46f88622e6ec2bbc09f403eeb9ec6122eb05931f lrnassar Thu Apr 30 15:41:01 2026 -0700 Releasing PrimateAI-3D and PromoterAI tracks to beta and RR. refs #37274 refs #37278 Drops the alpha tag from both tracks under predictionScoresSuper. Adds 'New' pennantIcons on primateAi and promoterAi pointing at the May 1, 2026 newsarch anchor, and an 'Updated' pennantIcon on the predictionScoresSuper supertrack. Adds a combined release post to newsarch.html with an HBB hg38 screenshot illustrating PrimateAI-3D coding-region calls alongside PromoterAI per-allele scores in the proximal promoter, and updates the indexNews.html sidebar. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index ad9d7a8b43c..590638ad2c8 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,121 @@ <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="050126"></a> +<h2>May 1, 2026 New PrimateAI-3D and PromoterAI variant impact tracks from Illumina</h2> +<p> +We are pleased to announce the release of two new variant-impact prediction tracks +from <a href="https://www.illumina.com/" target="_blank">Illumina</a>: +<a href="/cgi-bin/hgTrackUi?db=hg38&g=primateAi&position=default" target="_blank"><b>PrimateAI-3D</b></a>, +which scores every possible coding missense variant on the human GRCh38/hg38 and +GRCh37/hg19 assemblies, and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=promoterAi&position=default" target="_blank"><b>PromoterAI</b></a>, +which scores every possible non-coding single-nucleotide substitution in proximal +promoter regions on GRCh38/hg38. Together, these deep-learning predictors extend +pathogenicity prediction across both protein-coding and regulatory sequence. +Both tracks are grouped under the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=predictionScoresSuper&position=default" target="_blank">Deleteriousness +Predictions</a> container in the Phenotype and Disease Associations track group. +</p> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=primateAi&position=default" target="_blank">PrimateAI-3D</a> +track displays approximately 70.7 million scored missense variants per assembly, +covering every possible single-base coding change across all protein-coding genes. +PrimateAI-3D is a deep-learning model that learns variant pathogenicity from common +variation observed across 233 non-human primate species and large human population +databases. Each variant is colored +<span style="color:red">red (pathogenic)</span> or +<span style="color:blue">blue (benign)</span> based on Illumina's prediction +call. Items are labeled by default with the nucleotide change (e.g. +<code>C>T</code>); the corresponding amino acid change is shown on hover and +can be toggled as the on-feature label from the Track Settings. +</p> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=promoterAi&position=default" target="_blank">PromoterAI</a> +track provides pre-computed scores for every possible single-nucleotide substitution +within 500 bp of annotated transcription start sites, covering approximately +39.5 million genomic positions. Scores range from −1 to +1, where +<b>negative</b> values indicate predicted <b>under-expression</b> and <b>positive</b> +values indicate predicted <b>over-expression</b> of the associated transcript; the +magnitude reflects the predicted size of the expression change. The container track +includes: +</p> +<ul> + <li>Four <b>per-base score</b> subtracks – one bigWig for each alternate + allele (<b>A</b>, <b>C</b>, <b>G</b>, <b>T</b>). Bars are colored + <span style="color:red">red</span> for positive scores and + <span style="color:blue">blue</span> for negative scores. + </li> + <li>A <b>PromoterAI Overlaps</b> bigBed subtrack summarizing positions where + multiple transcripts overlap. Each item lists the contributing transcripts, + their per-transcript scores, and their strand orientation. About 90% of overlap + items lie at bidirectional promoters where transcripts on opposite strands + share regulatory sequence. + </li> +</ul> + +<div class="text-center"> + <img src="../images/illuminaPrimatePromoterNewsImage.png" + alt="Genome Browser screenshot at the HBB locus on hg38 showing PrimateAI-3D + pathogenicity calls across the coding region and PromoterAI per-allele scores + in the 5' UTR and proximal promoter" width='80%'> + <p class="gbsCaption"> + <em>PrimateAI-3D and PromoterAI at the start of <i>HBB</i> on hg38 + (chr11:5,226,883-5,227,212). PrimateAI-3D scores every coding missense variant + as red (pathogenic) or blue (benign), while the four PromoterAI per-allele + bigWig subtracks score every possible non-coding substitution in the 5′ + UTR and proximal promoter just upstream of the <i>HBB</i> start codon.</em> + </p> +</div> + +<p> +See the track description pages for Illumina's recommended interpretation +thresholds. +</p> + +<p> +Both tracks are distributed by Illumina under a license agreement and are not +available through the Table Browser, Data Integrator, REST API, or public +download. The full methods are described in +<a href="https://www.ncbi.nlm.nih.gov/pubmed/37262156" target="_blank">Gao +et al. 2023</a> (PrimateAI-3D, <i>Science</i>) and +<a href="https://www.ncbi.nlm.nih.gov/pubmed/40440429" target="_blank">Jaganathan +et al. 2025</a> (PromoterAI, <i>Science</i>). +</p> + +<p> +We would like to thank Hong Gao, Kishore Jaganathan, and the Illumina PrimateAI-3D +and PromoterAI teams for making these predictions available to the research +community. We also would like to thank Max Haeussler and Lou Nassar for the +creation and release of the UCSC Genome Browser tracks. +</p> + <a name="042226"></a> <h2>Apr. 22, 2026 New NMD Escape tracks on hg38</h2> <p> We are pleased to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&g=nmd" target="_blank"><b>NMD Escape</b></a> track on the human genome assembly (GRCh38/hg38). This track collection displays regions where premature termination codons (PTCs) are predicted to escape nonsense-mediated mRNA decay (NMD), a cellular quality control mechanism that normally degrades transcripts with premature stop codons. Identifying NMD escape regions is important for interpreting the clinical significance of truncating variants under the ACMG/AMP PVS1 criterion. </p> <p> The container track includes: </p>