spacer

IPD-MHC Database

Ovine (OLA) Nomenclature

The nomenclature guidelines presented here were proposed at a meeting of the comparative MHC nomenclature committee of the International Society for Animal Genetics on the 28th of September 2005. These guidelines are reproduced in Ellis et al. (2006) along with those from other species interest groups. In order to standardise MHC nomenclature as much as possible it was proposed by K. Ballingall and M. Stear that the OLA guidelines should follow those proposed for HLA and BoLA nomenclature. The principle exception will allow for differentiation between different species designations within the genus Ovis. For example sequences derived from domestic sheep Ovis aries will be prefixed Ovar while sequences derived from bighorn sheep Ovis canadensis will be prefixed Ovca. An update on these guidelines can be found in Ballingall et al.  (2011).

Class I

Class I nomenclature is based on the HLA nomenclature system. Allele names are based on amino acid sequence and consist of 5 to 9 digits. The first 3 digits indicate the allele 'group', the second 2 indicate coding change, the next 2 indicate non-coding change, and the last 2 indicate promoter/intron change - the last 4 digits are therefore rarely used. Names will only be given to full length cDNA sequences. A full length cDNA sequence will include both start and stop codons, however sequences amplified from cDNA will be included if the start and stop codons are included in the respective primers. .

The guidelines regarding assignment to an allele 'group' are that sequences within a group should have a maximum of 4 amino acid changes within the alpha 1 and 2 domains, plus up to 4 amino acid changes in any other part of the coding sequence. IPD alignments use the new nomenclature. Old nomenclature is included in a table for comparison.

Class I Locus Assignment

It is clear from genetic analyses of transcribed class I genes in sheep (Miltiadou, et al. 2005) that the repertoire of class I loci differs between haplotypes and that accurate assignment of individual alleles to a specific locus is not yet possible. As this appears similar to that described in cattle (Holmes, et al. 2003); it is proposed to follow the nomenclature suggested for BoLA class I. All class I alleles are prefixed 'N' to indicate 'not assigned', and numbered in a single series. Given the limited number of sequences available we do not propose to differentiate between putative classical and putative non-classical alleles at this time.

Class II

Allelic nomenclature:In domestic sheep (Ovis aries), DRB1 is the principal transcribed and polymorphic DRB locus.  To maintain consistency with other MHC loci, the following nomenclature for alleles at the Ovar-DRB1 locus was adopted.  The first two digits following the species and locus designation (Ovar-DRB1) represents the allelic family (Ovar-DRB1*01, *02 etc).  Alleles within a family differ by no more than four amino acids in the region encoded by the second exon.  The next two digits indicate coding change within the allelic family or elsewhere in the coding region (Ovar-DRB1*0101, Ovar-DRB1*0102) and the next two digits (Ovar-DRB1 *010102) may be used to indicate silent or synonymous substitutions within the coding region.  An additional two digits may be used to identify allelic differences within the intronic regions. Alleles from different sheep species will use the species specific prefix (Ovca for Ovis canadensis, Ovda for Ovis dalli) and will be named independently from Ovar-DRB1 alleles.  Ovar-DRB1*0101 will be used as the reference sequence for all sheep species in order to ease comparisons between species specific alignments. 

It is anticipated that sequence information covering ovine DQ loci will also be included in 2011.  The DQA and DQB loci appear to have been duplicated in all of the ovine MHC haplotypes analysed so far.  It is anticipated that alleles at the DQA1 and DQA2 loci will appear in independent lists.   DQA alleles that may represent a third locus (DQA3 or DQA2-like) will be listed independently as DQAN until their locus assignment can be fully characterised.   Likewise, it is proposed that DQB alleles will initially be listed in a single series termed DQBN.

Conditions for Acceptance of New OLA Alleles

  • Full length sequences are always preferable.
    • For class I genes full length sequences are required.
    • For class II genes we encourage submission of full length sequences for all class II loci with the exception of the principally transcribed and highly polymorphic DRB1 locus. For this locus the entire exon 2 must be included. Primer sites within exon 2 will not be accepted.
  • Sequencing should have been performed on both strands of the template DNA.
  • When a sequence is based on clones derived from PCR amplification, a minimum of three clones must have been sequenced.
  • When a sequence is based on clones derived from PCR amplification, sequences from 2 independent PCR reactions are required.
  • If a novel sequence is derived from direct sequencing of PCR products, material derived from at least two separate PCR reactions should have been sequenced.
  • Ensure that predicted amino acid sequences make sense with particular attention to unique/unusual amino acid substitutions. If in doubt sequence additional clones derived from a different PCR amplification.
  • An accession number in a nucleotide Database should have been obtained.
  • When possible the sequence should have been submitted for publication.
  • DNA or other material, in particular cell lines, should be available for future reference.
  • Submission of a sequence to the Nomenclature Committee should include a computer-readable copy of the sequence.

Submission of New OLA Sequences

To receive official names, sequences of new OLA genes or alleles should be submitted to the OLA interest group of the comparative MHC steering committee of the International Society for Animal Genetics using the submission tool which can be found on the IPD-MHC home page. Contributors are encouraged to submit sequences even if an identical sequence is already present within the IPD-MHC OLA database. This provides essential verification of the sequence and additional information regarding population and breed distribution.

Further Information

For more information on the OLA nomenclature please contact keith.ballingall@moredun.ac.uk. For information regarding the website and technical issues please contact IPD Support

 


spacer
spacer