aa807eaeadff6c4f4d3c19a2783a5677d4f3801f gperez2 Thu Jun 30 14:17:24 2022 -0700 Updating news for the hg38 gnomadPLI track, refs #29358 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2387ec5..8bf5380 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,55 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2006">2006 News</a></li> <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="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> <!-- ============= 2022 archived news ============= --> <a name="2022"></a> + +<a name="063022"></a> +<h2>June 30, 2022 New gnomAD Constraint Metrics track on GRCh38/hg38</h2> +<p> +We are pleased to announce the <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPLI">Genome +Aggregation Database (gnomAD) Constraint Metrics</a> track, previously only on hg19, +is now also available on the human GRCh38/hg38 genome assembly.</p> +<p> +These data show 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 four subtracks:</p> +<ul> + <li><b>Gene LoF</b> – gnomAD Predicted Loss of Function Constraint Metrics By Gene (pLI) + <li><b>Gene Missense</b> – gnomAD Predicted Missense Constraint Metrics By Gene (Z-scores) + <li><b>Transcript LoF</b> – gnomAD Predicted Loss of Function Constraint Metrics By Transcript (pLI) + <li><b>Transcript Missense</b> – gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores) +</ul> +<p> +More information on this track can be found in the <a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPLI#TRACK_HTML" +>track description page</a>, as well as the <a href="https://gnomad.broadinstitute.org/faq" target="_blank"> +gnomAD</a> site. We would like to thank the <a href="https://gnomad.broadinstitute.org/" target="_blank"> +Genome Aggregation Database Consortium</a> for making these data available. We would also like to thank Lou +Nassar, Maximilian Haeussler, Anna Benet-Pages, and Gerardo Perez for their work in creating and releasing these +tracks.</p> + <a name="062822"></a> <h2>June 28, 2022 Update to GTEx cis-eQTL for hg38</h2> <p> We are happy to announce an update to the <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gtexEqtlHighConf">GTEx cis-eQTL</a> track for the human assembly (GRCh38/hg38). The track shows genetic variants likely affecting proximal gene expression in 49 human tissues from the <a href="https://gtexportal.org/home/" target="_blank">Genotype-Tissue Expression (GTEx)</a> V8 data release. With this update, we are introducing the <a href="https://github.com/xqwen/dap" target="_blank">DAP-G</a> 95% credible set alongside the <a href="http://genetics.cs.ucla.edu/caviar/" target="_blank">CAVIAR</a> high-confidence set.</p> <p> Hovering over items in the track display will show the variant ID (often a dbSNP rsID), the target gene, tissue, and posterior probablity (Causal Posterior Probability (CPP) for CAVIAR; SNP Posterior Inclusion Probability (PIP) for DAP-G). Clicking an item will show the details of that interaction