Table 3.

DNA-based vs. RNA-based approaches, choosing the right starting material for TCR profiling.

Advantages
gDNA	mRNA
easier to obtain; very stable [49]; no requirement for reverse transcription (RT); better reflect the number of analyzed cells; accurate measurement of clonality without bias caused by variable expression levels in different cells.	higher number of copies in a single cell; large information at the gene transcription level; reduced interference of non-coding signals after the splicing process [50]; overall length sequence in the CDR region is easily available; non-productive receptor transcripts are underrepresented [51]. close proximity of V and C regions after the splicing process facilitates PCR amplification [13].
Disadvantages
gDNA	mRNA
higher concentration input; potential annealing of primers for multiple binding sites; presence of introns and “unused” segments in the sequence of interest that have to be amplified, causing challenges during PCR process [13]; Detection of all the TCR sequences whether they contribute to a productive or a nonproductive segment arrangement [13].	introduction of errors during retrotranscription [52]; easily degraded; high requirements for extraction, transportation and storage.