Summer newsletter 2020Newsletters ·
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 apace 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 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 4000 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
We have reached a major milestone in our VGNC project – 100,000 approved symbols! This breaks down per main species as:
12349 approved cat gene symbols
16873 approved chimpanzee symbols
15804 approved cow symbols
15626 approved dog symbols
14456 approved horse symbols
13114 approved rhesus macaque symbols
12963 approved pig symbols
We look forward to approving many more!
Archived complete HGNC datasets
Following community request, we now archive the complete HGNC dataset file (both in tab separated and JSON formats) each month and each quarter. These files are found in the archive section of our FTP site. Please note that the archives begin from the month of June 2020.
New HGNC gene groups
New gene groups from the past quarter of the year include:
Gene Symbols in the News
Recent news reports have discussed how which ABO gene variant you carry may affect your risk of catching, or becoming extremely ill, with COVID-19. Some studies have linked blood group A with a higher risk of both catching and suffering extreme symptoms of the disease, while blood group O has been associated with a lower risk. However, other studies have questioned this association.
Specific immunoglobulin gene segments have also recently been linked with severity of COVID-19: the presence of antibodies with regions derived from IGHV3-23, IGHV3-48, IGHV1-2, or IGHV4-34 gene segments are all associated with a more severe form of the disease. These same IGHV segments have been previously associated with response to other viruses, including influenza.
The hybrid gene CHRFAM7A (a fusion of duplicated exons from CHRNA7 and FAM7A), expressed by around 75% of people, has been implicated in a failure to respond to drugs that target acetylcholine concentrations to treat Alzheimer disease. So far, this association has only been tested in induced pluripotent stem cells, but if further studies confirm it, Alzheimer patients not carrying the CHRFAM7A fusion may benefit from treatment with drugs that were previously viewed as ineffective.
A new study has identified the GSTA4 gene as a target of existing and candidate multiple sclerosis treatments. The study shows that GSTA4 is involved in survival of oligodendrocyte cells during differentiation and there is hope that further study on this gene may improve the understanding and treatment of multiple sclerosis in the future.
On Thursday, Jun 25th, we took part in a virtual meeting with our colleagues from the mouse and rat genomic nomenclature committees. Although the meeting was a success, we look forward to the day we can meet these colleagues again in person! One useful outcome was that we are now members of a shared Slack channel with mouse and rat nomenclature advisors, making it much easier to raise quick issues with everybody.
Members of the HGNC/VGNC will be attending a couple of virtual conferences over the next few months. David Nelson, one of our collaborators for the CYP gene naming of the VGNC project has co-authored an abstract for, will be virtually attending, Genome Informatics 2020 with Elspeth, Susan and Tamsin from 14th-16th September. Ruth will be virtually attending The Complex Life of RNA – Virtual from 7th-9th October.
Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Guidelines for human gene nomenclature. Nat Genet. 2020 Aug;52(8):754-758 PMID:32747822 DOI:10.1038/s41588-020-0669-3
Thompson B, Davidson EA, Liu W, Nebert DW, Bruford EA, Zhao H, Dermitzakis ET, Thompson DC, Vasiliou V. Overview of PAX gene family: analysis of human tissue-specific variant expression and involvement in human disease. Hum Genet. 2020 Jul 29. PMID:32728807 [DOI:10.1007/s00439-020-02212-9] (https://link.springer.com/article/10.1007/s00439-020-02212-9)