808c426eb279a17a5539731811f1deda6e783e1e lrnassar Wed Sep 9 17:20:31 2026 -0700 Announcing the AlphaGenome Variant Impact (AVI) score track for hg38. refs #38261 Adds the Sept. 10 news archive entry with a figure of the AVI scores across the TERT locus, and adds the item to the front page news list, dropping the Jul. 22 entry to keep the list at six. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index e753af7ebec..8fe053fbf81 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,84 @@ <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="091026"></a> +<h2>Sep. 10, 2026 New AlphaGenome Variant Impact (AVI) score track for hg38</h2> +<p> +We are pleased to announce a new track showing the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=alphaGenome&position=default" target="_blank">AlphaGenome Variant Impact +(AVI) score</a> from Google DeepMind's AlphaGenome Atlas, on the human GRCh38/hg38 assembly. +The score combines AlphaGenome's predictions of how a variant affects gene regulation, covering +expression, splicing, chromatin accessibility and transcription factor binding across hundreds +of cell types, with AlphaMissense predictions for protein-altering changes. The result is a +single number that ranks how damaging a substitution is likely to be. Unlike most prediction +scores, it covers non-coding variants as well as coding ones, across the whole genome. +</p> + +<div class="text-center" style="margin-top: 1.5em;"> +<a href="https://genome.ucsc.edu/s/Lou/AlphaGenome" target="_blank"> +<img alt="AlphaGenome AVI scores across the TERT locus, showing four per-allele subtracks with +elevated scores over the gene's 5' end and its highlighted promoter" +src="/images/newsArchImages/alphaGenome.png" width='65%'></a> +<p class="gbsCaption"><em>AVI scores at the TERT locus on hg38, one subtrack per alternate +allele. Scores stay high across the highlighted promoter, shown in red as EH38E3622530, and fall +to background either side. The two promoter mutations most often seen in cancer sit inside it, +beyond the end of every TERT transcript.</em></p> +</div> + +<p> +The track shows the precomputed score for every possible single-base substitution, about 8.8 +billion in all, with one subtrack per alternate allele. Scores are PHRED-scaled, so 10 marks the +top 10 percent of substitutions genome wide, 20 the top 1 percent and 30 the top 0.1 percent. +Hover the mouse over any position to see the score, and zoom in to see individual bases. +</p> + +<p> +The AlphaGenome Variant Impact (AVI) score track can be found in the "Phenotype and Literature" +group, inside the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=predictionScoresSuper&position=default" target="_blank">Deleteriousness +Predictions</a> track collection, so it can be compared with other prediction scores such as +<a href="/cgi-bin/hgTrackUi?db=hg38&g=caddSuper1_7&position=default" target="_blank">CADD</a>, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=revel&position=default" target="_blank">REVEL</a>, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=eve&position=default" target="_blank">EVE</a>, +<a href="/cgi-bin/hgTrackUi?db=hg38&g=primateAi&position=default" target="_blank">PrimateAI</a> +and <a href="/cgi-bin/hgTrackUi?db=hg38&g=promoterAi&position=default" +target="_blank">PromoterAI</a>. AlphaGenome has not been validated +for, and is not approved for, any clinical use. +</p> + +<p> +We thank Google DeepMind for making the data available. See the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=alphaGenome&position=default" target="_blank">track description page</a> for +details on the data, methods and licensing. The AVI data cannot be redistributed by UCSC, so it +is not available for download or through the Table Browser, and for now we cannot show the +splicing and feature importance scores. We would like to thank Max Haeussler and Lou Nassar for +the development and release of this track. +</p> + <a name="090426"></a> <h2>Sep. 4, 2026 ENCODE Expression: mouse developmental time course bulk RNA-seq for mm10 and mm39</h2> <p> We are pleased to announce a new <b>ENCODE Expression</b> track container for the mouse <a href="/cgi-bin/hgTrackUi?db=mm10&g=mouseDevTimecourse&position=default" target="_blank">mm10/GRCm38</a> and <a href="/cgi-bin/hgTrackUi?db=mm39&g=mouseDevTimecourse&position=default" target="_blank">mm39/GRCm39</a> assemblies. The container shows bulk RNA-seq gene expression across mouse embryonic development, produced by the <a href="http://woldlab.caltech.edu/" target="_blank">Wold Lab</a> at Caltech as part of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE</a> project and described in <a href="https://doi.org/10.1038/s41586-020-2536-x" target="_blank">He <em>et al</em>., <em>Nature</em> 2020</a>. These tracks are turned on by default on both assemblies, so you will see them the next time you open the mouse browser. </p>