Maybe someone has an idea. I have performed TCR repertoire on blood from several patients with an autoimmune, genetic, disorder.
I have found they have a shorter CDR3B length than healthy controls (43.7 vs. 43.4 nucleotides. p<0.01)
BUT there are no differences in number of N insertions or deletions.
What else can explain a shorter TCR?
One way would just be to use TRBD1 a bit more often, as it’s shorter than TRBD2:
>K02545|TRBD1*01|Homo sapiens|F|D-REGION|82..93|12 nt|1| | | | |12+0=12| | | gggacagggggc >X02987|TRBD2*01|Homo sapiens|F|D-REGION|140..155|16 nt|1| | | | |16+0=16| | | gggactagcggggggg
However when you say that insertions/deletions are the same, you have to appreciate that those values are an artifact of how the sequences look in the final rearrangement, not actually what happened - e.g. you can’t tell the difference between a base being removed and then the same base being reintroduced.
If you combine that fact with two very small, very similar TRBD genes (which you won’t be able to distinguish in the majority of cases), it’s entirely possible that there are actually significant differences in non-templated insertion/deletions, and you’re just not able to see it.
only have found your post today! This sounds interesting - we’ve found shorter CDR3s in T1D (PMID:29176645), although clearly it was related to the different insertion/deletion pattern. I would look into VDJ usage, as Jamie suggested.
Also try to eliminate confounders - what was your repertoire source, PBMCs? Sorted cells? As different cell subsets might have different repertoire and a difference in ratio of CD4s to CD8s might explain a difference.
Also, I assume that patients/controls were processed together, so nothing like a batch effect?
One thing to consider is age, CDR3 length will increase with age (Rechavi, E. et al. Timely and spatially regulated maturation of B and T cell repertoire during human fetal development. Sci. Transl. Med. 7, 276ra25–276ra25 (2015); Hall, M. A., Reid, J. L. & Lanchbury, J. S. The distribution of human TCR junctional region lengths shifts with age in both CD4 and CD8 T cells. Int. Immunol. 10, 1407–1419 (1998).). If your controls are older, this might be a reason. However, this should co-incide with more N-insertions.