Table 1.

Methods for identifying paired TCR chains.

Technique	Beta %	Alpha %	Paired %	Amplified TCR regions	Strengths	Major limitations	Reference
PCR-based	N/A	35%	N/A	Full variable region	Limited number of primers	Low throughput Gives a limited assessment of TCR repertoire PCR product is not directly conducive with cloning	Ozawa et al., (2008)
PCR-based 5′-RACE	N/A	N/A	N/A	Full TCR chain	High throughput Compatible with subsequent in vitro studies	Fully human TCR construct, not compatible with in vivo mouse expression	Walchli et al., (2011)
PCR-based	55–75%	45–65%	N/A	CDR3	Limited number of primers	Low throughput Gives a limited assessment of TCR repertoire PCR product is not directly conducive with cloning	Dash et al., (2011)
PCR-based	27–85%	N/A	39%	CDR3	Limited number of primers	Low throughput PCR product is not directly conducive with cloning	Kim et al., (2012)
PCR-based	67%	61%	43%	Full TCR chain	Combines TCR identification with phenotype	Fully human TCR construct, not compatible with in vivo mouse expression	Eugster et al., (2013)
Gene capture	100%	100%	100%	N/A	High throughput	Necessary to generate T cell clones to identify Tcra and Tcrb genes Requires in silico assembly and de novo TCR construction	Linnemann et al., (2013)
Emulsion PCR	N/A	N/A	N/A	CDR3	High throughput Limited number of primers	PCR product is not directly conducive with cloning	Turchaninova et al., (2013)
PCR-based	N/A	N/A	13–72%	Full TCR chain	Limited number of primers Compatible with subsequent in vitro studies	Alpha and beta chains are cloned into separate vectors, non-stoichiometric expression Fully human TCR construct, not compatible with in vivo mouse expression	Kobayashi et al., (2013)
PCR-based	81–92%	87%	58–82%	CDR3	High throughput Combines TCR identification with phenotype	PCR product is not directly conducive with cloning	Han et al., (2014)
PCR-based	N/A	N/A	N/A	CDR3	Limited number of primers	Low throughput PCR product is not directly conducive with cloning Requires in silico assembly and de novo TCR construction Fully human TCR construct, not compatible with in vivo mouse expression	Guo et al., (2016)
RNA-seq	88–96%	74–96%	70–93%	Full TCR chain	High throughput Combines TCR identification with gene expression profile	RNA-seq is a prohibitive technique for many labs due to the associated cost TCR sequence information only, would require synthesizing TCR construct for expression (costly)	Stubbington et al., (2016)
Current protocol
PCR-based	63–89%	49–60%	45–59%	Full variable region	Compatible with subsequent in vitro and in vivo studies	Low throughput Gives a limited assessment of TCR repertoire

N/A = not available.