226898981d9edeea42f4c8bfb7eef501cbf770ac lrnassar Tue Jul 15 14:55:19 2025 -0700 Announcing two new pathogenicity prediction tracks, refs #35806 #35922 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 34b185225c3..4ce96db0343 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,58 @@ <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="071525"></a> +<h2>July 15, 2025 New pathogenicity prediction scores for human: MutScore and M-CAP</h2> +<p> +We have two new pathogenicity prediction score tracks available in our +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=predictionScoresSuper" +target="_blank">Deleteriousness Predictions</a> super track.</p> +<ul> +<li><a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=mutScore" +target="_blank">MutScore</a> (hg19/hg38) - MutScore is a pathogenicity predictor that integrates unsupervised +features of single DNA variants with information derived from such clusters. The predictive model +for MutScore was trained with a random forest approach on medically-relevant mutations and +subsequently tested against various genomic databases for both hereditary conditions and +cancer (ClinVar, HGMD, and DoCM) to achieve high performance.</li> +<li><a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=mutScore" +target="_blank">M-CAP</a> (hg19) - M-CAP is a pathogenicity classifier for +rare missense variants tuned to the high sensitivity required in the clinic. By combining previous +pathogenicity scores (including SIFT, Polyphen-2 and CADD) with novel features and a powerful +model, it yields an effective classifier, reducing a typical exome/genome rare (<1%) missense +variant (VUS) list from 300 to 120, while never mistaking 95% of known pathogenic variants as benign.</li></ul> +<p> +See the track description page +for more information and interpretation guidelines.</p> +<p> +We would like to thank the authors of <a href="https://mutscore.iob.ch/" +target="_blank">MutScore</a> and <a href="http://bejerano.stanford.edu/mcap/" +target="_blank">M-CAP</a> for creating and providing these data. We would also +like to thank Max Haeussler and Lou Nassar for the development and release of these tracks.</p> + <a name="070925"></a> <h2>July 09, 2025 Unusually Conserved Regions track for hg38</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=unusualcons" target="_blank">Unusually Conserved Regions</a> track for GRCh38/hg38. The supertrack consists of 12 tracks that show regions of unusual conservation in humans relative to other organisms. The full list of tracks, along with item count and coverage is summarized in the following table: </p> <p> <table class="stdTbl"> <tbody><tr> <th>Track</th> <th>Count</th> <th>Coverage in bp</th> </tr>