59fb440ba930a3f0eaee0af6e7fe6a2526b10551 gperez2 Wed Dec 3 11:49:31 2025 -0800 More updates to gnomadMpc.html and releasing/announcing the hg19 gnomAD MPC track, refs #36531 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 1eaf3d3943a..33d35aad9b6 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,61 @@ <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 found <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 our <a href="https://github.com/ucscGenomeBrowser/kent/commits/master" target=_blank>GitHub page</a>. Lastly, see our <a href="credits.html" target="_blank"> credits page</a> for acknowledgments of the data we host.</p> <!-- ============= 2025 archived news ============= --> <a name="2025"></a> + +<a name="120325"></a> +<h2>Dec. 03, 2025 New gnomAD Missense Deleteriousness Prediction by Constraint (MPC) track for hg19</h2> +<p> +We are happy to announce the release of the +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadMpc" + target="_blank">Missense Deleteriousness Prediction by Constraint (MPC) track</a> for hg19, +now available in the +<a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=gnomadSuper" + target="_blank">gnomAD superTrack</a>. This track shows a score that tries to identify +missense-depleted regions using the patterns of rare missense variation in 125,748 gnomAD v2.1.1 +exomes, compared to a null mutational model. Missense-depleted regions are enriched for ClinVar pathogenic +variants, de novo missense variants in individuals with neurodevelopmental disorders (NDDs), and +complex trait heritability. This track can be used to aid in interpreting missense variants.</p> +<p> +Transcript regions with constraint predictions are colored using the viridis palette, where yellow +indicates the lowest OE values and dark blue-purple indicates the highest.</p> +<div class="text-center"> +<img src="../../images/newsArchImages/gnomAD_mpc.png" width='80%'></a> +</div> +<p> +A corresponding MPC version for hg38 is planned for release by the gnomAD team in 2026.</p> +<p> +We would like to thank Kaitlin Samocha for suggesting this track and the +<a href="https://gnomad.broadinstitute.org/about" + target="_blank">Genome Aggregation Database Consortium (gnomAD)</a> for making the data +available. We would also like to thank Maximilian Haeussler, Luis Nassar, and Gerardo Perez for the +creation and release of this track.</p> + + + <a name="111425"></a> <h2>Nov. 14, 2025 Updated Varaico Variants track and new Varaico Variants (suppl) track for hg38 and hg19</h2> <p> We are pleased to announce the release 2 of the <b>Varaico Variants track</b> and the addition of a new <b>Varaico Variants (suppl) track</b> for the human assemblies <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=varsInPubs" target="_blank">hg38/GRCh38</a> and <a href="/cgi-bin/hgTrackUi?db=hg19&position=default&g=varsInPubs" target="_blank">hg19/GRCh37</a>. The Varaico tracks are generated using literature mining methods similar to those used for the <a href="http://bejerano.stanford.edu/AVADA/" target="_blank">AVADA</a> resource. With this update, the Varaico Variants track now contains more than 5.5 million variants.</p> <p> The Varaico Variants (suppl) track shows variants extracted from supplementary data files using