36cd91779b5cd2866c500c32a5892cfc959bfe06 lrnassar Fri May 29 10:30:15 2026 -0700 MPRA superTrack: news announcement, pennantIcon, attribution fix. refs #37359 Ship the user-visible release pieces for the Jun. 2, 2026 announcement of the MPRA superTrack (MPRA Base + MPRAVarDB) on hg38. News announcement: - Added a Jun. 2, 2026 entry to newsarch.html (anchor #060226) describing both subtracks, the data sources (MPRA Base / MPRAVarDB), and an Element-level vs Variant-level summary. Screenshot at the TERT promoter shows MPRA Base reporter activity for melanoma risk variants alongside filtered MPRAVarDB high-confidence variants from Kircher saturation mutagenesis. - Added the matching entry to indexNews.html ("New MPRA Base and MPRAVarDB tracks on hg38", 42 chars, under the ~50-char target); dropped the now-7th entry "Updated superTrack configuration page" to keep the 6-item limit. - Added the screenshot mpraNewsImage.png (3198x1015) referenced by the news div at 90% width. trackDb stanza: - Added "New" pennantIcon to the parent mpra superTrack pointing to the news anchor, matching the recount3 / promoterAi pattern. Attribution fix: - The parent mpra.html Credits section still attributed MPRAVarDB to "Tao Wang and colleagues". That attribution doesn't match the actual paper authors (Jin W, Xia Y, Nizomov J, Liu Y, Li Z, Lu Q, Chen L per PMID 39325859, DOI 10.1093/bioinformatics/btae578); replaced with "Weijia Jin and colleagues" to match mpraVarDb.html. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0dd74d8cedd..0a44fd8f6d3 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,126 @@ <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="060226"></a> +<h2>Jun. 2, 2026 New Massively Parallel Reporter Assay (MPRA) tracks on hg38</h2> +<p> +We are pleased to announce a new +<a href="/cgi-bin/hgTrackUi?db=hg38&g=mpra" target="_blank"><b>MPRAs</b></a> +container track on the human genome assembly (GRCh38/hg38), gathering +results from massively parallel reporter assays (MPRAs). MPRAs are +high-throughput methods that measure the regulatory activity of +thousands of candidate DNA sequences in parallel by linking each +fragment to a barcoded reporter gene and quantifying the resulting +reporter RNA. +</p> + +<p> +The container brings together two complementary data +sources: <b>tested enhancer elements</b> and <b>allele-resolved variant +effects</b>. MPRA Base captures element-level activity, identifying +which candidate DNA fragments function as regulatory elements in a +given cell line. MPRAVarDB captures variant-level allelic effects, +quantifying how individual SNPs change reporter activity between +reference and alternate alleles, useful for +fine-mapping GWAS signals and prioritizing causal regulatory variants. +</p> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=mprabase" target="_blank"><b>MPRA +Base</b></a> subtrack displays 40,938 experimentally tested cis-regulatory +elements curated from the +<a href="http://mprabase.ucsf.edu/app/mprabase" target="_blank">MPRA Base</a> +database (<a href="https://pubmed.ncbi.nlm.nih.gov/38045264/" target="_blank">Zhao +et al., 2023</a>), drawn from 10 MPRA, STARR-seq, and related reporter +experiments across six cell lines (HepG2, HUES64, mESC, NPC, HEK293FT, +and UACC903). Each item is colored by within-experiment percentile rank: +<span style="color:red">red</span> for the top quartile, +<span style="color:orange">orange</span> for the 50–74th percentile, and +<span style="color:blue">blue</span> for the bottom half. The track also +exposes the assayed oligo sequence and a variant-allele-type field +(<tt>reference</tt> / <tt>alternate</tt> / <tt>NA</tt>) so users can +distinguish standard enhancer-element tests from allelic comparisons. +</p> + +<p> +The <a href="/cgi-bin/hgTrackUi?db=hg38&g=mpraVarDb" target="_blank"><b>MPRAVarDB</b></a> +subtrack displays 239,028 variants tested for allelic regulatory effects +across 18 MPRA studies, more than 30 cell lines, and more than 30 human +diseases or traits (curated by +<a href="https://mpravardb.rc.ufl.edu/" target="_blank">MPRAVarDB</a>; +<a href="https://pubmed.ncbi.nlm.nih.gov/39325859/" target="_blank">Jin +et al., 2024</a>). Variants come from GWAS fine-mapping for +neurodegenerative, autoimmune, oncologic, and other disease loci, +eQTL fine-mapping in lymphoblastoid cells, saturation mutagenesis of +20 disease-associated regulatory elements, and several focused screens. +Items are colored by statistical significance: +<span style="color:#C80000;">dark red</span> for variants with FDR < 0.05, +<span style="color:#FFA500;">orange</span> for nominal p < 0.05 but +FDR ≥ 0.05, and <span style="color:#BEBEBE;">grey</span> for the rest. +</p> + +<div class="text-center"> + <img src="../images/mpraNewsImage.png" + alt="Genome Browser screenshot at the TERT promoter on hg38 showing MPRA Base + reporter elements for melanoma risk variants tested in HEK293FT and UACC903 + cells, and MPRAVarDB high-confidence variants from saturation mutagenesis of + the TERT promoter" + width='90%'> + <p class="gbsCaption"> + <em>MPRA Base elements and MPRAVarDB variants at the TERT promoter + (chr5, GRCh38/hg38). MPRA Base (top) shows reporter activity for + melanoma risk variants tested in HEK293FT and UACC903 cells + (Choi et al., 2020). MPRAVarDB (bottom) highlights + high-confidence allelic effects from saturation mutagenesis of the + TERT promoter (Kircher et al., 2019).</em> + </p> +</div> + +<p> +See the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=mprabase" target="_blank">MPRA Base</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=mpraVarDb" target="_blank">MPRAVarDB</a> +track description pages for the full list of contributing studies, +per-study scoring methodology, and notes on how to interpret raw scores +and log2 fold change across studies that use different statistical +frameworks. +</p> + +<p> +We would like to thank Varda Singhal, Jianyu Zhao, and the +<a href="https://pharm.ucsf.edu/ahituv" target="_blank">Ahituv Lab</a> +at UCSF for creating and curating the MPRA Base database, and Weijia Jin +and the +<a href="https://mpravardb.rc.ufl.edu/" target="_blank">MPRAVarDB team</a> +at the University of Florida for the variant-effect resource. 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="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.