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Nat Protoc. 2019 Aug;14(8):2571-2594. doi: 10.1038/s41596-019-0195-x. Epub 2019 Jul 24.

RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis.

Author information

1
Broad Institute of MIT and Harvard, Cambridge, MA, USA.
2
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
3
Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA.
4
Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark.
5
Integrated DNA Technologies, Redwood City, CA, USA.
6
Massachusetts Institute of Technology, Cambridge, MA, USA.
7
Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA. kennethj_livak@dfci.harvard.edu.
8
Translational Immunogenomics Lab, Dana-Farber Cancer Institute, Boston, MA, USA. kennethj_livak@dfci.harvard.edu.

Abstract

RNase H-dependent PCR-enabled T-cell receptor sequencing (rhTCRseq) can be used to determine paired alpha/beta T-cell receptor (TCR) clonotypes in single cells or perform alpha and beta TCR repertoire analysis in bulk RNA samples. With the enhanced specificity of RNase H-dependent PCR (rhPCR), it achieves TCR-specific amplification and addition of dual-index barcodes in a single PCR step. For single cells, the protocol includes sorting of single cells into plates, generation of cDNA libraries, a TCR-specific amplification step, a second PCR on pooled sample to generate a sequencing library, and sequencing. In the bulk method, sorting and cDNA library steps are replaced with a reverse-transcriptase (RT) reaction that adds a unique molecular identifier (UMI) to each cDNA molecule to improve the accuracy of repertoire-frequency measurements. Compared to other methods for TCR sequencing, rhTCRseq has a streamlined workflow and the ability to analyze single cells in 384-well plates. Compared to TCR reconstruction from single-cell transcriptome sequencing data, it improves the success rate for obtaining paired alpha/beta information and ensures recovery of complete complementarity-determining region 3 (CDR3) sequences, a prerequisite for cloning/expression of discovered TCRs. Although it has lower throughput than droplet-based methods, rhTCRseq is well-suited to analysis of small sorted populations, especially when analysis of 96 or 384 single cells is sufficient to identify predominant T-cell clones. For single cells, sorting typically requires 2-4 h and can be performed days, or even months, before library construction and data processing, which takes ~4 d; the bulk RNA protocol takes ~3 d.

PMID:
31341290
DOI:
10.1038/s41596-019-0195-x

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