Summer newsletter 2020
28 Aug 2020
Fewer changes, other species, and no more dates – the new HGNC guidelines have been released!
We are delighted to announce that we have published a comment article about updates to our nomenclature guidelines. The citation in Nature Genetics can be viewed in the ‘Publications’ section below. A summary of our latest guidelines can be found on our website.
The major reasons for recent updates to our guidelines are as follows: The world of genomics, especially clinical genomics, has moved on swiftly, since our guidelines were last in print in 2002. We had been making necessary updates to our online guidelines over the years, but these changes had not been published in a peer-reviewed journal. To support the world of clinical genomics, we have had a seismic shift in our philosophy away from “gene nomenclature should evolve with new technology rather than be restrictive as sometimes occurs when historical and single gene nomenclature systems are applied” to “the stability of gene symbols, particularly those associated with disease, is now a key priority”. The latest guidelines reflect this change and include reference in our main guidelines to the role of Vertebrate Gene Nomenclature Committee (VGNC) in assigning equivalent gene nomenclature to selected vertebrate species.
One key feature in our paper is a section explaining the scenarios that merit updates to HGNC nomenclature. We had not anticipated the social media storm that would occur in response to the news, mentioned in this section, that we had updated a set of gene symbols that were being auto-converted to dates when entered in Microsoft Excel.
We have been aware of this issue for many years and initially tried to publicise how to change settings in Excel to prevent the auto-conversion, but it became clear that we could not possibly reach everybody that uses Excel to list gene symbols. Our work with the Transforming Genetic Medicine Initiative (TGMI) project alerted us to the scale of the problem in clinical settings and our subsequent discussion with users and with our Scientific Advisory Board galvanised us to begin the process of seeking updates to these problematic symbols. Our initial consultation with the research community that publish on the genes in question had mixed results, and it took several rounds of communication before we went ahead throughout 2019 and changed all symbols beginning MARCH# to begin MARCHF#, all symbols beginning MARC# to MTARC# (MTARC1 and MTARC2), all symbols beginning SEPT# to SEPTIN#, and the symbol DEC1 to DELEC1.
The resulting tweets included elation: ‘THRILLED by this announcement’, ‘Finally good news for 2020’, ‘Welcome news for anyone who has worked with gene lists in Excel’, and incredulity: ‘I almost thought it’s a joke’, ‘Is this an out-of-season April fools joke?’. The response was big enough to catch the attention of journalists: the Verge website contacted us for comments ahead of their article and we were featured on at least 22 other news sites in a variety of languages. We were pleased that EMBL also featured our article in a news announcement, and we would also like to thank all of our newsletter readers who responded to the news of our publication. All of this media attention has resulted in a high Altmetric score and over 4,000 downloads of the guidelines paper!
Report tags are now searchable on genenames.org
There are three kinds of report tags that can appear at the top of genenames.org symbol reports:
Ambiguous – present if the locus type of the gene ambiguous, e.g. it is not certain whether the gene encodes a protein or is a pseudogene
Placeholder Symbol – present if the symbol is one of HGNC’s systematic placeholder symbols; applies to C#orf, KIAA# and FAM# symbol reports
Stable Symbol – present when the symbol has been reviewed by an HGNC curator and a decision has been made that the symbol should not be subject to future change (it is important to note that the lack of this tag does not mean that the HGNC considers all other symbols are subject to change)
We have recently made these report tags searchable via the ‘Applied filters’ function on genenames.org search results. The ‘Filter by symbol report tag’ is at the bottom of the filters. If you select ‘Gene symbol reports’ from under the ‘Gene data’ tab, you will get the full list of our symbol reports and be able to filter the 137 reports with an ‘Ambiguous’ tag, the 895 reports with a ‘Placeholder symbol’ tag and the 1773 reports with a ‘Stable’ tag.
100,000 approved VGNC gene symbols