9fc19d1c120f23370047d73268806e2fa019811a Merge parents 73365345ad5 b88a0d542ed mspeir Tue Feb 25 08:10:50 2025 -0800 resolving merge conflict in indexNews and newsarch files diff --cc src/hg/htdocs/goldenPath/newsarch.html index 40da810e818,e064855ac81..bfc5a0eec5f --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@@ -51,58 -51,75 +51,103 @@@ </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="022425"></a> + <h2>Feb. 24, 2025 enGenome VarChat track for human (hg38 and hg19)</h2> + <p> + We are happy to announce the release of the enGenome VarChat track for the + <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=varChat&position=default" >hg38/GRCh38</a> + and <a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg19&g=varChat&position=default">hg19/GRCh37</a> human assemblies, + available in the Variants in Papers superTrack. + <a target="_blank" href="https://varchat.engenome.com/">VarChat</a> is an open platform that + leverages the power of generative artificial intelligence to support the genomic variant + interpretation process by searching the available scientific literature for each variant and + condensing it into a brief yet informative text. + </p> + + <p> + The track shows how many papers the variant was observed in, its gene, its HGVS nomenclature, and + dbSNP rsID. Variants are color-coded based on the level of literature support, as shown in the + table below:</p> + <table> + <thead> + <tr> + <th style="border-bottom: 2px solid #6678B1;">Color</th> + <th style="border-bottom: 2px solid #6678B1;">Level of literature support</th> + </tr> + </thead> + <tbody> + <tr> + <td style="background-color: #012840; width: 50px;"></td> + <td align="left">High: at least 25 papers mention the variant</td> + </tr> + <tr> + <td style="background-color: #03738C; width: 50px;"></td> + <td align="left">Medium: between 10 and 24 papers mention the variant</td> + </tr> + <tr> + <td style="background-color: #96D2D9; width: 50px;"></td> + <td align="left">Low: fewer than 10 papers mention the variant</td> + </tr> + </tbody> + </table> + <p> + We would like to thank VarChat for providing the data to UCSC. We would also like to thank Lou + Nassar, Max Haeussler, and Gerardo Perez for their efforts on this release.</p> + +<a name="022125"></a> +<h2>Feb. 21, 2025 New AlphaMissense scores track for hg38 and hg19</h2> +<p> +We are pleased to announce the addition of AlphaMissense tracks to the hg38 and +hg19 reference genomes. AlphaMissense scores predict the pathogenicity of +missense variants for all possible single amino acid substitutions in the human +proteome. +</p> + +<p> +To access these tracks on the Genome Browser, please visit their description +pages below and change the tracks' visibility: +</p> +<ul> + <li><a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg38&g=alphaMissense&position=default">AlphaMissense + on hg38/GRCh38</a></li> + <li><a target="_blank" + href="/cgi-bin/hgTrackUi?db=hg19&g=alphaMissense&position=default">AlphaMissense + on hg19/GRCh37</a></li> +</ul> +<p> +To learn more about the AlphaMissense dataset, please see the +publication by <a +href="https://www.science.org/doi/full/10.1126/science.adg7492" +target="_blank">Cheng et al. Science. 2023.</a> +</p> + <a name="021425"></a> <h2>Feb. 14, 2025 CIViC track for hg19 and hg38 is now available</h2> <p> We are excited to announce the release of the CIViC track for <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg19&g=civic&position=default">hg19/GRCh37</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=civic&position=default" target="_blank">hg38/GRCh38</a>. The <a target="_blank" href="https://civicdb.org/welcome"> Clinical Interpretation of Variants in Cancer</a> (CIViC) is an online database of clinically relevant variant interpretations from expert- and crowd-sourced peer-reviewed literature, clinical trials, and some conference abstracts. The details page for a feature will list diseases and therapies that have been associated with a genomic variant. Visiting the CIViC page for a variant will allow browsing the Molecular Profiles associated with that variant, and in turn each Molecular Profile shows the Clinical Evidence and Assertions for various diseases and therapies. </p>