Frequency of clonally expanded T cells evaluated by PCR from a single cell

In analyses of antigen-specific immune responses, it is essential to estimate the frequency of individual T cell clonotypes. This frequency has been estimated, however, only indirectly by the frequency of T cell receptor (TCR) mRNA. We have developed a method to determine T cell frequency directly by cell count using reverse transcription polymerase chain reaction (RT-PCR) amplification of TCR beta genes from single cell-derived cDNA (single cell PCR). In a study of clinical samples, the frequency of clonally expanded T cells estimated by TCR frequency analysis was found to be higher than that by single cell PCR. Single cell PCR can estimate T cell frequency accurately, as it is not affected by skewed PCR amplification or different TCR mRNA expressions in individual T cells.