Check nomenclature in PMID:9971792

[ustervbo]

The nomenclature used in PMID:9971792 seems to follow Kabat

The TCR information in the paper is

v.beta	cdr3.beta	j.beta	d.beta	v.alpha	cdr3.alpha	j.alpha
Vβ17.1	CASMGNSAGANVLTFG	Jβ2.6
Vβ17.1	CASMGNSAGANVLTFG	Jβ2.6
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVNEQFFG	Jβ2.1
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVNEQFFG	Jβ2.1
Vβ17.1	CASMGNSAGANVLTFG	Jβ2.6
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ8	CASSSVSEAFFG	Jβ1.1
Vβ8	CASSSVNEQFFG	Jβ2.1
Vβ8	CASSSANYGYTFG	Jβ1.2
Vβ13.1	CASSYQTGTGNYGYTFG	Jβ1.2
Vβ13.1	CASSYSGHVYEQYFG	Jβ2.7
Vβ13.1	CASRGQGFSYEQYFG	Jβ2.7
Vβ6	CASSFLGLNEQFFG	Jβ2.1
Vβ6	CASSLDIPSYNEQFFG	Jβ2.1
Vβ6.4	CASSLGGNLYEQYFG	Jβ2.7
Vβ6.4	CASSSHDTGGYNSPLHFG	Jβ1.6
Vβ6.4	CASSFRDYGNYEQYFG	Jβ2.7
Vβ6.4	CASSLIGVSSYNEQFFG	Jβ2.1
Vβ6.4	CASSSHDRQGASSPLHFG	Jβ1.6
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ14.1	CASKVGAGGLYEQYFG	Jβ2.7
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ7.1	CASSQAALAGFGYEQYFG	Jβ2.7
Vβ7.2	CASSPARNTEAFFG	Jβ1.1
Vβ7.2	CASSPSRNTEAFFG	Jβ1.1
Vβ7.2	CASSPHRNTEAFFG	Jβ1.1
Vβ6.4	CASSLGGNLYEQYFG	Jβ2.7	Vα4.1	CILRGGGADGLTFG	Jα45
Vβ9.2	CASSQEEGVZRDPDQRYEQYFG	Jβ2.7	Vα4.1	CILRGGGADGLTFG	Jα45
Vβ6.4	CASSSHDTGGYNSPLHFG	Jβ1.6
Vβ6.4	CASSSHDTGGYNSPLHFG	Jβ1.6
Vβ6.4	CASSFRDYGNYEQYFG	Jβ2.7
Vβ6.4	CASSFRDYGNYEQYFG	Jβ2.7
Vβ6.4	CASSFRDYGNYEQYFG	Jβ2.7
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ14.1	CASSIGPALNTEAFFG	Jβ1.1
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1	Vα6.1	CAMREGMDSSYKLIFG	Jα31
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1	Vα6.1	CAMREGMDSSYKLIFG	Jα31
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1	Vα6.1	CAMREGMDSSYKLIFG	Jα31
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ6.4	CASSLHDRGSRTEAFFG	Jβ1.1
Vβ14.1	CASKVGAGGLYEQYFG	Jβ2.7
Vβ6.4	CASSLIGVSSYNEQFFG	Jβ2.1	Vα3.1	CATVLRMDSSYKLIFG	Jα21
Vβ6.4	CASSLIGVSSYNEQFFG	Jβ2.1	Vα3.1	CATVLRMDSSYKLIFG	Jα31
Vβ6.4	CASSLIGVSSYNEQFFQ	Jβ2.1	Vα3.1	CATVLRMDSSYKLIFG	Jα31
Vβ6.4	CASSSHDRQGASSPLHFG	Jβ1.6

[mikessh]

Hmm, Kabat is a numbering scheme for defining CDR1-3 positions (which differs from IMGT), not segment naming convention. Naming conventions are listed at http://imgt.org/IMGTrepertoire/index.php?section=LocusGenes&repertoire=nomenclatures&species=human&group=TRBV

[ustervbo]

Do you know there the Vβ annotation comes from? I can't find it anywhere, and just assumed it was from Kabat's 'Sequences of Proteins of Immunological Interest'.

I am believe the annotation used in this paper it is not an abbreviation of the IMGT annotation. First, there is no TRVB14-1 or TRVB13-1 (there is only a TRBV14 or TRBV13) and I have worked with a mouse TRB originally identified with Vβ8.2 which is TRBV13-2 in the present IMGT reference set.

[ustervbo]

It is amazing what you can get from tracing papers. It is an old nomenclature which is replaced by the Arden nomenclature.

In the 1995 papers 'Human T-cell receptor variable gene segment families' (PMID:8550092) and 'Mouse T-cell receptor variable gene segment families' (PMID:8550093) there are tables devoted to corrospondence between 'Official designation' and 'Previous designation'. I will scrutinize these tables and see how it matches with the annotation in this and #302 and #303