c9a757f239030036c1f4c4a01ff757c27037a341 gperez2 Thu Jun 25 05:27:40 2026 -0700 Announcing the Varaico release 3 tracks, refs #37658 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d4371fe3ec5..49187ac6890 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,58 @@ <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="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) +Varaico data remains available in our +<a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/hg38/varaico/" + target="_blank">download archive</a>. +For more information, please visit the <a href="https://varaico.com/" + target="_blank">Varaico website</a>.</p> +<p> +Please note that the <b>Genomenon Mastermind Variants</b> track has been retired at +the data provider's request and is no longer updated or displayed.</p> +<p> +We would like to thank Johannes Birgmeier for generating and making the Varaico +data available. We would also like to thank Maximilian Haeussler and Gerardo Perez +for their efforts on this release.</p> + <a name="062326"></a> <h2>Jun. 23, 2026 Non-canonical ORFs track collection on hg38</h2> <p> We are pleased to announce a new <a href="/cgi-bin/hgTrackUi?db=hg38&g=ncOrfs" target="_blank"><b>Non-canonical ORFs</b></a> track collection on the human genome assembly (GRCh38/hg38), bringing together several public databases of open reading frames (ORFs) that fall outside annotated protein-coding genes. While the human genome has roughly 20,000 annotated protein-coding genes, ribosome profiling (Ribo-seq) and proteomics have revealed widespread translation of ORFs in regions long considered non-coding, including 5' and 3' UTRs, long non-coding RNAs, pseudogenes, and alternative reading frames of known genes. </p> <p> @@ -1457,32 +1485,32 @@ item.</em> </p></a> </div> <p> We would like to thank Mike Schatz, Evan Eichler, and all <a href="https://colorsdb.org/membership" target="_blank">CoLoRSdb investigators</a> for generating and making the data publicly available. We would also like to thank Karen Wang and Jairo Navarro Gonzalez for the creation and release of these tracks. </p> <a name="091925"></a> <h2>Sep. 19, 2025 Developmental Disorders Gene2Phenotype (DDG2P) for hg38 and hg19</h2> <p> We are pleased to announce the release of the <a href="https://www.deciphergenomics.org/ddd/ddgenes" target="_blank">Developmental Disorders Genotype-to-Phenotype (DDG2P)</a> track for -<a href="/cgi-bin/hgTrackUi?db=hg19&g=g2p&position=default" target="_blank">hg19</a> and -<a href="/cgi-bin/hgTrackUi?db=hg38&g=g2p&position=default" target="_blank">hg38</a>. The DDG2P +<a href="/cgi-bin/hgTrackUi?db=hg19&g=ddg2p&position=default" target="_blank">hg19</a> and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=ddg2p&position=default" target="_blank">hg38</a>. The DDG2P track displays genes associated with severe developmental disorders. The track can be used to filter genomic sequencing data of people with genetic disorders to identify likely causative variants and accelerate diagnosis. </p> <p> Items in this track are colored according to the likelihood that the gene-disease association is true:</p> <ul> <li> <font style="color: green;"><b>Green</b></font> - Definitive</li> <li> <font style="color: blue;"><b>Blue</b></font> - Strong</li> <li> <font style="color: orange;"><b>Orange</b></font> - Moderate</li> <li> <font style="color: red;"><b>Red</b></font> - Limited</li> <li> <font style="color: gray;"><b>Gray</b></font> - Refuted</li> </ul>