Saturday 10 November 2018

Making coding T cell receptor sequences from V-J-CDR3

If, like me, you work on T cell receptors, occasionally you’re probably going to want to express a particular TCR in cells. However you're not always going to have the sequence, at either nucleotide or protein sequence level.

Not a problem, you can sort this out. You can look up all the relevant germline sequences from IMGT, trim away all the non-used bits, add in the non-templated stuff, then manually stitch it all together and have a look to see if it still makes what you were expecting. You can do all that... or you can just use the code I wrote.

StiTChR does it all: give it a V gene, a J gene, and a CDR3 amino acid sequence and it'll look up, trim and stitch together all the relevant TCR nucleotide sequences for you, back-translating the non-templated region using the most frequent codon per residue. It also translates it all, and will run a quick rudimentary alignment against a known partial protein sequence if you have one for a visual confirmation that it's made the right thing.

You can then take the alpha/beta TCR sequences it generates, bang them into an expression vector (typically split by a T2A sequence or something) and transduce your cells of interest.

I wrote this code to save me a bit of time in future, but hopefully it can do the same for some of you!