What's New at HGMD
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What's New at HGMD |
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From time to time, HGMD will be updated with regard to its content and structure. This page will inform users of changes to the site, and should answer any questions regarding those changes.
We shall also include any information regarding the database in general.
The new HGMD professional release becomes available with a total of 120,004 mutation entries. This represents a growth of 2,727 mutations over the previous release.
HGMD cDNA codon numbering
HGMD has instituted a policy of numbering cDNAs with the ATG starting at codon 1 (to better comply with HGVS nomenclature). All HGMD cDNA sequences and mutations are now numbered from ATG=1 by default. Legacy numbering is provided for older genes (e.g. F8, LDLR, Collagens, Haemoglobins) to assist with this transition.
Mutation Mart
A new batch mode has been made available as part of the HGMD Advanced Search. Users may search HGMD by submitting lists of dbSNP, PubMed or Entrez gene identifiers.
HGMD News
Genomic chromosomal coordinates based on NCBI build 36.3 of the genome (hg18) will not be available for future releases of HGMD Professional, as HGMD is standardising coordinates based on on hg19. Users still requiring coordinates based on hg18 should use LiftOver, based at UCSC.
HGMD (Cardiff) now has over 49,000 registered users.
The new HGMD professional release becomes available with a total of 117,277 mutation entries. This represents a growth of 4,030 mutations over the previous release.
Genomic coordinates and HGVS nomenclature (splicing mutation dataset)
The HGMD splicing mutations have now been mapped to both builds of the reference genome (NCBI37.2 / hg19 and legacy NCBI36.3 / hg18). Approximately 96% of splicing mutations have been successfully mapped. HGVS nomenclature is also provided for this dataset. The vast majority (~98% overall) of HGMD micro-lesions have now been mapped to the reference genome.
HGMD (Cardiff) now has over 48,000 registered users.
The new HGMD professional release becomes available with a total of 113,247 mutation entries. This represents a growth of 2,475 mutations over the previous release.
New search features
The reference search has been upgraded, and will now allow the searching of both the primary and secondary (additional) references present in HGMD.
Genomic coordinates
HGMD mutations (missense/nonsense, regulatory, small deletions, small insertions and small indels) have now been mapped to the new build of the reference genome (NCBI37.2 / hg19). Coordinates displayed in HGMD should now be considered to be hg19 unless otherwise stated. Legacy NCBI36.3 / hg18 coordinates will continue to be provided (via LiftOver) until the end of 2011.
cDNA reference sequences
Many of our cDNA reference sequences have now either been updated to newer versions, or replaced entirely if a new RefSeq sequence was available for that gene.
HGMD (Cardiff) now has over 46,000 registered users.
The new HGMD professional release becomes available with a total of 110,772 mutation entries. This represents a growth of 2,726 mutations over the previous release.
New search features (Professional version only)
The gene search has been updated to allow users search HGMD without utilising boolean fulltext indexing. The new non-boolean search does not use the fulltext index and there is no minimum word length (features that exist with the boolean fulltext search).
A new mutation search is now available. Mutations may now be searched via chromosomal coordinate (currently build 36.3/hg18). Single coordinates, a range of coordinates or mutations mapped to a whole chromosome may be returned via this search function.
The HGMD F.A.Q. now has its own search page.
HGMD (Cardiff) now has over 43,000 registered users.
The new HGMD professional release becomes available with a total of 108,046 mutation entries. This represents a growth of 2,911 mutations over the previous release.
New advanced search features (Professional version only)
HGMD has initiated the process of annotating mutation data with structural and functional information derived from (i) in vitro and/or in vivo experimentation and (ii) in silico based predictions. This is to facilitate ascertainment of the molecular mechanism underlying the functional effect(s) of a given mutation. It is planned that HGMD should eventually store (and be searchable for) annotations pertaining to more than 50 different types of functional site e.g. exonic splice enhancers, post-translational modifications, transcription factor binding sites etc.
HGMD now also includes data derived from the application of methods useful in the context of personal genome interpretation, such as SIFT and MutPred, thereby facilitating the prediction of deleterious missense mutations.
The recent study by the 1000 Genomes Project Consortium published in Nature utilises HGMD data.
HGMD (Cardiff) now has over 41,000 registered users.
The new HGMD professional release becomes available with a total of 105,135 mutation entries. This represents a growth of 2,702 mutations over the previous release.
Links to the NCBI RefSeqGene project (Professional version only)
Where identified, links to the NCBI RefSeqGene project are now available on a gene-wise basis.
HGMD (Cardiff) now has over 39,000 registered users.
The new HGMD professional release becomes available with a total of 102,433 mutation entries. This represents a growth of 2,104 mutations over the previous release.
HGMD now has over 37,000 registered users.
The new HGMD professional release becomes available with a total of 100,329 mutation entries. This represents a growth of 3,698 mutations over the previous release.
Genomic coordinates extended (Professional version only)
Genomic coordinate data has been extended to the regulatory mutation data set to complement the missense/nonsense, small deletion, small insertion and small indel data sets which have already been mapped.
HGMD layout change (Professional version only)
The summary mutation pages have been altered to make the HGVS nomenclature more prominent, which should greatly facilitate data interpretation for users used to the HGVS standard.
HGMD now has over 34,000 registered users.
The new HGMD professional release becomes available with a total of 96,631 mutation entries. This represents a growth of 3,284 mutations over the previous release.
HGMD now has over 32,000 registered users.
The new HGMD professional release becomes available with a total of 93,347 mutation entries. This represents a growth of 2,214 mutations over the previous release.
HGVS nomenclature has been extended to the small deletion, small insertion and small indel mutation data sets to complement the missense/nonsense HGVS nomenclature launched in release 2009.1 (March 2009).
Genomic coordinates extended (Professional version only)
Genomic coordinate data been extended to the small deletion, small insertion and small indel mutation data sets to complement the missense/nonsense coordinate data launched in release 2008.3 (September 2008).
dbSNP entries (Professional version only)
Validated dbSNP entries may now be viewed alongside HGMD mutation and disease-associated/functional polymorphism data, to provide a more complete overview of alleleic variation for the genes present in HGMD. This feature is currently only available for missense/nonsense mutations, with other mutation types to follow.
Advanced search (Professional version only)
The transcription factor binding sites available in TRANSFAC have been mapped to the regulatory mutation and disease-associated/functional polymorphism dataset. Users may search HGMD to identify which regulatory mutations/polymorphisms disrupt or create a particular binding site.
The results of queries using the advanced search may now be downloaded as a custom genome browser track, ready to import into UCSC's genome browser. This feature allows users to visualize HGMD data alongside the genomic annotations provided by UCSC.
Comments added (Public site)
Editorial comments (for mutation data) are now available to view in the public version of HGMD for the first time.
HGMD now has over 30,000 registered users.
The new HGMD professional release becomes available with a total of 91,133 mutation entries. This represents a growth of 2,816 mutations over the previous release.
Highly Commended award presented by the Cardiff University Innovation Network for the collaboration between BIOBASE and the School of Medicine, Department of Medical Genetics, for the development of the Human Gene Mutation Database (HGMD).
cDNA sequences (Professional version only)
Users may optionally display translated protein sequence alongside the (recently updated) HGMD cDNA sequence.
HGMD now has over 28,000 registered users.
The new HGMD professional release becomes available with a total of 88,317 mutation entries. This represents a growth of 2,759 mutations over the previous release.
HGMD is pleased to announce the integration of the official mutation nomenclature proposed by den Dunnen JT and Antonarakis SE (2001) Hum Genet 109: 121-24. Users may search for specific mutations using nomenclature terms, which will also be displayed alongside individual HGMD entries. This feature is currently only available for missense/nonsense mutations, with other mutation types to follow as they are mapped to the Genome.
Additional references added to HGMD entries
Additional references will now be displayed for certain HGMD mutation and functional polymorphism entries. These references fall into two main categories; functional characterisation reports (e.g. in vitro expression studies) and other additional reports (e.g. additional or further description of the mutation, additional phenotypes etc). Coverage of these additional references is not comprehensive, as reports will only be added if the HGMD curators deem that the additional report acts to enhance the mutation entry.
There are currently 2,860 mutation/functional polymorphism entries in HGMD with at least one additional reference.
New cDNA sequences
The HGMD cDNA sequences have been updated to reflect the latest release of the NCBI refseq sequence database. Most HGMD entries that previously relied on older GenBank cDNA sequences have now been updated. These sequences will also be available on the pubic site in due course.
HGMD now has over 26,000 registered users.
The new HGMD professional release becomes available with a total of 85,558 mutation entries. This represents a growth of 1,830 mutations over the previous release.
HGMD is pleased to announce the integration of the Gene Ontology Project's ontology terms (as provided by the Gene Ontology Consortium, Nat Genet (2000) 25: 25-9) into HGMD professional. Ontology terms may be searched for directly (e.g. 'DNA binding') or by accession number (e.g. 'GO:0003677'). HGMD genes may also be browsed according to assigned gene ontology via the gene search link. Gene-specifc ontologies are displayed on each individual gene page.
New search options
Users may now additionally browse HGMD genes by chromosomal location (1-22, X and Y). The ability to view pre-queried HGMD data (a random HGMD gene entry, genes newly added for the current release, genes updated with new mutation data for the current release, or genes sorted by ontology term) is also available.
HGMD now has over 23,000 registered users.
The new HGMD professional release becomes available with a total of 83,728 mutation entries. This represents a growth of 2,841 mutations over the previous release.
HGMD is pleased to announce the first release of its uniquely comprehensive human disease-associated/functional polymorphism database.
Polymorphisms included are either disease-associated (in many cases with some additional supporting functional evidence), or are of in vivo or in vitro functional significance albeit with no reported disease association as yet. These data are sub-localised within HGMD under the same mutation categories as our existing disease-causing mutation data (i.e. missense/nonsense, regulatory etc), but are specifically marked as polymorphisms. Corresponding dbSNP numbers are provided where possible. Users should soon be able to search this sub-dataset utilising the existing Advanced Search toolset. Please also read our inclusion criteria for these polymorphisms.
There are currently 3983 disease-associated/functional polymorphisms in 1493 different genes logged in HGMD. This total is expected to continue to grow in line with the existing disease-causing mutation dataset.
Genomic coordinates of mutations
HGMD is pleased to announce the inclusion of genomic coordinates for the missense/nonsense mutation dataset. Data of this type have been mapped to build 36.3 of the Human Genome curated at the NCBI (analogous to the hg18 assembly of the UCSC Genome Browser). The mapping process for missense/nonsense mutations is approximately 92% complete. Coordinates for other mutation types will be included in future releases of HGMD.
HGMD search
Genes can now be searched for using known gene name aliases to complement the recently added gene symbol alias search.
HGMD now has over 22,000 registered users.
The new HGMD professional release (now designated 2008.2) becomes available with a total of 80,887 mutation entries. This represents a growth of 1,809 mutations over the previous release.
Genes can now be searched for using known gene symbol aliases, the HGNC Nomenclature Committee ID and the Entrez Gene ID in addition to the official HGNC Nomenclature Committee gene symbol.
Protein sequences from several organisms (other than Mus musculus) have been added to HGMD Professional for use by the protein sequence alignment tool for missense mutations. Protein sequences from Rattus norvegicus, Gallus gallus, Canis lupus familiaris, Felis catus, Sus scrofa, Ovis aries, Bos taurus, Macaca mulatta, Takifugu rubripes, and Pan troglodytes have recently been included. For some of the organisms listed, only a small number of orthologous protein sequences are currently characterised by the NCBI Entrez protein reference database. We will therefore continue to add new sequences as they appear.
HGMD has exceeded 20,000 registered users in a little over 2 years. A continuing tremendous response from our users.
The new HGMD professional release (8.1) becomes available with a total of 79,078 mutation entries. This represents a growth of 3,067 mutations over the previous release.
Users may now browse HGMD genes in an alphabetical (A-Z) fashion.
The Advanced Search now allows searching for relevant keywords that are present in the published abstract. This complements the existing feature of searching article titles.
HGMD has exceeded 18,000 registered users in a little over 21 months. A continuing tremendous response from our users.
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The contribution of HGMD to the work of the Institute of Medical Genetics (Cardiff University) was recently recognised by the award of the Queen's Anniversary Prize for "Transforming healthcare for families with inherited disorders" to the Institute in November 2007. |
The new HGMD professional release (7.4) becomes available with a total of 76,011 mutation entries. This represents a growth of 2,600 mutations over the previous release.
Users may now sort mutation data in several different ways when retrieving mutations for each gene. Data may be sorted by location, disease/phenotype, author name or year of publication.
More detailed statistics for small indels have now been added and are accessible through the HGMD Professional statistics page.
HGMD has exceeded 15,500 registered users in a little over 18 months. A continuing tremendous response from our users.
The new HGMD professional release (7.3) becomes available with a total of 73,411
mutation entries. This represents a growth of 1,566 mutations
over the previous release.
HGMD can now be searched by codon number.
All mutations in a single gene can now be viewed by clicking on the 'Get all mutations' button available on each gene page adjacent to the mutation total.
HGMD has exceeded 12500 registered users in a little over 15 months. A continuing tremendous response from our users.
The new HGMD professional release (7.2) becomes available with a total of 71,845 mutation entries. This represents a growth of 2,111 mutations over the previous release.
Pairwise alignments for missense mutations with the corresponding mouse protein sequence are now available for over 1800 of the genes in HGMD. Over 92% of missense mutations will now display an associated alignment.
HGMD has exceeded 11,000 registered users in a little over 12 months. A continuing tremendous response from our users.
Users of the Cardiff website may now see an example entry (GH1 gene) from HGMD Professional 7.2.
The recent publication by the Macaque Genome Consortium in Science utilises HGMD data.
The new HGMD professional release (7.1) becomes available with a total of 69,734 mutation entries. This represents a growth of 2,704 mutations over the previous release.
HGMD can now be searched for mutation-specific attributes. This feature currently only supports HGMD accession number searches. Please refer to the help page for further details.
Missense mutations now have extra information, including further descriptions of each mutation with amino acid sequence context and alignments with the corresponding mouse sequence where currently available (APC, BRCA1, BRCA2, CFTR, FGFR3, GALT, GJB1, NF1, RET and TP53 at present). Amino acid properties are also displayed for each missense mutation.
Wolfenbüttel, Germany: BIOBASE today announced a new advanced search facility to allow comprehensive interrogation of HGMD data. The advanced search facility will be available to HGMD Professional subscribers from the next release.
The advanced search facility allows the user to
HGMD has exceeded 9000 registered users in a little over 9 months. A continuing tremendous response from our users.
The new HGMD professional release (6.4) becomes available with a total of 67,030 mutation entries. This represents a growth of 2,779 mutations over the previous release.
HGMD has exceeded 6000 registered users in a little over 6 months. A continuing tremendous response from our users.
The new HGMD professional release (6.3) becomes available with a total of 64,251 mutation entries. This represents a growth of 2,069 mutations over the previous release.
HGMD has exceeded 3000 registered users in a little over 3 months. A continuing tremendous response from our users.
The new HGMD professional release (6.2) becomes available with a total of 62,182 mutation entries. This represents a growth of 2,518 mutations over the previous release.
Wildcard (*) searching and alternate spellings for search terms have recently been added to the public search tool.
HGMD has exceeded 1000 registered users in a little over 3 weeks. A tremendous response from our users which clearly shows how widely HGMD is used by both the academic and commercial scientific community.
625 new entries added to HGMD this month.
Access to the mutation data held in the public version of HGMD in Cardiff will remain free only for registered users from academic institutions/non-profit organisations. Both commercial and academic/non-profit users wishing to access the most up-to-date version of the database may license HGMD and the accompanying programs from BIOBASE, our commercial partner. Please vistit our registration page for further details.
482 new entries added to HGMD this month.
HGMD has been on the web for 10 years this month. Coincidentally, we have also exceeded 60,000 mutation entries!
1032 new entries added to HGMD this month.
The first release of HGMD professional (release 6.1) becomes available with a total of 59,664 mutation entries.
423 new entries added to HGMD this month.
1361 new entries added to HGMD this month.
HGMD collaboration with Biobase begins January 2006. BIOBASE, based in Wolfenbüttel (Germany) and Beverly MA (USA), is the leading content provider of biological databases. This cooperative agreement covers the exclusive worldwide marketing of the Human Gene Mutation Database (HGMD) to both academic and commercial users. The initial 5-year contract will guarantee the continuity of HGMD. You can read the latest news on the Biobase website (PDF).
The new HGMD search facility is now available. HGMD can still be searched in the same way - by gene symbol, gene name, OMIM number, GDB number and disease keyword. The old version of HGMD will no longer be updated, therefore we would ask our users to use the new search from now on.
969 new entries added to HGMD this month.
475 new entries added to HGMD this month.
307 new entries added to HGMD this month.
626 new entries added to HGMD this month.
476 new entries added to HGMD this month.
549 new entries added to HGMD this month.
642 new entries added to HGMD this month.
Our 5 year exclusive collaboration with Celera Genomics has now come to an end.
378 new entries added to HGMD this month.
455 new entries added to HGMD this month.
469 new entries added to HGMD this month.
353 new entries added to HGMD this month.
Meta-analysis of gross insertions published in Human Mutation.
573 new entries added to HGMD this month.
The total number of unique inherited gene lesions recorded by HGMD surpassed 50,000 this month.
409 new entries added to HGMD this month.
635 new entries added to HGMD this month.
464 new entries added to HGMD this month.
471 new entries added to HGMD this month.
339 new entries added to HGMD this month.
532 new entries added to HGMD this month.
A companion paper to the Rat Genome Consortium Nature article is published in Genome Biology.
864 new entries added to HGMD this month.
534 new entries added to HGMD this month.
257 new entries added to HGMD this month.
The recent publication by the Rat Genome Consortium in Nature utilises HGMD data.
561 new entries added to HGMD this month.
665 new entries added to HGMD this month.
613 new entries added to HGMD this month.
79 new entries added to HGMD this month.
515 new entries added to HGMD this month.
607 new entries added to HGMD this month.
494 new entries added to HGMD this month.
842 new entries added to HGMD this month.
547 new entries added to HGMD this month.
434 new entries added to HGMD this month.
341 new entries added to HGMD this month.
An updated description of HGMD was recently published in Human Mutation (2003) 21:577-81.
387 new entries added to HGMD this month.
464 new entries added to HGMD this month.
245 new entries added to HGMD this month.
559 new entries added to HGMD this month.
449 new entries added to HGMD this month.
289 new entries added to HGMD this month.
599 new entries added to HGMD this month.
407 new entries added to HGMD this month.
435 new entries added to HGMD this month.
613 new entries added to HGMD this month.
239 new entries added to HGMD this month.
1433 new entries added to HGMD this month.
1016 new entries added to HGMD this month.
275 new entries added to HGMD this month.
856 new entries added to HGMD this month.
791 new entries added to HGMD this month.
249 new entries added to HGMD this month.
266 new entries added to HGMD this month.
268 new entries added to HGMD this month.
455 new entries added to HGMD this month.
422 new entries added to HGMD this month.
570 new entries added to HGMD this month.
665 new entries added to HGMD this month.
HGMD now contains links to unpublished mutation data available in online public locus-specific mutation databases. These links have been established in order to provide HGMD users with easy and comprehensive access to both published and unpublished mutation data.
540 new entries added to HGMD this month.
Our new permanent web address is www.hgmd.org. Our old address will remain functional for as long as necessary, but please use the new address to reach the HGMD home page.
HGMD has recently entered into a licensing agreement with Celera Genomics of Rockville, MD, USA. As part of this agreement, the University of Wales College of Medicine in Cardiff has undertaken to provide Celera with a period of exclusive access to new information added to HGMD. Thus HGMD data will, together with the SNP Reference Database, be made available to subscribers as part of Celera's web-based Discovery System™. The agreement also allows for future collaborations including joint software and database development. After the period of exclusivity, new HGMD data are made publically available on the Cardiff site. This collaboration with Celera not only guarantees the future of HGMD but will also allow us to greatly improve and expand our service on the public website whilst still maintaining our scientific research programme.
The total number of nuclear genes with reported mutations surpassed 1000 on April 15th.
HGMD can now be searched for mitochondrial genes which contain disease causing mutations. The resulting gene page contains a link to Mitomap, along with the usual links to OMIM, GDB and the HUGO Nomenclature database.
An updated description of HGMD was recently published in Human Mutation 15:45-51, 2000.
A list of recent journal articles written utilising HGMD data and published by authors within HGMD can be found on the HGMD articles page.
The total number of unique inherited gene lesions recorded by HGMD surpassed 20,000 on 1st Dec 1999. This represents an increase of 10,000 in 2 1/2 years.
HGMD has been on the web for 3 years this month
HGMD now includes disease-associated polymorphisms that are reported in the literature. As of this month, there are over 150 entries of this type in HGMD. Further information can be obtained from our Background page.
The new link is located under External Links on each gene home page where there is a corresponding page at GeneClinics.
The new link is located under External Links on each gene home page. The Nomenclature Database provides information regarding the official symbol for each gene.
The new link is located under External Links on each gene home page. We now have bi-directional links with GenAtlas. The link is intended to supplement the data already provided by our links with OMIM and GDB.
This new option is located under Associated Data on each gene home page. The link goes to a text file containing approximately 25 bp either side of the splice junction for each exon/intron boundary. Note that this is only available for certain genes (currently about 50). We hope to be able to bring more of these sequences online as they become available. Further information regarding this feature can be obtained from our Background page.
A paper produced by members of the HGMD team was published in the American Journal of Human Genetics. This paper describes research carried out utilising our data on single base-pair substitutions within gene coding regions.
HGMD has been picked as a top site by BioMedNet.
The New Genes page can be accessed through a link on our Search page. This page details which genes have been added to HGMD in the last 2 months. The associated phenotype(s) are also given, along with links to the relevant gene pages.
The layout for the HGMD webpages was redesigned. Each gene now has its own "home page". Each home page contains a table detailing the type and number of mutations in HGMD, and links to the mutation pages. Further information can be obtained from our Background page.
An updated description of HGMD was published in Nucleic Acids Res. 26:285-287, 1998.
This link is found at the bottom of each page under Associated Data. Each map gives a graphical representation of all reported missense/nonsense mutations, deletions and insertions superimposed onto the amino acid sequence for that gene.
HGMD reaches a landmark, now cataloguing over 10,000 unique inherited gene lesions.
On each page under Associated Data, there is now a link to a text file containing the derived reference cDNA sequence, numbered by codon.
HGMD picked as a "cool site" by Netscape.
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