def0bb04c307aae1c09c50cbec6ea568e2937341 lrnassar Mon Sep 28 15:19:53 2020 -0700 News announcement for clinvar + clinGen changes refs #24818 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 34fae10..7492c5b 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,112 @@ <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="093020"></a> +<h2>Updates to ClinVar and ClinGen (GRCh37/hg19)(GRCh38/hg38)</h2> +<p> +We have updated the <b>ClinVar Variants track (hg19/hg38)</b>, and made changes to the current +<b>ClinGen CNVs track (hg19/hg38)</b>. We have also added three new tracks in support of a new +ClinGen composite. These changes have been made in an effort to support our clinical users, +with an emphasis on facilitating Genome Browser use in variant interpretation.</p> + +<a name="093020a"></a> +<h3>Updates to ClinVar Variants track</h3> +<p> +The <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=clinvar">ClinVar Variants +track</a> has been reorganized based on variant length. +The previous tracks, ClinVar Short Variants (<= 100bp) and +ClinVar Long Variants (> 100bp), are now ClinVar SNVs (< 50bp) and +ClinVar CNVs (>= 50bp). We have also added a mouse-over from the track display which +shows phenotype and clinical significance information. In addition, +the CNV track now has the following improvements:</p> +<ul> +<li>The <a target="_blank" href="/goldenPath/help/trackDb/trackDbHub.html#mergeSpannedItems"> +mergeSpannedItems</a> feature has been enabled which collapses all CNVs that span a larger +genomic region than the browser's window display. Merged items can be shown by right-click.</li> +<li>CNVs now have a color gradient according to the clinical significance for easy +identification of pathogenic variants.</li></ul> +<p> +Lastly, multiple feature options have been added to both tracks independently:</p> +<ul> +<li>Filtering by variant length is available on both tracks.</li> +<li>Filter by variation (INS, DEL, etc.) now available on both tracks.</li> +<li>Filter by clinical significance (benign, conflicting, etc.) now available on both tracks.</li> +<li>Filter on allele origin (somatic, germ line, de novo, etc.) now available on both tracks.</li> +<li>Filter by molecular consequence (stop lost, nonsense, intron variant, etc.) now available +on short variants track.</li> +</ul> +<p> +Below is an example of the filter options available for the <b>ClinVar SNVs track</b>. For +additional details on the updated display, see the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=clinvar">track description page</a>.</p> + +<p class="text-center"> + <img class='text-center' src="../images/clinVarFilters.png" width='60%' +alt="Example of filter options in ClinVar SNVs track"> +</p> + +<a name="093020b"></a> +<h3>Changes to ClinGen and new tracks</h3> +<p> +We have created a new composite track, <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=clinGenComp">ClinGen</a>, and deprecated the previous +<a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&c=chr1&g=iscaComposite"> +ClinGen CNVs track</a>. The ClinGen CNVs track will continue to be available, however, +the data will no longer be updated. This was done by request of ClinGen, as all the +data, as well as further updates, can be found in the <a target="_blank" +href="/cgi-bin/hgTrackUi?db=hg38&g=clinvar">ClinVar Copy Number Variants (ClinVar CNVs) track</a>.</p> +<p> +The new <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp">ClinGen composite +track</a> includes three new tracks described below:</p> +<ul> +<li><b>ClinGen Dosage Sensitivity Map - Haploinsufficiency</b> - Shows evidence supporting or +refuting haploinsufficiency (loss) as mechanisms for disease at gene-level and larger genomic +regions.</li> +<li><b>ClinGen Dosage Sensitivity Map - Triplosensitivity</b> - Shows evidence supporting or +refuting triplosensitivity (gain) as mechanisms for disease at gene-level and larger genomic +regions.</li> +<li><b>ClinGen Gene-Disease Validity Classification (ClinGen Validity)</b> - Provides a +semi-qualitative measurement for the strength of evidence of a gene-disease relationship.</li> +</ul> + +<p class="text-center"> + <img class='text-center' src="../images/clinGenComp.png" width='90%' +alt="Example of three new ClinGen Composite tracks"> +</p> + +<p> +For more information on these tracks, including display conventions, scores, and classifications, +see the <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=clinGenComp">track description +page</a>.</p><br> +<p> +We would like to thank May Flowers and Erin Riggs as well as the rest of the ClinGen team. We +would also like to thank ClinVar for making these data available. Track development and release +was made possible by Anna Benet-Pages, Christopher Lee, Max Haeussler, and Lou Nassar.</p> + <a name="092520"></a> <h2>Sept. 25, 2020   New data and visualization types: Covid GWAS (Lollypop) and Family Trios (VCF Trios)</h2> <h3>Covid GWAS meta-analysis</h3> <p> We are happy to announce the first COVID-19 tracks in our human genome browsers <a href="../../cgi-bin/hgGateway?db=hg19">GRCh37/hg19</a> and <a href="../../cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>, the COVID-19 GWAS meta-analysis. This track brings together data from 17 international GWAS studies and aims to identify genetic determinants of SARS-CoV-2 infection susceptibility and disease severity. These data are from the <a href="https://www.covid19hg.org/results/" target="_blank"> COVID-19 Host Genetics Initiative (HGI)</a>, a collaborative effort to analyze and share viral host genetics research. More resources are available on our page: <a href="../../covid19.html">COVID-19 Resources at UCSC</a>. </p>