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September 7, 2020

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

Nature Biotechnology - 2020



Authors: Pierre Barennes, Valentin Quiniou, Mikhail Shugay, Evgeniy S. Egorov, Alexey N. Davydov, Dmitriy M. Chudakov, Imran Uddin, Mazlina Ismail, Theres Oakes, Benny Chain, Anne Eugster, Karl Kashofer, Peter P. Rainer, Samuel Darko, Amy Ransier, Daniel C. Douek, David Klatzmann, and Encarnita Mariotti-Ferrandiz.

  • puce

    Monitoring the T cell receptor (TCR) repertoire is crucial for understanding immune responses, but the accuracy of current TCR sequencing (TCRseq) methods is uncertain. This study compared nine TCRseq methods, including six RACE-PCR and three multiplex-PCR approaches, on the same T cell sample. Significant differences were found in accuracy and reproducibility for TCR α (TRA) and β (TRB) chains.

  • puce

    Most methods had difficulty capturing TRA diversity, especially with low RNA input. 5′ RACE-PCR methods were consistent with each other but differed from RNA-based multiplex-PCR results. A genomic DNA-based method and two non-UMI RNA-based methods were more sensitive in detecting rare clonotypes, although UMI methods were more accurate in clonotype quantification.

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