Which Is Robust, economical, and Versatile

Oakes, T, Heather, JM, Best, K, Byng-Maddick, R, Husovsky, C, Ismail, M, Joshi, K, Maxwell, G, Noursadeghi, M, Riddell, Natalie , Ruehl, T, Turner, CT, Uddin, I and Chain, B (2017) Quantitative Characterization of the t Cell Receptor Repertoire of Naïve and Memory subsets Using an Integrated experimental and Computational Pipeline Which Is Robust, economical, and Versatile Frontiers in Immunology, 8, 1267.

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Abstract

The T cell receptor (TCR) repertoire can provide a personalized biomarker for infectious and non-infectious diseases. We describe a protocol for amplifying, sequencing, and analyzing TCRs which is robust, sensitive, and versatile. The key experimental step is ligation of a single-stranded oligonucleotide to the 3′ end of the TCR cDNA. This allows amplification of all possible rearrangements using a single set of primers per locus. It also introduces a unique molecular identifier to label each starting cDNA molecule. This molecular identifier is used to correct for sequence errors and for effects of differential PCR amplification efficiency, thus producing more accurate measures of the true TCR frequency within the sample. This integrated experimental and computational pipeline is applied to the analysis of human memory and naive subpopulations, and results in consistent measures of diversity and inequality. After error correction, the distribution of TCR sequence abundance in all subpopulations followed a power law over a wide range of values. The power law exponent differed between naïve and memory populations, but was consistent between individuals. The integrated experimental and analysis pipeline we describe is appropriate to studies of T cell responses in a broad range of physiological and pathological contexts.

Item Type: Article
Divisions : Faculty of Health and Medical Sciences > School of Biosciences and Medicine
Authors :
NameEmailORCID
Oakes, TUNSPECIFIEDUNSPECIFIED
Heather, JMUNSPECIFIEDUNSPECIFIED
Best, KUNSPECIFIEDUNSPECIFIED
Byng-Maddick, RUNSPECIFIEDUNSPECIFIED
Husovsky, CUNSPECIFIEDUNSPECIFIED
Ismail, MUNSPECIFIEDUNSPECIFIED
Joshi, KUNSPECIFIEDUNSPECIFIED
Maxwell, GUNSPECIFIEDUNSPECIFIED
Noursadeghi, MUNSPECIFIEDUNSPECIFIED
Riddell, Natalien.riddell@surrey.ac.ukUNSPECIFIED
Ruehl, TUNSPECIFIEDUNSPECIFIED
Turner, CTUNSPECIFIEDUNSPECIFIED
Uddin, IUNSPECIFIEDUNSPECIFIED
Chain, BUNSPECIFIEDUNSPECIFIED
Date : 12 October 2017
Funders : EPSRC
Identification Number : 10.3389/fimmu.2017.01267
Copyright Disclaimer : Copyright © 2017 Oakes, Heather, Best, Byng-Maddick, Husovsky, Ismail, Joshi, Maxwell, Noursadeghi, Riddell, Ruehl, Turner, Uddin and Chain. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Uncontrolled Keywords : T cell receptor, repertoire analysis, naive T cells, memory T cells, unique molecular identifier
Depositing User : Melanie Hughes
Date Deposited : 12 Oct 2017 09:17
Last Modified : 12 Oct 2017 09:17
URI: http://epubs.surrey.ac.uk/id/eprint/842523

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