94d4368e9b539a8c369e16a8a950e14799f03cab jnavarr5 Tue Aug 11 16:13:45 2026 -0700 Announcing the ClinPred pathogenicity score track for hg19 and hg38, refs #37510 Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d420173c47f..e2a0d82b51b 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,89 @@ <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> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> +<a name="081126"></a> +<h2>Aug. 11, 2026 Deleteriousness Predictions: ClinPred for hg19 and hg38</h2> +<p> +We are pleased to announce the release of the ClinPred pathogenicity score track for +<a href="/cgi-bin/hgTrackUi?db=hg19&g=clinPred" target="_blank">hg19</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=clinPred" target="_blank">hg38</a>. +ClinPred is a machine-learning predictor of pathogenicity for nonsynonymous (missense) +single-nucleotide variants, combining existing pathogenicity scores with population allele +frequency from gnomAD. It was trained on confidently annotated disease-causing and benign +variants from ClinVar. Pre-computed scores are provided for all possible human missense +variants in the exome. +</p> + +<p> +Scores range from 0 to 1, with higher values indicating a greater predicted likelihood +that a variant is disease-relevant. The authors recommend a score of ≥ 0.5 as evidence +of pathogenicity. As with any pathogenicity prediction score, ClinPred is intended as +supporting evidence rather than a stand-alone classifier. +</p> + +<p> +There are four subtracks in this collection, one for each possible alternate nucleotide +(A, C, G, T). At every exome position covered by ClinPred, three of the four subtracks +show a score (one per non-reference base), and the fourth, corresponding to the reference +base, is set to 0. Synonymous alternates are also set to 0, since ClinPred only scores +missense variants. Positions with no exome coverage are shown as gaps. +</p> + +<div class="text-center" style="margin-top: 1.5em;"> +<a href="https://genome.ucsc.edu/s/bkitiyakara/share_JMwPz7ty" target="_blank"> +<img alt="Genome Browser screenshot of the ClinPred track" src="/images/newsArchImages/ClinPred.png" +width='55%'></a> +<p class="gbsCaption"><em>ClinPred pathogenicity scores for all possible single-nucleotide +substitutions (A, C, G, and T) at a genomic locus (chr7, GRCh38/hg38). The four ClinPred +subtracks display predicted pathogenicity scores for each possible alternate allele, where +higher scores indicate a greater likelihood that the variant is disease-causing.</em></p> +</div> + +<p> +Items in this track are colored according to score: +</p> + +<ul> + <li><span style="color:red;"><b>Red</b></span> – Likely pathogenic (≥ 0.5)</li> + <li><span style="color:blue;"><b>Blue</b></span> – Likely benign (< 0.5)</li> +</ul> + +<p> +<b>Note:</b> Zoom in until every base is visible at the top of the display; otherwise, +multiple nucleotides will fall under a single pixel, and no score will be shown on the +mouseover tooltip. +</p> + +<p> +We would like to thank the ClinPred authors for making the pre-computed scores publicly +available. This track was developed by Lou Nassar and Max Haeussler with QA by Eliza Alde, +Jairo Navarro, and Barali Kitiyakara. +</p> + <a name="072226"></a> <h2>Jul. 22, 2026 ENCODE4 cCREs and ENCODE4 Regulation tracks released for human (hg38) and mouse (mm10)</h2> <p> We are excited to announce our major release of the ENCODE4 data collection on the UCSC Genome Browser for both the human (hg38/GRCh38) and mouse (mm10/GRCm38) assemblies. This release consists of two major components: the <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=cCREs&position=default" target="_blank"> <b>ENCODE Registry of cCREs</b></a> (candidate Cis-Regulatory Elements) container, and the new <a href="/cgi-bin/hgTrackUi?db=hg38&c=chr7&g=wgEncodeReg4&position=default" target="_blank"> <b>ENCODE4 Regulation</b></a> container, both described in <a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank"> Moore <em>et al</em>., <em>Nature</em> 2026</a>. </p>