b63002965b8608c38af0c85ede421e7e79bd8d0d jnavarr5 Wed Dec 11 11:53:28 2024 -0800 Announcing the DDG2P track, refs #34097 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index b99d9bf..73eaf49 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,64 @@ <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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="121024"></a> +<h2>Dec. 10, 2024 DDG2P Developmental Disorders Genotype-to-Phenotype tracks for Human (hg19/hg38)</h2> +<p> +We are pleased to introduce the DDG2P (Developmental Disorders Genotype-to-Phenotype) track within +our genomic database, now available for both the +<a href="/cgi-bin/hgTrackUi?db=hg19&g=decipherDDG2P&position=default" target="_blank">GRCh37/hg19</a> +and +<a href="/cgi-bin/hgTrackUi?db=hg38&g=decipherDDG2P&position=default" target="_blank">GRCh38/hg38</a> +human genome assemblies. This track is specially curated to enhance understanding of genetic +variants associated with developmental disorders. This track facilitates the visual exploration and +analysis of complex genetic variations that may influence developmental disorders.</p> + +<p> +The DDG2P track incorporates an intuitive color-coding system alongside detailed tooltips for an +enhanced user experience:</p> + +<ul> + <li><font color="red">Red:</font> Indicates a loss of genetic material (deletions).</li> + <li><font color="blue">Blue:</font> Signifies a gain of genetic material (duplications).</li> + <li><font color="grey">Grey:</font> Marks areas with deletions or duplication (indel).</li> +</ul> + +<p>The DDG2P track's <b>mouseover</b> tooltip provides the following information about the data:</p> +<ul> + <li><b>Position:</b> Chromosomal range of the CNV.</li> + <li><b>Type of CNV:</b> Loss, gain, or deletions/duplications.</li> + <li><b>Frequency:</b> Prevalence of the CNV in the population.</li> + <li><b>Observations:</b> Times the CNV was noted in the dataset.</li> + <li><b>Sample Size:</b> Number of samples analyzed.</li> +</ul> +<p> +We would like to thank <a href="https://www.deciphergenomics.org/" target="_blank">DECIPHER</a> for +making the data publicly available. We would also like to thank Yesenia Puga, Gerardo Perez, and +Jairo Navarro for the creation and release of the DDG2P track on the UCSC Genome Browser.</p> <a name="110824"></a> <h2>Nov. 8, 2024 New GENCODE gene tracks: Human V47 (hg19/hg38) - Mouse M36 (mm39)</h2> <p> We are happy to announce new GENCODE Gene annotation tracks, which correspond to <a href="https://www.ensembl.info/2024/10/18/ensembl-113-has-been-released/" target="_blank">Ensembl 113</a>, for three assemblies: <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV47lift37">hg19/GRCh37</a>, <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38&c=chr1&g=wgEncodeGencodeV47">hg38/GRCh38</a>, and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=mm39&c=chr12&g=wgEncodeGencodeVM36">mm39/GRCm39</a>. For human, the GENCODE V47 annotations were mapped to hg38/GRCh38 and then back-mapped to the hg19/GRCh37 assembly. For all three assemblies, the gene sets contain the following tracks:</p> <ul>