enclone can look for evidence that T cells are iNKT or MAIT cells. This evidence may be
displayed e.g. with LVARSP=inkt or LVARSP=mait, see
enclone help lvars. One may also filter to show
only cells with some evidence, using the INKT and MAIT options, see
enclone help filter.
enclone looks for both gene and junction (CDR3) evidence. The rules for this are likely to be tweaked over time. Junction evidence is discussed later. For gene evidence, the following rules are used currently:
As an example,
enclone TCR=101287 LVARSP=mait CDR3=CSAGQGDTEAFF[1] GROUP = 1 CLONOTYPES = 1 CELLS
[1.1] CLONOTYPE = 1 CELLS
βββββββββββββββ¬βββββββββββββββββββββββββββββββββββββββββββ¬βββββββββββββββββββββββββββββββ
β β CHAIN 1 β CHAIN 2 β
β β 596|TRBV20-1 β 535|TRBD1 β 536|TRBJ1-1 β 454.1.1|TRAV1-2 β 419|TRAJ33β
β ββββββββββββββββββββββββββββββββββββββββββββΌβββββββββββββββββββββββββββββββ€
β β 111111111111 β 111111111111 β
β β 000111111111 β 5 000000111111 β
β β 789012345678 β 9 456789012345 β
β β ββββCDR3ββββ β ββββCDR3ββββ β
βreference β β¦β¦β¦β¦β¦β¦β¦β¦β¦β¦β¦F β P β¦β¦β¦β¦β¦β¦β¦β¦β¦LIW β
βdonor ref β β¦β¦β¦β¦β¦β¦β¦β¦β¦β¦β¦F β P β¦β¦β¦β¦β¦β¦β¦β¦β¦LIW β
βββββββββββββββΌβββββββββββββββββββββββββββββββββββββββββββΌβββββββββββββββββββββββββββββββ€
β# n mait β ............ u const β . ............ u const β
β1 1 π°gjπ±g β CSAGQGDTEAFF 5 TRBC1 β P CAVMDSNYQLIW 1 TRAC β
βββββββββββββββ΄βββββββββββββββββββββββββββββββββββββββββββ΄βββββββββββββββββββββββββββββββ
displays a single cell showing evidence for the cell being a MAIT cell, encoded using
the string π°gjπ±g. This stands for "gene and junction evidence on the alpha
chain, and gene evidence on the beta chain" (i.e. π°gj = alpha gene and junction).
Please we aware that detection of junction evidence is limited by the completeness of the lists on which they are based (see below), and these lists are incomplete! They are also likely to change over time as more data studying iNKT and MAIT cells emerge. Note that while iNKT and MAIT cells are described as "invariant", a more accurate description would be "semi-invariant", or "limited variant" as V and J gene recombinations that generate iNKT and MAIT TCRs can still generate considerable nucleotide and amino acid diversity within the CDR3.
For junction evidence, enclone tests for presence of a given chain's CDR3 amino acid sequence in a fixed list. Here is the list for human iNKT: