d52cbc57618c1635024918518f864f9a5f79ca12 max Tue Dec 10 03:52:17 2019 -0800 updating HGMD to 2019 version, refs #24625 diff --git src/hg/makeDb/trackDb/human/hgmd.html src/hg/makeDb/trackDb/human/hgmd.html index 6f56311..00b6771 100644 --- src/hg/makeDb/trackDb/human/hgmd.html +++ src/hg/makeDb/trackDb/human/hgmd.html @@ -1,90 +1,92 @@ <h2>Description</h2> <div class="warn-note" style="border: 2px solid #9e5900; padding: 5px 20px; background-color: #ffe9cc;"> <p><span style="font-weight: bold; color: #c70000;">NOTE:</span><br> HGMD public is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the HGMD public database is open to all academic users, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.</p> <p><span style="font-weight: bold; color: #c70000;">DOWNLOADS:</span><br> As requested by Qiagen, this track is not available for download or mirroring but only for limited API queries, see below. </p></div> <p> This track shows the genomic positions of variants in the public version of the Human Gene Mutation Database (<a href="http://www.hgmd.cf.ac.uk/ac/index.php" target="_blank">HGMD</a>). UCSC does not host any further information and provides only the coordinates of mutations. </p> <p> To get details on a mutation (bibliographic reference, phenotype, disease, nucleotide change, etc.), follow the "Link to HGMD" at the top of the details page. Mouse over to show the type of variant (substitution, insertion, deletion, regulatory or splice variant). For deletions, only start coordinates are shown as the end coordinates have not been provided by HGMD. Insertions are located between the two annotated nucleic acids. </p> <p> The HGMD public database is produced at Cardiff University, but is free only for academic use. Academic users can register for a free account at the <a href="http://www.hgmd.cf.ac.uk/docs/register.html" target=_"blank">HGMD -User Registration</a> page. Download and commercial use requires a license for the <a -href="https://www.qiagenbioinformatics.com/products/human-gene-mutation-database/" target="_blank">HGMD Professional</a> +User Registration</a> page. Download and commercial use requires a license for the <a href="https://www.qiagenbioinformatics.com/products/human-gene-mutation-database/" target="_blank">HGMD Professional</a> database, which also contains many mutations not yet added to the public version of HGMD public. The public version is usually 1-2 years behind the professional version. </p> <p>The HGMD database itself does not come with a mapping to genome coordinates, but there is a related product called "GenomeTrax" which includes HGMD in the UCSC Custom Track format. Contact Qiagen for more information.</p> <h2>Batch queries</h2> <p>Due to license restrictions, the HGMD data is not available for download or for batch queries in the Table Browser. However, it is available for programmatic access via the <a href="https://ga4gh.org/#/beacon">Global Alliance Beacon API</a>, a web service that accepts queries in the form (genome, chromosome, position, allele) and returns "true" or "false" depending on whether there is information about this allele in the database. For more details see our <a href="hgBeacon">Beacon Server</a>. </p> -<p>Subscribers of the HGMD database can also download the full database or use -the HGMD API to retrieve full details, please contact Qiagen support +<p>Subscribers of the HGMD database can also download the full database or use the HGMD API to retrieve full details, please contact Qiagen support for further information. Academic or non-profit users may be able to obtain a limited version of HGMD public from Qiagen.</p> <h2>Display Conventions and Configuration</h2> <p> Genomic locations of HGMD variants are labeled with the gene symbol and the accession of the mutation, separated by a colon. All other information is shown on the respective HGMD variation page, accessible via the "Link to HGMD" at the top of the details page. </p> +<p>HGMD variants are originally annotated on RefSeq transcripts. You can show +all and only those transcripts annotated by HGMD by activating the HGMD +subtrack of the track "NCBI RefSeq".</p> + <h2>Methods</h2> <p> The mappings displayed on this track were obtained from Qiagen and reformatted at UCSC as a <a href="../goldenPath/help/bigBed.html">bigBed</a> file. </p> <h2>Credits</h2> <p> Thanks to HGMD, Frank Schacherer and Rupert Yip from Qiagen for making these data available. </p> <h2>References</h2> <p> Stenson PD, Mort M, Ball EV, Shaw K, Phillips A, Cooper DN. <a href="https://dx.doi.org/10.1007/s00439-013-1358-4" target="_blank"> The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine</a>. <em>Hum Genet</em>. 2014 Jan;133(1):1-9. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24077912" target="_blank">24077912</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3898141/" target="_blank">PMC3898141</a> </p>