750e46fd9085b25b3e40445330c196cc85232b52 lrnassar Wed Dec 23 10:09:17 2020 -0800 News announcement for clinvar interpretations track refs #26330 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 506483a..0dadaf9 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,71 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="122320"></a> +<h2>Dec. 23, 2020 New ClinVar Interpretations track for human (hg19/hg38)</h2> +<p> +We are pleased to release a new track, <b>ClinVar Interpretations</b>, for the hg19/GRCh37 and +hg38/GRCh38 human assemblies. This track can be found as part of the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">ClinVar Composite</a>. It is the first +track to use our bead graph display, which is a variation of our existing <a target="_blank" +href="#062019">lollipop display</a>.</p> +<p> +The <b>ClinVar Interpretations track</b> displays the genomic positions of individual variant +submissions and interpretations of the clinical significance, as well as their relationship +to disease in the ClinVar database. As seen on the image below, the variants are classified into +six categories each on a separate horizontal line:</p> + +<p class="text-center"> + <img class='text-center' src="../images/clinVarInt.png" width='100%' +alt="ClinVar Interpretations track with Franklin display"> +</p> + +<ul> +<li><font color="d20000"><b>P</b> - Pathogenic</font></li> +<li><font color="d20000"><b>LP</b> - Likely Pathogenic</font></li> +<li><font color="000088"><b>VUS</b> - Variant of Unknown Significance</font></li> +<li><font color="#00d200"><b>LB</b> - Likely Benign</font></li> +<li><font color="#00d200"><b>B</b> - Benign</font></li> +<li><font color="#888"><b>OTH</b> - Others</li></font></ul> + +<p> +The size of the bead on the line represents the number of submissions at that genomic position. +The color of the beads aids to distinguish the categories further. Hovering on the track +items shows the genomic variations which start at that position and the +number of individual submissions with that classification. Additional information on the variants +can be found by clicking into the item.</p> +<p> +For more information see the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr10&g=clinvar">track description page</a>.</p> +<p> +We would link to thank <a target="_blank" href="https://www.ncbi.nlm.nih.gov/clinvar/">ClinVar</a> +for making these data available, as well as Brian Joseph Raney, Ana Benet Pages, Gerardo Perez, +and Lou Nassar for the development and release of this track.</p> + <a name="121620"></a> <h2>Dec. 16, 2020 New In-Silico PCR feature for assembly hubs</h2> <p> We are excited to announce assembly hubs can now perform In-Silico PCR. Assembly hub developers have long been able to activate DNA and amino acid BLAT searches on their hubs by running gfServers from their institution, and now with the new isPcr setting, they can enable In-Silico PCR searches too using the same running gfServers. In-Silico PCR searches a sequence database with a pair of PCR primers, using an indexing strategy for fast performance to find target regions across the genome. Browser users without an institution to host gfServers can still benefit from this new feature by downloading and installing a virtual machine <a href="help/gbib.html">Genome Browser in a Box (GBiB)</a>, and alternatively running gfServers on the GBiB, all locally from a laptop. For more information see the <a href="http://genomewiki.ucsc.edu/index.php/Assembly_Hubs" target="_blank">Assembly Hub Wiki</a> and the <a href="help/hubQuickStartAssembly.html" target="_blank">Quick Start Guide to Assembly Hubs</a>.</p> <p>