Questions: Is it possible to detect TCR gamma/delta chains in the V(D)J assay?
Answer: The Single Cell V(D)J Enrichment Kits target constant regions of TCR alpha and beta chains and will not enrich for gamma/delta chains. It is possible that custom primers could be designed to capture these sequences. The User Guide describes the assay scheme and configuration (with oligo sequence info and primer concentrations for target enrichment steps), which can be used for designing a custom assay: https://support.10xgenomics.com/single-cell-vdj/index/doc/user-guide-chromium-single-cell-vdj-reagent-kit
Because this is not supported, unfortunately we cannot provide any further guidance on custom assay development.
In principle, the cellranger vdj pipeline should be able to assemble and annotate the chains irrespective of the chain type. However, please note that our annotation algorithms are tuned to work with human and mouse TRA and TRB or IgH and IgL chains. Therefore there may be unforeseen performance issues in annotating the D/G chain types.
Products: Single Cell VDJ