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Allele

IMGT sequence polymorphisms
How are alleles determined?
Requirements for the assignment of new alleles
IMGT RFLP polymorphisms

An allele is a polymorphic variant of a gene.

The 'allele' concept is part of the 'CLASSIFICATION' concept of IMGT-ONTOLOGY[8]

Alleles are defined (i) for the sequence polymorphisms described at the nucleotide level, and (ii) for the Restriction Fragment Length Polymorphisms (RFLP) detected by Southern hybridization.

IMGT sequence polymorphisms

Their description is according to the IMGT allele nomenclature for sequence polymorphisms which has been set up for IG and TR of human and other vertebrates (IMGT Scientific chart). The allele polymorphism mutations are described according to the IMGT description of mutations.
An allele is identified by the mutations of its sequence compared to the reference sequence designated as *01. Full description of mutations and allele name designations are only recorded for the core sequences (V-REGION, D-REGION, J-REGION, C-REGION). They are reported in Alignments of alleles [1] and Tables of alleles [2-6] (IMGT Repertoire), and in IMGT/GENE-DB.
Allele IMGT reference sequences are described according to the IMGT unique numbering [7] (IMGT Scientific chart). The sets of sequence fragments isolated from the allele IMGT reference sequences and used for the IMGT/V-QUEST tool constitute the IMGT reference directory and can be downloaded in FASTA format from the IMGT Repertoire.
Allele sequences of highly homologous duplicated genes cannot, in some cases, be correctly assigned to one or the other gene(s) when these sequences are not mapped. These sequences are therefore described as "alleles" of the gene selected by IMGT and compared to the allele *01 of that gene. However, it is not excluded that some of these "alleles" belong exclusively to the other (e.g. not selected) gene(s) (for example, see Mouse (Mus musculus) TRAV11 and TRAV11D).

How are alleles determined?

Alleles displayed in the Alignments of alleles represent "potential" alleles. They are based on nucleotide differences in the core region of the genomic germline V, D and J genes (V-REGION, D-REGION, J-REGION) and of the C genes (C-REGION).

For each potential allele, one sequence (accession number in red) is selected as "reference sequence" (based on one or, whenever possible, several of the following criteria: germline sequence, first sequence published, longest sequence, mapped sequence).

Alignments of alleles allow to know how many times the alleles have been sequenced. Alleles which have been sequenced once may represent either rare alleles or sequencing errors. When a sequencing error is strongly suspected, the nucleotide and amino acid differences are shown in italics and in black and/or a note is added.

When the allele has been confirmed by several groups (identical sequence found by more than one investigator, evidence they are not PCR errors), by genetic studies (segregated in family studies) or by expression studies (both alleles expressed in antibodies in one person), a plus + is added in the column "confirmed by genetics and/or data" in Table of alleles).

Requirements for the assignment of new alleles

Requirements for the assignment of new alleles for variable (V), diversity (D) and joining (J) genes of immunoglobulin (IG) and T cell receptor (TR) genes are the following:

sequences of new alleles should be from genomic DNA and from V, D and J genes in germline configuration.
sequences of new alleles should include the complete gene unit, that is:
- L-V-GENE-UNIT (or exceptionally V-GENE-UNIT)
- D-GENE-UNIT
- J-GENE-UNIT.
sequences should be submitted to GenBank, EMBL-Bank or DDBJ.

Be aware that:

Allele numbers are provided on a chronological basis, and as the IMGT nomenclature committee (IMGT-NC) becomes aware of new alleles.
Sequences are entered in IMGT/LIGM-DB only when sequences become publicly available.

Therefore authors who would like to keep the anteriority of new alleles, should contact the IMGT nomenclature committee with the submitted sequences and accession numbers.

IMGT RFLP polymorphisms

IMGT RFLP polymorphisms are described in the section "Probes and RFLP" of the IMGT Repertoire.

References:
[1]	Lefranc, M.-P. et al., Nucleic Acids Res., 26, 297-303 (1998) PMID: 9399859, LIGM:195.
[2]	Pallarès, N. et al., Exp. Clin. Immunogenet., 15, 8-18 (1998) PMID: 9619396, LIGM:200
[3]	Barbié, V. and Lefranc, M.-P., Exp. Clin. Immunogenet., 15, 171-183 (1998) PMID: 9813414, LIGM:207
[4]	Martinez, C. and Lefranc, M.-P., Exp. Clin. Immunogenet., 15, 184-193 (1998) PMID: 9813415, LIGM:208
[5]	Pallarès, N. et al., Exp. Clin. Immunogenet., 16, 36-60 (1999) PMID: 10087405, LIGM:210
[6]	Ruiz, M. et al., Exp. Clin. Immunogenet., 16, 173-184 (1999) PMID: 10394055, LIGM:211
[7]	Lefranc, M.-P., The Immunologist, 7, 132-136 (1999) LIGM:217.
[8]	Giudicelli, V. and Lefranc, M.-P., Bioinformatics, 15, 1047-1054 (1999) PMID: 10745995, LIGM:221

See also:

Created: 03/12/1999
Last updated: Wednesday, 29-Jun-2011 17:02:00 CEST
Authors: Véronique Giudicelli and Marie-Paule Lefranc
Editors: Manuel Ruiz and Chantal Ginestoux
Contact: Marie-Paule Lefranc

Software material and data coming from IMGT server may be used for academic research only, provided that it is referred to IMGT®, and cited as "IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)." References to cite: Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) Cover of NAR; Ruiz, M. et al., Nucleic Acids Research, 28, 219-221 (2000); Lefranc, M.-P., Nucleic Acids Research, 29, 207-209 (2001); Lefranc, M.-P., Nucleic Acids Res., 31, 307-310 (2003); Lefranc, M.-P. et al., In Silico Biol., 5, 0006 (2004) [Epub], 5, 45-60 (2005); Lefranc, M.-P. et al., Nucleic Acids Res., 33, D593-D597 (2005) Full text; Lefranc, M.-P. et al., Nucleic Acids Research 2009 37: D1006-D1012; doi:10.1093/nar/gkn838 Full text.
For any other use please contact Marie-Paule Lefranc Marie-Paule.Lefranc@igh.cnrs.fr.

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