bbddaf74c88b5e590f0943b73dd5c0d40f42e42d lrnassar Fri Jul 24 15:22:34 2026 -0700 Update Long-read SVs announcement counts for cardSv/noyvertSv additions. refs #37888 Bump the container from 14 to 16 studies and roughly 2.3 to 2.6 million merged SV sites, and add NIH CARD (Americas) and Noyvert 888 (1000 Genomes) to the region summary table. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d0ee164fdec..c717f432ddb 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -215,43 +215,43 @@ improving the expansive track hubs for ENCODE4 and for iterating with us to bring them to the browser as native tracks. We also thank the <a href="https://www.encodeproject.org/" target="_blank">ENCODE Consortium</a>, the ENCODE production laboratories, and the ENCODE Data Coordination Center for generating and processing the underlying experiments, and Gerardo Perez, Brian Raney, Max Haeussler, and Lou Nassar for building and reviewing these tracks. </p> <a name="071626"></a> <h2>Jul. 16, 2026 Long-read Structural Variants tracks for human (hg38 and hs1)</h2> <p> We are excited to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&g=longReadVariants&position=default" target="_blank"><b>Long-read Structural Variants</b></a> container track on the human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&g=longReadVariants&position=default" target="_blank">GRCh38/hg38</a> and <a href="/cgi-bin/hgTracks?db=hs1&position=default" target="_blank">T2T-CHM13/hs1</a>. -The container track brings together structural variant (SV) callsets from 14 long-read +The container track brings together structural variant (SV) callsets from 16 long-read sequencing studies worldwide into a single place where you can compare large genomic rearrangements (deletions, insertions, duplications, inversions, and complex events) across populations, cohorts, and calling strategies. Long-read technologies span repetitive regions and resolve complex loci that are difficult to detect with short reads, giving more precise breakpoints and better sensitivity for large variants. </p> <p> At the center of the container track is an <a href="/cgi-bin/hgTrackUi?db=hg38&g=lrSvAll&position=default" target="_blank"><b>All long-read SVs merged</b></a> track that unifies every source callset on identical -position, type, and length into roughly 2.3 million distinct SV sites, each carrying +position, type, and length into roughly 2.6 million distinct SV sites, each carrying per-database allele counts so you can see at a glance how many studies support a given variant and at what frequency. This merged track is the best place to start: we recommend using it to survey structural variation across all studies at a locus, then turning to the individual dataset tracks for cohort-specific allele frequencies, genotypes, and annotations on the variants you want to follow up. </p> <div class="text-center"> <img src="../images/longReadSVsAnnouncementImage.png" alt="Long-read Structural Variants container track at the UGT2B17 locus on hg38. The merged track shows a common whole-gene deletion of about 117 kb, echoed by overlapping calls in the individual dataset tracks below. A mouseover reports a 79% allele frequency for the deletion in the Chinese Pangenome Consortium." width='80%'> <p class="gbsCaption"><em>The Long-read Structural Variants container track at @@ -272,32 +272,32 @@ let you narrow by SV type, source study, variant length, allele frequency, or the number of supporting studies, in any combination. </p> <p> The container track pulls together cohorts from across the world. A high-level summary is shown below; a complete table with per-study sample counts, cohorts, sequencing coverage, and SV counts is on the <a href="/cgi-bin/hgTrackUi?db=hg38&g=longReadVariants&position=default" target="_blank">track description page</a>. </p> <table class="stdTbl"> <tr><th>Region / theme</th><th>Contributing studies</th></tr> <tr><td>East Asia</td><td>Han Chinese 945, ToMMo Japan, Chinese Pangenome Consortium</td></tr> - <tr><td>1000 Genomes (global)</td><td>1KG ONT 100 (Gustafson), 1KG ONT Vienna (1,019)</td></tr> - <tr><td>Americas</td><td>All of Us, GA4K (pediatric rare disease), SVatalog (cystic fibrosis)</td></tr> + <tr><td>1000 Genomes (global)</td><td>1KG ONT 100 (Gustafson), 1KG ONT Vienna (1,019), Noyvert 888</td></tr> + <tr><td>Americas</td><td>All of Us, GA4K (pediatric rare disease), SVatalog (cystic fibrosis), NIH CARD (brain)</td></tr> <tr><td>Europe</td><td>deCODE (Iceland)</td></tr> <tr><td>Middle East</td><td>Arab Pangenome Reference</td></tr> <tr><td>Global reference & pangenome callsets</td><td>CoLoRSdb, HPRC v2.1, HGSVC2, HGSVC3</td></tr> </table> <p> Six of these datasets (CoLoRSdb, 1KG ONT Vienna, HGSVC3, HPRC v2.1, Arab Pangenome Reference, and the Chinese Pangenome Consortium) are also released on the <a href="/cgi-bin/hgTracks?db=hs1&position=default" target="_blank">T2T-CHM13/hs1</a> assembly in native coordinates. </p> <p> License restrictions on some sources limit redistribution; see the track description page for per-study details.