cf87c27669523cb325d1d2d52e11e6f18d24504e gperez2 Wed Aug 26 18:36:04 2026 -0700 Announcing the gnomAD v4.1.1 and MPC tracks. Adding pennantIcons to the new and updated tracks. refs #38166 refs #37351 refs #37478 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 901a4a30d7e..48d9d8f085b 100644 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -52,30 +52,80 @@ <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> <!-- ============= 2026 archived news ============= --> <a name="2026"></a> +<a name="082626"></a> +<h2>Aug. 26, 2026 gnomAD v4.1.1 and MPC tracks for hg38</h2> +<p> +We are excited to announce the updated +<b>Genome Aggregation Database (gnomAD) v4.1.1 tracks</b> for human assembly +hg38/GRCh38, along with a +new <b>gnomAD MPC track</b>, both found in the <a target=_blank href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants">gnomAD superTrack</a>. The tracks are:</p> +<ul> + <li><b><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariantsV4.1" target="_blank">gnomAD v4.1.1</a></b> + (composite track): Shows exome and genome variants. This release revises the LOFTEE END_TRUNC + GERP distance threshold from -58.0 to 0.0, reclassifying about 79,920 predicted loss-of-function + variants from high-confidence to low-confidence.</li> + <li><b><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadPLI" target="_blank">gnomAD Constraint Metrics</a></b> + (composite track): The v4.1.1 constraint metrics were recomputed + using a Bayesian framework instead of the previous frequentist approach, expanded the coverage model + from a depth cutoff to allele number, and now include chrX and chrY. gnomAD's recommended LOEUF + threshold changed from <0.35 to <0.45 accordingly. The two v4.1.1 subtracks: + <ul> + <li><b>Transcript LoF v4.1.1</b>: gnomAD Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI)</li> + <li><b>Transcript Missense v4.1.1</b>: gnomAD Predicted Missense Constraint Metrics By Transcript (Z-scores)</li> + </ul> + </li> + <li><b><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadMpc" target="_blank">gnomAD MPC</a></b> (composite + track): Shows a machine-learning score that predicts which missense variants are likely to be + deleterious, computed from the gnomAD v4.1.1 release of 730,947 exomes. The score is shown as four + allele-specific tracks (A, C, G, T).</li> + <li><b><a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadMpcOverlaps" target="_blank">gnomAD MPC overlaps</a></b>: + Covering the small subset of variants (about 250,000, or 0.4% of the ~70 million scored variants) + that are scored against more than one transcript.</li> +</ul> + +<div class="text-center" style="margin-top: 1.5em;"> +<a href="https://genome.ucsc.edu/s/gperez2/gnomADv4.1.1" target="_blank"> +<img alt="Genome Browser screenshot of the gnomAD v4.1.1 and MPC tracks" src="/images/newsArchImages/gnomadV4.1.1_MPC.png" +width='75%'></a> +<p class="gbsCaption"><em>gnomAD v4.1.1 exomes and genomes variants, the LoF and missense +constraint tracks, and the four gnomAD MPC allele tracks plus MPC overlaps, at the KCNH1 locus +on hg38.</em></p> +</div> + +<p> +For more information about the v4.1.1 update, see the <a href="https://gnomad.broadinstitute.org/news/2026-03-gnomad-v4-1-1/" target="_blank">gnomAD +blog post</a>.</p> + +<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, and Caitlin Samocha for +providing the MPC score data. We would also like to thank Christopher Lee, Maximilian Haeussler, +and Gerardo Perez for their efforts on this release.</p> + <a name="081126"></a> <h2>Aug. 11, 2026 Deleteriousness Predictions: ClinPred for hg19 and hg38</h2> <p> We are pleased to announce the release of the ClinPred pathogenicity score track for <a href="/cgi-bin/hgTrackUi?db=hg19&g=clinPred&position=default" target="_blank">hg19</a> and <a href="/cgi-bin/hgTrackUi?db=hg38&g=clinPred&position=default" target="_blank">hg38</a>. ClinPred is a machine-learning predictor of pathogenicity for nonsynonymous (missense) single-nucleotide variants, combining existing pathogenicity scores with population allele frequency from gnomAD. It was trained on confidently annotated disease-causing and benign variants from ClinVar. Pre-computed scores are provided for all possible human missense variants in the exome. </p> <p> Scores range from 0 to 1, with higher values indicating a greater predicted likelihood