Fig. 5: Example individual clonotype.
From: Single-cell T-cell receptor repertoire profiling in dogs
Individual cell-specific TRA and TRB clonotypes are resolved to the nucleotide level. Illustrated here is a single such TRB clonotype from Melanoma_B (CDR3: CASSSVQLAERYF). a A specific VDJ recombination with complete TRBV4-2, TRBD1, and TRBJ2-6 and a portion of TRBC is depicted. The Universal Reference (based on IMGT V(D)JC reference sequences) is shown in the first row. Germline variants in the analyzed sample, relative to the Universal Reference, are depicted in the Donor Reference line. The germline/donor sequence is inferred by the cellranger software, by determining shared sequence between multiple clonotypes, in different cells, that use the same gene segment. The Consensus row and subclonotype row(s) show additional variants from the Donor and Universal Reference that were presumably introduced during joining of gene segments. The consensus represents the sequence of the first exact subclonotype for a receptor chain within the clonotype. In this case, only a single subclonotype for a single barcode is shown. But, in other cases, multiple subclonotypes may be grouped together, each represented by one or more cell barcodes. Subclonotypes may have small nucleotide differences or share a TRA chain but have missing TRB chain or vice versa. Single nucleotide changes are shown in orange and small deletions shown in purple. b and c are zoomed into the base pair level to visualize the variants.
