A characteristic of many Hematological malignancies is that one or a few clones dominate the peripheral lymphocyte repertoire. Currently, many clinical labs use spectrotype-like analyses to identify the presence/absence of a malignant cancer clones. Over-abundance of a PCR product in the one size that uses the same family of V genes is interpreted as evidence of a clonal repertoire. However, high-throughput sequencing (HTS) of antigen receptors provides an alternative method to identify clonality which using the actual sequences of the T-cell receptors (TCR) carried by clones as opposed to interpreting clonality using a proxy (V gene usage or size).
Adaptive Biotechnologies new software tool, betaSEQ, allows direct comparisons of TCR CDR3 Spectrotype and Betamark data to HTS TCR CDR3 sequencing data. Here you can see that size data can be misleading. Based on V gene usage, this individual appears to have a huge TCR that uses TRBV28 and dominates their peripheral TCR repertoire (Fig 1). However, using TCR sequencing data it becomes apparent that this spike is due to lots of different T cells, and no one T-cell receptor sequence represents more than 13% of the T-cell receptor repertoire (Fig 2). On top of that, the most frequent TCR cone doesn’t even use TRBV28! though, the 2nd most frequent clone does…
Fig.1: TCR frequency by V gene usage
Fig. 2: TCR frequency based on HTS TCR sequencing data
