Table 3.
CDR3 sequences with known antigen reactivity. These sequences were found at higher abundance in IBD patients compared with their healthy co-twins. Column 3 lists the pathogens which they were found to be reactive to, according to VDJdb.28 Column 4 indicates whether the V region of the antigen reactive clonotype was the same in our own data. Identical CDR3 regions with different V genes may or may not recognise the same antigen.
| CDR3 region | Chain | Antigen reactivity | V gene concordance with VDJdb |
|---|---|---|---|
| CAVSSNDYKLSF | alpha | Influenza A,39 yellow fever40 | No |
| CAVMNYGGSQGNLIF | alpha | CMV41 | No |
| CAVEDSNYQLIW | alpha | CMV41 | No |
| CAASGGGSYIPTF | alpha | CMV, EBV41 | No |
| CSARDRVGNTIYF | beta | EBV42 | Yes |
| CASSLGYEQYF | beta | CMV, EBV41,43 | No |
| CSVGAGGTNEKLFF | beta | EBV42 | Yes |
IBD, inflammatory bowel disease; V[D]J, variable diversity joining; CMV, cytomegalovirus; EBV, EpsteinBarr virus.