d1480f47eaefcb26436f4818ea85befb187f1958 gperez2 Mon Feb 24 09:17:11 2025 -0800 Announcing the release of the enGenome VarChat track, refs #35081 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0eb433811bf..93900cc6f20 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,75 @@ </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: less 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="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>