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

P. Barennes, V. Quiniou, M. Shugay, ES. Egorov, AN. Davydov, DM. Chudakov, I. Uddin, M. Ismail, T. Oakes, B. Chain, A. Eugster, K. Kashofer, PP. Rainer, S. Darko, A. Ransier, DC. Douek, D. Klatzmann, E. Mariotti-Ferrandiz

. 2021 ; 39 (2) : 236-245. [pub] 20200907

Language English Country United States

Document type Journal Article, Research Support, N.I.H., Intramural, Research Support, Non-U.S. Gov't

Persistent link   https://www.medvik.cz/link/bmc21011548

Grant support
Department of Health - United Kingdom

E-resources Online Full text

NLK ProQuest Central from 2000-01-01 to 1 year ago
Health & Medicine (ProQuest) from 2000-01-01 to 1 year ago

Links

PubMed 32895550
DOI 10.1038/s41587-020-0656-3
Knihovny.cz E-resources

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.

References provided by Crossref.org

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