aaead1eeb6e454442e1a6c6dcb6a7c41cf3991d6 lrnassar Tue Jun 30 16:49:27 2026 -0700 varFreqs: July 1, 2026 release announcement, newsarch + indexNews + pennantIcon. refs #36642 Adds the New SNV Frequencies supertrack release entry to newsarch.html (anchor #070126) and indexNews.html for the upcoming July 1, 2026 release. The newsarch entry features rs4986893, the CYP2C19 East Asian founder stop-gained variant, as the screenshot example. Updates the varFreqs supertrack pennantIcon to point to the new anchor with hover text "Released Jul. 1, 2026". diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 49187ac6890..f5d79cdff8d 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,130 @@ <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="070126"></a> +<h2>Jul. 1, 2026 New SNV Frequencies supertrack on hg38</h2> +<p> +We are pleased to announce a new +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqs" target="_blank"><b>SNV +Frequencies</b></a> supertrack on the human assembly (GRCh38/hg38). The +collection unifies single-nucleotide variant allele frequencies from 30+ +population resequencing and biobank projects worldwide, covering roughly +1.7 million genomes, exomes, and genotyping arrays, into a single place +where a variant's frequency can be compared across populations, ancestries, +and disease cohorts. +</p> + +<p> +The collection includes three combined tracks that aggregate the source +data along different lines: +</p> +<ul> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqsBackground" target="_blank"> + <b>Population reference</b></a> (default view): 1.24 billion variants + pooled across general-population and biobank cohorts plus the + unaffected/control arms of the disease studies.</li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqsAffected" target="_blank"> + <b>Disease cohorts</b></a>: 133 million variants in the affected or + case arms of five disease-study cohorts (SFARI SPARK WES and WGS, SCHEMA, + GREGoR, GA4K). Each variant also carries its background frequency for + easy case-vs-population comparison.</li> + <li><a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqsArray" target="_blank"> + <b>Genotyping Array Databases Combined</b></a>: 14.7 million variants + from three array cohorts (TPMI Taiwan, Mexico Biobank, UK Biobank + imputed), kept separate from the sequencing-based tracks because chip + data has different per-variant confidence.</li> +</ul> + +<div class="text-center"> + <img src="../images/snvFrequenciesNewsarch.png" + alt="SNV Frequencies mouseover at rs4986893, a CYP2C19 stop-gained variant common in East Asian populations" + width='80%'> + <p class="gbsCaption"><em>rs4986893, a CYP2C19 stop-gained variant common in + East Asian populations. The mouseover ranks ToMMo Japan, KOVA Korea, and WBBC + China at the top, well above the 1.6% pooled background AF.</em></p> +</div> + +<p> +Each variant in the combined tracks is colored by predicted protein +consequence +(<b style="color:#FF0000">loss-of-function</b>, +<b style="color:#1F77B4">missense</b>, +<b style="color:#008000">synonymous</b>, +<b style="color:#808080">non-coding</b>), and +carries pooled allele counts and pooled allele frequencies (sum AC / sum +AN) across the contributing cohort arms. Cross-database filters allow +you to narrow to variant type, consequence, source database, length, or +any combination of per-track AC/AF/AN ranges. +</p> + +<p> +The supertrack pulls together cohorts from across the world. A high-level +summary of the regions and contributing projects is shown below; a +complete table with per-cohort sample counts, data types, sub-populations +and download status is on the +<a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varFreqs" target="_blank">supertrack +description page</a>. +</p> + +<table class="stdTbl"> + <tr><th>Region</th><th>Contributing cohorts</th></tr> + <tr><td>East Asia</td><td>ToMMo, GenomeAsia, NPM, KOVA, WBBC, ChinaMAP, TPMI</td></tr> + <tr><td>South Asia</td><td>IndiGen, GenomeIndia</td></tr> + <tr><td>Africa</td><td>Tishkoff</td></tr> + <tr><td>Americas</td><td>AllOfUs, TOPMed, ABraOM, Mexico Biobank</td></tr> + <tr><td>Europe</td><td>FinnGen, SweGen, GoNL, HRC, UK Biobank, ALFA</td></tr> + <tr><td>Middle East</td><td>Saudi</td></tr> + <tr><td>Oceania</td><td>MGRB</td></tr> + <tr><td>Disease cohorts</td><td>SFARI SPARK (WES + WGS), SCHEMA, GREGoR, GA4K</td></tr> + <tr><td>Global reference panels</td><td>SGDP, gnomAD HGDP+1kG</td></tr> + <tr><td>Long-read / linked-read</td><td>GA4K, CoLoRSdb, SVatalog</td></tr> +</table> + +<p> +License restrictions on some sources limit redistribution; see the +supertrack description page for per-cohort details. +</p> + +<p> +We plan to continue updating this track as more population-scale +allele-frequency datasets become available. If you are involved with a +project that publishes variant frequencies and would like to contribute, +please <a href="/contacts.html" target="_blank">reach out</a>. +</p> + +<p> +We would like to thank the millions of participants worldwide who donated +samples and shared health information to make this data possible; the +investigators who provided the variant files, including Matthew Hansen +(Tishkoff lab), Insoo Jang (KOVA), and Andreas Lahner (MGZ) for feedback; +and Alex Ioannidis (UCSC) for the motivation behind the track. The track +was developed by Maximilian Haeussler with QA and review by Lou Nassar. +</p> + <a name="062526"></a> <h2>Jun. 25, 2026 Release 3 update of the Varaico Variants and Varaico Variants (suppl) tracks for hg38 and hg19</h2> <p> We are happy to announce release 3 of the <b>Varaico Variants</b> and <b>Varaico Variants (suppl)</b> tracks for the human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varsInPubs" target="_blank">hg38/GRCh38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=varsInPubs" target="_blank">hg19/GRCh37</a>. This release contains a precision improvement and an update of the underlying literature. The Varaico tracks are created using literature mining, similar to <a href="http://bejerano.stanford.edu/AVADA/" target="_blank">AVADA</a>.</p> <p> The Varaico Variants (suppl) track contains variants extracted from supplementary data files using similar methods as in the Varaico track. The previous (release 2)