157a2aba6a9a20bd1f995daf6b799f552a20c77c jnavarr5 Fri Sep 19 12:56:24 2025 -0700 Announcing the DDG2P track for hg38 and hg19, refs #35054 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 14335735bad..d551c70ae13 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,79 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be found <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> +<a name="091925"></a> +<h2>Sep. 19, 2025 Developmental Disorders Gene2Phenotype (DDG2P) for hg38 and hg19</h2> +<p> +We are pleased to announce the release of the <a href="https://www.deciphergenomics.org/ddd/ddgenes" +target="_blank">Developmental Disorders Genotype-to-Phenotype (DDG2P)</a> track for +<a href="/cgi-bin/hgTrackUi?db=hg19&g=ddg2p&position=default" target="_blank">hg19</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=ddg2p&position=default" target="_blank">hg38</a>. The DDG2P +track displays genes associated with severe developmental disorders. The track can be used to +filter genomic sequencing data of people with genetic disorders to identify likely causative +variants and accelerate diagnosis. +</p> +<p> +Items in this track are colored according to the likelihood that the gene-disease +association is true:</p> +<ul> + <li> <font style="color: green;"><b>Green</b></font> - Definitive</li> + <li> <font style="color: blue;"><b>Blue</b></font> - Strong</li> + <li> <font style="color: orange;"><b>Orange</b></font> - Moderate</li> + <li> <font style="color: red;"><b>Red</b></font> - Limited</li> + <li> <font style="color: gray;"><b>Gray</b></font> - Refuted</li> +</ul> + +<p>Each <b>mouseover</b> tooltip provides the following information:</p> +<ul> + <li><strong>G2P ID</strong>: Unique identifier assigned by the Gene2Phenotype (G2P) database.</li> + <li><strong>Number of PubMed IDs</strong>: Count of publications associated with the variant.</li> + <li><strong>Molecular Mechanism</strong>: Description of the molecular processes and interactions + causing pathogenic effects.</li> + <li><strong>Allelic Requirements</strong>: Number of alleles required at a locus to produce a + pathogenic phenotype (e.g., monoallelic, biallelic).</li> + <li><strong>Variant Consequence</strong>: Predicted effect each allele of a variant has on a + transcript.</li> + <li><strong>Disease Name</strong>: Name of the disease associated with the variant.</li> + <li><strong>Date of Last Review</strong>: Most recent date the entry was manually reviewed.</li> +</ul> + +<div class="text-center"> + <a href="https://genome.ucsc.edu/s/jnavarr5/ddg2p_announcement"> + <img src="../images/newsArchImages/ddg2p.png" + alt="DDG2P track with the mouseover tooltip on the BRCA1 gene." width='75%'> + <p class="gbsCaption"> + <em>Genome Browser screenshot of the DDG2P track with the mouseover tooltip on the BRCA1 gene.</em> + </p></a> +</div> +<p> +We would like to thank the <a href="https://www.ebi.ac.uk/gene2phenotype/about/project" +target="_blank">G2P project</a> for making this data publicly available. We would also like to thank +Jaidan Jenkins-Kiefer and Jairo Navarro Gonzalez for the creation and release of the Genome Browser +tracks.</p> <a name="082125"></a> <h2>Aug. 21, 2025 MaveDB Experiment Heatmaps and Alignment track for hg38</h2> <p> We are excited to announce the release of the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=mavedb_maps">MaveDB Experiment Heatmaps and Alignment</a> track for hg38. This release provides heatmaps of <b>m</b>ultiplexed <b>a</b>ssays of <b>v</b>ariant <b>e</b>ffects (MAVE) from <a target="_blank" href="https://mavedb.org/">MaveDB</a>. Each heatmap presents the results of an experiment where many small substitutions were tested within a gene to examine their functional consequences. Accompanying tracks display alignments of each experiment sequence to the genome. </p> <p> Please note that only a subset of MaveDB experiments could be displayed as heatmaps; the sequence alignments in this track only cover those experiments.</p>