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ASHG01-NW Summary

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Summary of "The Proposal of New Human Gene Nomenclature Guidelines"

Participants
Cindy Smith (MGD), Hester Wain (HGNC), Sue Povey (HGNC), Elspeth Bruford (HGNC), Cara Hunsberger (Molecular Therapy and Genomics), Donna Maglott (NCBI/LocusLink), Stephen Scherer (HGAC), Panos Deloukas (Sanger), Gerard Manning (Kinases, Sugen), Chris Porter (GDB), Alan Scott (OMIM), Kim Pruitt (Ref_Seq), Lucy Osborne (WBS Region), Lap-Chee Tsui (HUGO).

Updates from this meeting have now been incorporated into the guidelines.
A list of the issues discussed and actions recommended is detailed below:

  • Definition of a gene: Does this include objects which are never transcribed?  Yes, pseudogenes.
  • Would we change any gene symbols retrospectively to conform with the new guidelines? No.
  • Definition of a locus:   There was much discussion about this, and no agreement was reached, so for the meantime we will maintain the MGD definition.
  • Antisense and intronic transcripts are given their own symbol in the mouse, not one that reflects the other gene.  Antisense genes in human will only be assigned an AS suffix if there is proven regulatory function but no other known structure or function on which to base a gene name.   Genes of unknown function on the opposite strand which have no proven regulatory function should be assigned the suffixOS for "opposite strand".
  • Anonymous gene families: MGD are proposing an alternative to theFAM scheme (usingGG for gene grouping).  We are looking into this.
  • Aliases: All known aliases should be added to the gene entry including  those used for proteins.  The accession ID for each alias is not currently stored in Genew.
  • Pseudogene symbol: An alternative ofPS instead ofP was suggested to make pseudogenes more easily identifiable in searches.  However, it was felt this would be no better than P and that information is required from another field i.e. name or function, to ascertain whether the object was a pseudogene.  We may be able to introduce a function field to the Genew database in the future.  The change in numbering system was discussed and it was agreed to maintain already used systems but to encourage authors when submitting new families of pseudogenes to identify each with its own number and then the suffixP.
  • The reason for not approving unique symbols such asRING# andBING# was also discussed.  These are not approved because the symbols have seriously misled a number of scientists into believing that these genes are related when they are not. C#orfsymbols were suggested as a reasonable temporary solution to this type of problem.
  • Orthologous genes:  Genes which are initially identified in another organism e.g. mouse, will usually be assigned  the same symbol in human.  However, we do add the original organism to the gene name.  It was decided that we would update all previously assigned gene names that indicated organism orthology in a consistent manner to improve database searching.  Thus, all gene names containing organism specifications will now indicate the organism in parentheses at the end of the gene name e.g.DEF6 for "differentially expressed in FDCP (mouse homolog) 6" will become: "differentially expressed in FDCP 6 (mouse)".
  • Ribosomal RNA gene symbols: We are looking into guidelines for these symbols.
  • LocusXRef:  This is the private database that HGNC edits which exports directly to LocusLink.  At present, to maintain confidentiality, we sometimes have to create a new entry even if the gene sequence already has an entry.  We are investigating other alternatives to generating two gene records that then subsequently need to be merged.
  • Ref_Seq: There was a query regarding the identification of the sequence used by Ref_Seq.  HGNC maintains its own archived copy of the submitted sequence with each gene symbol.