982b5bcbc18ff3816dcc364f7800cca2a6d2056f abenetpa Fri Apr 24 19:15:41 2020 -0700 newsarch announcement pLI and SV tracks refs #20394 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 22ae45a..a4baad6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -38,30 +38,99 @@ </ul> </div> <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="042820"></a +> +<h2>Apr. 28, 2020 gnomAD Constraint Metrics and Structural Variants data now available +on human (GRCh37/hg19) assembly</h2> + +<p> +We are pleased to announce two new Genome Aggregation Database (gnomAD) tracks, +<a target="_blank"href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=gnomadPLI">Predicted Constraint Metrics</a> and +<a target="_blank"href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=gnomadStructuralVariants">Structural Variants</a>, +for the human (GRCh37/hg19) assembly. +</p> + +<h3>Predicted Constraint Metrics</h3> +<p> +This data shows various metrics of pathogenicity per-gene as predicted for gnomAD v2.1.1 and +identifies genes subject to strong selection against various classes of mutation. It is comprised +of three subtracks: + +<ul> +<li> +<b>gnomAD Gene Constraint</b> - gnomAD Predicted Constraint Metrics By Gene +</li> +<li> +<b>gnomAD Transcript Constraint</b> - gnomAD Predicted Constraint Metrics By Transcript +<li> +<b>gnomAD Regional Constraint</b> - gnomAD Predicted Constraint Metrics By Transcript Regions +</li> +</ul> +</p> + +<h3>Structural Variants</h3> +<p> +This data shows structural variants calls (>=50 nucleotides) from the gnomAD v2.1 release on +10,847 unrelated genomes. It is comprised of three subtracks: + +<ul> +<li> +<b>All SV's</b> - gnomAD Structural Variants All +</li> +<li> +<b>Control Only SV's</b> - gnomAD Structural Variants Controls Only +<li> +<b>Non-neuro SV's</b> - gnomAD Structural Variants Non-neuro Only +</li> +</ul> +</p> + +<p> +This data can be found as part of the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&g=gnomadSuper">gnomAD</a> super-track. More information on +this track can be found in the track description pages, as well as the <a target="_blank" +href="https://gnomad.broadinstitute.org/faq">gnomAD</a> site. +</p> + +<p class="text-center"> + <img class='text-center' src="../images/GnomadConstraintStructruralVarRelease.PNG" width='80%' +alt="Example of Constraint Metrics and Structural Variants tracks"> +</p> + +<p> +We would like to thank the <a target="_blank" +href="https://gnomad.broadinstitute.org">Genome Aggregation Database Consortium</a> for making +these data available. We would also like to thank Christopher Lee, Maximilian Haeussler, Lou Nassar, +Jairo Navarro, Robert Kuhn and Anna Benet-Pages for their effort in the creation of these tracks. +</p> + + + <a name="2020"></a> <h2>Apr. 20, 2020 New video on the Browser's YouTube channel</h2> <p> We have released a new video to the Browser's <a href = "https://www.youtube.com/channel/UCQnUJepyNOw0p8s2otX4RYQ/videos" target = _blank>YouTube channel</a>. </p> <p> <b> Browser Basics, Part Two — Configuring the Browser </b> </p> <p> @@ -500,31 +569,30 @@ we have updated the Mastermind Variants track and expanded it to hg38.</p> <p class="text-center"> <img class='text-center' src="../images/variantsInPapersNewsArch2020.png" width='80%' alt="Example of AVADA and Mastermind tracks"> </p> <h3>Avada Variants</h3> <p> The Avada Variants track shows the genomic positions of variants in the <a target="_blank" href="http://bejerano.stanford.edu/AVADA/">AVADA database</a>. AVADA is a database of variants built by machine learning software that analyzes full text research articles in PDF format to find genes and variants that look most relevant for genetic diagnosis.</p> <p> Additional information can be found on the <a target="_blank" -href="../../cgi-bin/hgTrackUi?db=hg19&g=avada">track description</a> page as well as the <a target="_blank" href="https://doi.org/10.1038/s41436-019-0643-6">AVADA publication</a>.</p> <h3>Mastermind Variants</h3> <p> The <a href="#032619">Mastermind Variants</a> track is now available for the hg38 assembly alongside hg19. Both tracks will now be updated on a quarterly cycle. The track is also now filtered to make the data more specific by removing longer non-indels that are not directly mentioned in the text.</p> <p> Additional information on Mastermind Variants can be found in the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&g=mastermind">track description page</a>.</p> <p> We would like to thank Gill Bejerano and Johannes Birgmeier for making the AVADA data available, as well as Genomenon for the Mastermind track. We would also like to thank Maximilian Haeussler, Lou Nassar, and the rest of the Genome Browser team for the