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!

Getting CDR3 nucleotide sequence out of Decombinator

I was recently asked whether CDR3translator (the CDR3 extraction component of the Decombinator suite of T-cell receptor analysis scripts) has an option to output the CDR3 nucleotide, rather than amino acid sequence.

There currently is not, and I don't think there's much call to institute it as a in built feature, but I knocked together a bodge for them and it's an easy one line change so I'm posting it here in case anyone else has use of it:


This just exploits the way that the script currently finds CDR3s: it reconstructs the whole V/J nucleotide sequence from the five part Decombinator index (storing it in the 'nt' variable), translates this into its amino acid sequence ('aa') and then looks for the conserved motifs at the appropriate positions ('start_cdr3' and 'end_cdr3').

If you multiply each of these by 3 then you get the correct positions to extract the CDR3 nucleotide sequence, running from the conserved V-gene cysteine to the J-gene phenylalanine. If you want the GXG portion of the FGXG motif then you’ll need to add '+12' before the final closing square bracket.