c9401e6585d6b2dd85971d55120d7d7c3bc0d2e8 jnavarr5 Tue Mar 19 11:13:11 2024 -0700 Staging the gnomAD v4 constraints metrics announcemnt, refs #33084 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 2e734b9..536de4a 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,30 +51,53 @@ </div> <p>You can sign-up to get these announcements via our <a target=_blank href="https://groups.google.com/a/soe.ucsc.edu/g/genome-announce?hl=en">Genome-announce</a> email list. We send around one short announcement email every two weeks.</p> <p>Smaller software changes are not announced here. A summary of the three-weekly release changes can be <a target=_blank href="https://genecats.gi.ucsc.edu/builds/versions.html">here</a>. For the full list of our daily code changes head to <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>our GitHub page</a>.</p> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<!-- +<a name="032224"></a> +<h2>Mar. 22, 2024 gnomAD v4 Constraint Metrics for hg38</h2> +<p> +We are pleased to announce the release of the gnomAD v4 constraint metrics for human assembly +hg38/GRCh38. These tracks contain metrics of pathogenicity per-gene as predicted for gnomAD v4.0 and +identifies genes subject to strong selection against various classes of mutation.</p> +<p> +There are two new tracks in this update:</p> +<ol> + <li><b>Transcript LoF Constraint track</b>: Predicted constraint metrics at the whole transcript + evel for three different types of variation: missense, synonymous, and predicted loss of + function.</li> + <li><b>Transcript Missense Constraint track</b>: The missense constraint tracks are built + similarly to the LoF constraint tracks, however the items displayed are based on missense Z + scores. All items are colored black, and individual Z scores can be seen on mouseover. +</ol> +<p> +We would like to thank the <a href="https://gnomad.broadinstitute.org/about" target="_blank">Genome +Aggregation Database Consortium</a> for making these data available. We would also like to thank +Chris Lee and Jairo Navarro for the creation and release of these tracks.</p> +--> + <a name="030724"></a> <h2>Mar. 07, 2024 New Prediction Scores super track and BayesDel track for hg19</h2> <p> We are happy to announce the new Human Prediction Scores super track for the <a href="/cgi-bin/hgTrackUi?db=hg19&g=predictionScoresSuper">GRCh37/hg19</a> assembly. This super track currently includes the <a href="/cgi-bin/hgTrackUi?db=hg19&g=bayesDel">BayesDel track</a>, which can be used for clinical variant classification research. <a href="https://fenglab.chpc.utah.edu/BayesDel/BayesDel.html" target="_blank">BayesDel</a> is a deleteriousness meta-score for coding and non-coding variants, single nucleotide variants, and small insertion/deletions. The range of the score is from -1.29334 to 0.75731. The higher the score, the more likely the variant is pathogenic. There are eight subtracks for the BayesDel track: four include pre-computed MaxAF-integrated BayesDel scores for missense variants, one for each base. The other four are of the same format, but scores are not MaxAF-integrated.</p> <p> We would like to thank the