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Check nomenclature in PMID:9971792 #301

Open ustervbo opened 5 years ago

ustervbo commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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 commented 5 years ago

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