9288a378d249add61e2ab0dc4b6d87ac96eb1003 lrnassar Tue Sep 29 09:39:25 2020 -0700 Changing date to proper title, reordering credits refs #24818 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 7052edf..41e6bc9 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -41,31 +41,32 @@ <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> +<h2>Sept. 30, 2020 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, @@ -85,31 +86,31 @@ <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>Sept. 25, 2020   Changes to ClinGen and new tracks</h3> +<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> @@ -118,31 +119,31 @@ 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 +We would like to thank Erin Riggs and May Flowers 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