IPD - KIR Database

Conditions for acceptance of new allele sequences.

As emphasised in previous reports and releases from the database, there are required conditions for the acceptance of new sequences for official names. Please read the following conditions carefully before submitting sequences.

1. Where a sequence is obtained from cDNA or where PCR products are subcloned prior to sequencing, several clones should have been sequenced.
2. Sequencing should always be performed in both directions.
3. If direct sequencing of PCR amplified material is performed, products from at least two separate PCR reactions should have been sequenced.
4. In individuals who are heterozygous for a locus, where one of the alleles is novel, the novel allele must be sequenced in isolation from the second allele. Thus an allele sequence which is derived using a sequence based typing (SBT) methodology, where both alleles of a heterozygous individual are sequenced together, is insufficient evidence for assignment of an official designation.
5. Sequence derived solely from the primers used to amplify an allele should not be included in the sequence that is submitted.
6. Where possible, a novel sequence should be confirmed by typing of genomic DNA using a method such as PCR-SSOP or PCR-SSP. Where a new sequence contains either a novel mutation or a previously unseen combination of nucleotides (sequence motif), this must be confirmed by a DNA typing technique. This may require the use of newly designed probes or primers to cover the new mutation; these reagents should also be described.
7. An accession number in a databank must have been obtained. Sequences may be submitted to these databases online at the following addresses:
   EMBL: http://www.ebi.ac.uk/Submissions/index.html
   GenBank: http://www.ncbi.nlm.nih.gov/Genbank/index.html
   DDBJ: http://www.ddbj.nig.ac.jp/sub-e.html
8. Full length sequences are preferable though not essential.
9. Where possible, a paper in which the new sequence is described should be submitted for publication. Draft publications can submitted to the database by e-mail (IPD Contact Details).
10. DNA or other material, preferably cell lines, should, wherever possible, be made available in a publicly accessible repository or alternatively, at least in the originating laboratory. Documentation on this will be maintained by the WHO Nomenclature Committee.
11. Submission of a sequence to the Nomenclature Committee should be performed using the online tool available at http:/www.ebi.ac.uk/ipd/kir/submit_stage_1.html. Researchers will be expected to complete the following questionnaire relating to the sequence and provide a comparison of their new sequence with known related alleles. If the sequence cannot be submitted using the online web tools researchers should contact IPD directly for details of alternative submission methods.

It should be noted with some caution that cells from which only partial sequences have been obtained may later be shown to represent different or novel alleles when further sequencing is performed. This is of particular importance in cases where several different cells have been partially sequenced for an allele. In such cases, all cell lines have been listed in the database.

Official designations are currently being assigned to new alleles in the period between Nomenclature Committee meetings, provided they meet the criteria outlined above. 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 preempt formal designations such as "KIR2DL9", "KIR2DL1*0109" before consideration by the Nomenclature Committee is strongly discouraged.

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