Condition of acceptence for new alleles

The IPD-IMGT/HLA Database has a set of minimum requirements for sequence and metadata. Please review these requirements carefully before making a submisison to the database.

Requirements checklist

  1. If direct sequencing of PCR amplified material is performed, products from at least two separate PCR reactions must have been sequenced.
  2. Sequence derived from primers used to amplify an allele must not be included in the sequence that is submitted.
  3. An accession number in a databank must have been obtained. Sequences may be submitted to these databases online at the following addresses:
    • EMBL: /embl/Submission/index.html
    • GenBank: http://www.ncbi.nlm.nih.gov/Genbank/submit.html
    • DDBJ: http://www.ddbj.nig.ac.jp/submission-e.html
  4. The minimum requirements for a sequence to be named are exons 2 and 3 for an HLA class I sequence and exon 2 for an HLA class II sequence
  5. Where a novel sequence differs only within an intron or other non-coding part of the gene, a full length sequence must be obtained, which covers all coding and non-coding regions. In the absence of a full length genomic sequence from the most closely related allele, it may be required that this also be sequenced and submitted before a name can be assigned to the novel sequence.
  6. Where possible, a paper in which the new sequence is described should be submitted for publication. Draft publications can be submitted to the database by email.
  7. When HLA typing patients with haematological malignancies it is to essential confirm the presence of any novel alleles in the germline. This is possible by using DNA collected by buccal swab. Sequences derived solely from tumour material, or without sufficient evidence of the additional work to confirm the sequence in the germline will not be considered for nomenclature.
  8. The complete HLA type for HLA-A, -B, -DRB1 genes must be submitted for the material in which a novel allele has been defined. In addition the sample should have been characterised for the second allele at the locus of interest in a heterozygous individual.

Although at present it is only a recommendation that full-length sequences of the coding region of novel alleles be submitted it was widely felt that in the future this should become a requirement for submission. Such requirement would remove many of the currently encountered ambiguities in the assignment of names to alleles for which partial sequences have been submitted and should not be burdensome as sequencing techniques have improved substantially since the submission conditions were first devised. In cases where novel mutations or polymorphisms are detected in non-coding regions of the gene, it will be a requirement that full-length sequences be submitted of both the novel allele and its most closely related allele.

It should be noted with some caution that cells from which only partial sequences have been obtained may later be shown to have different or novel alleles when further sequencing is performed. This is of particular importance in cases where partial sequences of what appears to be the same allele have been obtained from several different cells. In such cases, all cells studied have been listed in this report.

Current practice is that official designations will be promptly assigned to newly described alleles in periods between Nomenclature Committee meetings, provided that the submitted data and its accompanying description meet the criteria outlined above. A list of the newly reported alleles is published each quarter in nomenclature updates in the journals HLA, Human Immunology and the International Journal of Immunogenetics. The listing of references to new sequences does not imply priority of publication. The use of numbers or names for alleles, genes or specificities which pre-empt assignment of official designations by the Nomenclature Committee is strongly discouraged.