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Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases

Barennes, P; Quiniou, V; Shugay, M; Egorov, ES; Davydov, AN; Chudakov, DM; Uddin, I; ... Mariotti-Ferrandiz, E; + view all (2021) Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases. Nature Biotechnology , 39 pp. 236-245. 10.1038/s41587-020-0656-3. Green open access

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Abstract

Monitoring the T cell receptor (TCR) repertoire in health and disease can provide key insights into adaptive immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is unclear. In this study, we systematically compared the results of nine commercial and academic TCRseq methods, including six rapid amplification of complementary DNA ends (RACE)-polymerase chain reaction (PCR) and three multiplex-PCR approaches, when applied to the same T cell sample. We found marked differences in accuracy and intra- and inter-method reproducibility for T cell receptor α (TRA) and T cell receptor β (TRB) TCR chains. Most methods showed a lower ability to capture TRA than TRB diversity. Low RNA input generated non-representative repertoires. Results from the 5' RACE-PCR methods were consistent among themselves but differed from the RNA-based multiplex-PCR results. Using an in silico meta-repertoire generated from 108 replicates, we found that one genomic DNA-based method and two non-unique molecular identifier (UMI) RNA-based methods were more sensitive than UMI methods in detecting rare clonotypes, despite the better clonotype quantification accuracy of the latter.

Type: Article
Title: Benchmarking of T cell receptor repertoire profiling methods reveals large systematic biases
Location: United States
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41587-020-0656-3
Publisher version: http://dx.doi.org/10.1038/s41587-020-0656-3
Language: English
Additional information: This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions.
Keywords: Next-generation sequencing, VDJ recombination
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/10110106
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