8caadf44150cd873343bb6af062f064cf039ce33 jnavarr5 Fri Apr 10 16:04:39 2026 -0700 Announing the STR superTrack and the gnomAD STR track, refs #36652 and #35420 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 84dc1b69b22..0b9c316c753 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,105 @@ <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="041026"></a> +<h2>Apr. 10, 2026 New Short Tandem Repeat (STR) tracks on hg38</h2> +<p> +We are pleased to announce several new Short Tandem Repeat (STR) tracks on the +human genome assembly (GRCh38/hg38). +</p> +<p> +A new <a href="/cgi-bin/hgTrackUi?db=hg38&g=strVar" target="_blank"><b>Tandem Repeat +Variation</b></a> track collection brings together population-level tandem repeat variation +data from multiple sources: +</p> +<ul> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=webstr" target="_blank"><b>WebSTR</b></a> – + 1,710,833 STR loci from the + <a href="https://github.com/gymrek-lab/EnsembleTR" target="_blank">EnsembleTR</a> panel with + allele frequency distributions for five continental populations from the + <a href="https://www.internationalgenome.org/" target="_blank">1000 Genomes Project</a> + (3,550 individuals). The EnsembleTR panel represents consensus calls from four STR + genotyping methods (HipSTR, GangSTR, ExpansionHunter, and AdVNTR). + </li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=strchive" target="_blank"><b>STRchive</b></a> – + 75 disease-associated tandem repeat expansion loci curated from published literature by the + <a href="https://strchive.org" target="_blank">STRchive</a> project. Each locus includes + the pathogenic repeat motif, minimum pathogenic repeat count, mode of inheritance, and + associated disease. Items are colored by inheritance mode. + </li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=trexplorer" target="_blank"><b>TRExplorer V2</b></a> + – 5,599,658 tandem repeat loci (STRs and VNTRs) from the + <a href="https://trexplorer.broadinstitute.org" target="_blank">TRExplorer</a> catalog at + the Broad Institute, compiled from 17 sources including perfect repeats in the reference, + polymorphic TRs from T2T assemblies, and curated disease-associated loci. Includes + population allele frequency histograms from TenK10K and HPRC256 cohorts. + </li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=tommoStr" target="_blank"><b>ToMMo 61K STR</b></a> + – 174,300 STR loci with allele count distributions from 61,000 Japanese individuals + from the <a href="https://jmorp.megabank.tohoku.ac.jp" target="_blank">Tohoku Medical + Megabank Organization (ToMMo)</a>, genotyped with Expansion Hunter. + </li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&g=viennaVntr" target="_blank"><b>1KG Vienna ONT + VNTR</b></a> – 361,362 VNTR loci with allele statistics from 1,019 samples of the + <a href="https://github.com/marschall-lab/project-ont-1kg" target="_blank">1000 Genomes + ONT Vienna project</a>, genotyped with VAMOS from Oxford Nanopore long-read sequencing. + Unlike the other tracks which use short-read data, this track can span longer repeat regions. + </li> +</ul> +<p> +Additionally, a new +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadStr" target="_blank"><b>gnomAD STR</b></a> +track has been added under the gnomAD Variants collection. This track displays genotype data +for 87 disease-associated STR loci from +<a href="https://gnomad.broadinstitute.org/" target="_blank">gnomAD</a> v3.1.3, including +loci associated with Huntington disease, fragile X syndrome, Friedreich ataxia, and various +spinocerebellar ataxias. The data were generated using +<a href="https://github.com/Illumina/ExpansionHunter" target="_blank">ExpansionHunter v5</a> +on 18,511 whole-genome sequenced samples across 10 populations. Each locus shows the +distribution of repeat allele sizes, providing a reference for normal and expanded allele +ranges. +</p> +<p> +We would like to thank Melissa Gymrek (UC San Diego) and the +<a href="https://webstr.ucsd.edu" target="_blank">WebSTR</a> team for providing the +WebSTR data, Harriet Dashnow (University of Colorado) and the +<a href="https://strchive.org" target="_blank">STRchive</a> team for their curated +disease-associated loci, Ben Weisburd, Egor Dolzhenko, and the +<a href="https://trexplorer.broadinstitute.org" target="_blank">TRExplorer</a> team at the +Broad Institute for their tandem repeat catalog, the +<a href="https://jmorp.megabank.tohoku.ac.jp" target="_blank">Tohoku Medical Megabank +Organization</a> for the ToMMo STR data, the 1000 Genomes ONT Vienna consortium and the +Marschall Lab at Heinrich Heine University Düsseldorf for the VNTR data, and the +<a href="https://gnomad.broadinstitute.org/about" target="_blank">gnomAD production +team</a> for making the STR genotype data available. We would also like to thank +Max Haeussler and Jairo Navarro Gonzalez for the creation and release of these +tracks. +</p> + <a name="040326"></a> <h2>Apr. 3, 2026 New heatmap display mode for bigBed tracks</h2> <p> We are pleased to announce a new <a href="/goldenPath/help/heatmap.html" target="_blank"><b>heatmap</b> display mode</a> for the Genome Browser.</p> <p> Heatmaps replace the standard block-and-line gene display with a color-coded grid: each block position along the item (e.g., an exon) becomes a column, each row represents a sample or condition, and cells are colored by score using a customizable gradient. This makes it easy to spot patterns in multi-sample quantitative data—such as variant effects, gene expression, or methylation levels—directly in their genomic context. </p> <div class="text-center">