Question: My data has a clonotype (say clonotype1) where the TRB chain is paired with a TRA chain and a second clonotype (say clonotype2) that has only TRB chain whose sequence is same as the TRB chain of clonotype1. Could you please explain the reason why cellranger vdj assigned the same TCR chain to different clonotypes?
Answer:
In Cell Ranger implementations prior to v5, two cells were merged into a clonotype if the nucleotide sequences of the CDR3 of all productive chains in the cells are an exact match.
For example, if cell1 has productive TRB and TRA chains while cell2 has a productive TRB chain and no TRA chain, they will be assigned to separate clonotypes even if the CDR3 nucleotide sequences of the TRB chains match between cell1 and cell2. In this example while TRBs match, there is no match for the TRA chain between cell1 in cell2, so not all productive chains match between the cells.
TRA is generally expressed at at lower levels than TRB. Therefore, sometimes the TRA chain is not detected or not annotated as productive. This might be a cause for the missing or nonproductive TRA in cell2 in the above example.
In Cell Ranger v5 or later, the algorithms have been upgraded such that cells with just the TRA or TRB chains are also merged into the same clonotype as those cells with both chain types, thus outputting biologically relevant clonotypes.