HGNC/HGVS Copy Number Variation Workshop

Summary

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Joint meeting of HGNC and HGVS: Room 209, Helsinki Fair Centre, Finland 31 May 2006( ~80 people in attendance)

Following a vote VCN genes will now be referred to as copy number variant or CNV genes (10 votes for CNV, 2 votes for VCN)

As a result of this meeting the HGNC formulated the following summary which will shortly be refined and incorporated into our Guidelines:

• HGNC is not a variation database.
• HGNC agrees with the need to 'name' individual copies of CNV genes.
• HGNC will continue to provide a unique "gene symbol" for all unique "genes".
• A unique "CNV symbol" will be available for "CNV genes".
• "CNV symbol" will be a new category in the HGNC database, with a unique symbol identifier which can be placed on a reference genome and the CNV symbol entry will include links to other databases.
• When a gene is identified as CNV then there will be a link in the gene symbol entry to any associated CNV symbol entries and to the Database of Genomic Variants.
• The CNV symbol entries will link to their stem symbol entry.
• "CNV symbols" will use the appropriate unique "gene symbol" stem with the addition of either a numeral or a letter depending on the last character in the stem symbol. eg: for the gene symbol "DEFB104" there will be 2 CNV symbols "DEFB104A" and "DEFB104B", whereas the gene symbol "ABO" could be given CNV symbols "ABO1", "ABO2" etc.
• "CNV symbols" will not have the same status in the HGNC database as "gene symbols".
• Standard gene search will only retrieve "gene symbols", eg DEFB104.
• The advanced search option to include CNV entries would retrieve DEFB104, DEFB104A, DEFB104B
• The use of CNV status means that there is no need for the addition of any extra identifiers in the gene name.
• HGNC will provide a "CNV symbol" upon request when the following criteria are reached:
• The "CNV gene" is listed in the Database of Genomic Variants
• NCBI and VEGA (if annotated by VEGA) agree upon the co-ordinates for the CNV copy in a reference sequence
• The "CNV genes" are greater than 97% identical

CNV Gene Nomenclature Updates

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NOVEMBER 2005 UPDATE: Due to the enthusiastic response we received to the Hot Topic (see below) we decided to focus on this issue at the ASHG05 conference in Salt Lake City. We presented a poster and organised a meeting to discuss the issues relating to the nomenclature of variable copy number genes. The meeting brought together some eminent scientists in segmental duplication/copy number variation and representatives from NCBI, Sanger, UCSC and OMIM as well as members of the HGVS and HGNC. JUNE 2006 UPDATE: HGNC and HGVS (Human Genome Variation Society) organised a satellite workshop at HGM2006 with a focus on Copy Number Variation (CNV). During the meeting it was agreed that a method of naming CNV genes was required and several suggestions were made for how this could be achieved. The points included in the workshop summary will shortly be refined and incorporated into our Guidelines. MAY 2007 UPDATE: The HGNC presented their hierarchical database structure in a talk at the HGVS and in a poster at HGM2007 in Montreal, Canada. This hierarchical database structure will be public once populated with >100 copy number variants. If you have a CNV gene submission please complete our online gene symbol request form, specifying the CNV status in the additional  comments and information field. Variable copy number gene nomenclature The research community is increasingly becoming aware that genes previously believed to be single copy, can be present in variable copy numbers in different individuals (PMID:15286789, 15273396 and 15918152). The nomenclature of these 'complex' loci has previously been dealt with on a case-by-case basis; however, as more such genes are identified, the HGNC would like to determine if a standard approach would be of benefit to the scientific community. Examples of HGNC 'case-by-case' approved scenarios include: 1. The RNR1-5 loci, which contain arrays of ribosomal RNA at p12 of the acrocentric chromosomes 13, 14, 15, 21, and 22 respectively. There are 150-300 copies of ribosomal genes in the human genome that are homogenised by concerted evolution, recombination and gene conversion. The individual rRNA genes in each RNR# cluster are not approved by the HGNC. 2. DEFA1A3 (defensin, alpha 1 and alpha 3, variable copy number locus) at 8p23.1 comprises variable copy number tandem repeats that include the DEFA1, DEFA3 and DEFT1P genes, each present in the current human genome build. We also have three separate approved gene records for DEFA1, DEFA3 and DEFT1P, as they can be distinguished by sequence although some individuals do not possess any DEFA3 copies (PMID:15944200, 16039093 and 15588320). 3. The KIR2DL5A and KIR2DL5B variable copy number genes. Although there is only one of these genes in the current human genome build, and some individuals do not possess both, the KIR2DL5A and KIR2DL5B genes are not in tandem and can be distinguished by sequence. The NCBI creates separate gene records for different genes so they have also created two separate Entrez Gene records for these (PMID:12185535).   As illustrated above there is currently no consensus for naming variable copy number genes and, indeed, it may not be feasible to apply a standard nomenclature system to all cases. We would greatly appreciate your opinion and thoughts regarding the potential problems of the current nomenclature systems, benefits and pitfalls of a standard nomenclature, and ideas for an ideal new nomenclature scheme for variable copy number genes. Please email hgnc@genenames.org with your view.