2019790b4445ac76dfc6e591fc1575abac740b5a gperez2 Fri Jan 17 18:24:02 2025 -0800 Renaming DDG2P announcement to DECIPHER Population CNVs, refs #35053 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index d8e9809..3805cf1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -99,63 +99,61 @@ <p> This track was created using the latest <a href="https://ftp.ncbi.nih.gov/gene/DATA/" target="_blank">NCBI files</a> (gene2accession and gene_orthologs). More information on this track can be found on the <a href="/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite#TRACK_HTML" target="_blank">track description</a> page.</p> <p> We would like to thank <a href="https://www.ncbi.nlm.nih.gov/" target="_blank">NCBI</a> for making this data available. We would also like to thank Jeltje van Baren, Mark Diekhans, Max Haeussler, and Gerardo Perez for the creation and release of this track. </p> <a name="121024"></a> -<h2>Dec. 10, 2024 DDG2P Developmental Disorders Genotype-to-Phenotype tracks for Human (hg19/hg38)</h2> +<h2>Dec. 10, 2024 DECIPHER Population CNVs 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> +We are pleased to introduce the DECIPHER Population CNVs track for both the +<a href="/cgi-bin/hgTrackUi?db=hg19&g=decipherPopulation&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> +<a href="/cgi-bin/hgTrackUi?db=hg38&g=decipherPopulation&position=default" target="_blank">GRCh38/hg38</a> +human genome assemblies. This track shows common copy-number variants (CNVs) and their population +frequencies.</p> <p> -The DDG2P track incorporates an intuitive color-coding system alongside detailed tooltips for an -enhanced user experience:</p> +The Population CNVs 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> +<p>The Population CNVs 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> +Jairo Navarro for the creation and release of the Population CNVs 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>