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.

TCR trivia part one - translating T cell receptor sequences

Here's the first in what's likely to a be pretty niche series of posts – but hopefully useful to some – on various bits of TCR trivia I've gleaned during my PhD. This installment: translating TCR sequences.

Whether you're doing high- or low-throughput DNA TCR sequencing, it's highly likely that at some point you'll want to translate your DNA into amino acid sequences.

There's usually a few main goals to bear in mind when translating; to check the frame, and (potential) functionality of the sequence (i.e. lacking premature stop codons), before defining the hypervariable CDR3 region.

Assuming your reads are indel free, sequencing variable antigen receptors will always involve a bit more thought about checking the reading frame than regular amplicon sequencing, due to the non-templated addition and deletion of nucleotides that occurs during V(D)J recombination.

So how do can we tell whether our final recombined sequence is in frame or not?

This will mostly depend on how your sequencing protocols work.

If, say you've somehow managed to sequence an entire TCR mRNA sequence, then it's easy; you can just take the sequence from the start codon of the leader region to the stop codon of the constant region and if it divides exactly by three then it's in frame. Assuming there's no stop codons in between and the CDR3 checks out, chances are good your sequence encodes a productively rearranged TCR chain.

Given today's technology, that's unlikely to be the case; whether you're cloning into plasmids and Sanger sequencing or throwing libraries into some next-gen machine, chances are good that the sequence you'll be working with is actually just a small window around the recombination site.

What's likely is that you have amplified from a constant or J region primer at one end, to a V or RACE/template-switching primer at the other. Sorting out the frame is then just a matter of finding sequences on either side of the rearrangement that you know should be in frame, and seeing whether they are.

So far so self-explanatory. Here's the first of the fiddlier bits of TCR trivia I want to impart, the thing I need to remind myself of every time I tweak my TCR translating scripts: in fully-spliced TCR message the last nucleotide of the J region makes up the first nucleotide of the first codon of the constant region.

This means that if you go from the first nucleotide of the V (or the leader sequence, all functional leader sequences being divisible by three) to either the second to last nucleotide of the J, or the second nucleotide of the C (if you've started with mRNA instead of gDNA) then presto, you'll be in frame!

This feature also produces another noteworthy feature, at least in one chain; while every TRBJ ends in the same nucleotide, there are functional TRAJ genes ending in each base. This means that the first residue of the constant region of the alpha chain can be one of four different amino acids – which can be a bit off-putting if you don't know this and you're looking at what's supposed to be constant.

Once you've translated your TCR the next step is to find the CDR3, which should surely be the easiest bit; just run from the second conserved cysteine to the phenylalanine in the FGXG motif, right, just as IMGT says? Simple, or so it might seem.

Both sides of the CDR3 offer their own complications. First off, finding the second conserved cysteine isn't as easy as just picking the second C from the 5', or the 5'-most one upstream of the rearrangement, as some Vs have more than two germline cysteines, and it's feasible that new ones might be generated in the rearrangement. At some point you're just going to have to do an alignment of all the different Vs, and record the position of all the conserved cysteines.

The FGXG is also trickier than it might seem, by merit of the fact that there are J genes in both the alpha and gamma loci* that (while supposedly functional) lack the motif, being either FXXG or XGXG. If you're only looking for CDR3s matching the C to FGXG pattern, then there's going to be whole J genes which never seem to get used by your analysis!

There you have it, a couple of little tips that are worth bearing in mind when translating TCR sequence**.

Addendum - it's actually a little bit more complicated. Naturally.

* If you're interested (or don't believe me), they are: TRAJ16, TRAJ33, TRAJ38, TRGJP1 and TRGJP2.

** Note that everything written here is based on human TCR sequence as that's what I work with, but most of it will probably apply to other species as well.