c611e789c10f1fceb3d7b0b7935598eb0d7dddce mspeir Tue Jul 15 15:54:45 2025 -0700 tweaking hrefs on indexNews to point to unique spots on newsarch page diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index ed4da9f7502..6c52af82c06 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,59 +52,59 @@ <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> +<a name="071525b"></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=mcap" 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> +<a name="071525a"></a> <h2>July 15, 2025 ENCODE4 Long-read RNA-seq Transcripts</h2> <p> We are pleased to announce the release of the ENCODE4 long-read RNA-seq transcripts track for <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=encode4LongRnaTranscripts" target="_blank">hg38</a> and <a href="/cgi-bin/hgTrackUi?db=mm10&position=default&g=encode4LongRnaTranscripts" target="_blank">mm10</a>. This track annotates trancripts using numerical triplets representing the identity of the start site, exon junction chain, and transcript end site of each transcript. This is presented alongside sample enrichment information to show how promoter selection, splice pattern, and 3’ processing are deployed across human tissues. </p> <div class="text-center">