5d9669325edefa6193f94910b74dc48f9655ffc7 gperez2 Sun Sep 29 17:50:32 2024 -0700 Releasing the six new gnomAD v4.1 tracks, #34511 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 52e9a7d..8bd7554 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -54,30 +54,80 @@ <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> <!-- ============= 2024 archived news ============= --> <a name="2024"></a> +<a name="093024"></a> +<h2>Sep. 30, 2024 New gnomAD v4.1 tracks for hg38</h2> +<p> +We are excited to release six new +<a target=_blank href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadVariants"> +Genome Aggregation Database (gnomAD) v4.1 tracks</a> for human assembly hg38/GRCh38. The new tracks +are found in the gnomAD superTrack:</p> +<ul> + <li><b>gnomAD v4.1 (composite track)</b>:</li> + <ul> + <li><b>Genome variants</b>: Variants from 76,215 genomes</li> + <li><b>Exome Variants</b>: Variants from 730,947 exomes</li> + </ul> + <li><b>gnomAD Constraint Metrics (composite track)</b>: + <ul> + <li><b>Transcript LoF v4.1</b>: Predicted Loss of Function Constraint Metrics By Transcript (LOEUF and pLI) v4.1</li> + <li><b>Transcript Missense v4.1</b>: Predicted Missense Constraint Metrics By Transcript (Z-scores) v4.1</li> + </ul> + <li><b>gnomAD Rare CNV Variants</b>: Rare CNV variants (<1% overall site frequency)</li> + <li><b>gnomAD Structural Variants</b>: Structural Variants v4.1</li> +</ul> +<p> +<b>gnomAD v4.1</b>: The gnomAD v4.1 data release replaces the v4 Pre-Release track and fixes the allele +number <a target="_blank" +href="https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/"> +issue</a>. The data contains two subtracks from a total of 807,162 individuals: one for genome +variant calls and one for exome variants.</p> +<p> +<b>gnomAD Constraint Metrics</b>: Contains metrics of pathogenicity per-gene as predicted for +gnomAD v4.1 and identifies genes subject to strong selection against various classes of mutation. +The release of the gnomAD v4.1 constraint metrics consists of two new subtracks in the gnomAD +Constraint Metrics composite: Transcript LoF v4.1 and Transcript Missense v4.1</p> +<p> +<b>gnomAD Rare CNV Variants</b>: Displays rare autosomal coding copy number variants (CNVs) with an +overall site frequency of less than 1%. These variants were identified from exome sequencing (ES) +data of 464,297 individuals.</p> +<p> +<b>gnomAD Structural Variants</b>: Shows structural variants calls (>=50 nucleotides) from +63,046 unrelated genomes. It mostly (but not entirely) overlaps with the genome set used for the +gnomAD short variant release.</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. We would also like to thank +Chris Lee, Ana Benet-Pagès, Luis Nassar, and Gerardo Perez for the creation and release of +these tracks.</p> + + + + <a name="092424"></a> <h2>Sept. 24, 2024 Nuclear mitochondrial DNA segments (NuMTs) for hg38</h2> <p> We are happy to announce the release of a new track, <a href="/cgi-bin/hgTrackUi?db=hg38&position=default&g=nuMtSeq">NuMTs Sequence</a>, for human assembly (GRCh38/hg38). This track is a collection of Nuclear mitochondrial DNA segments, provided in BED format with the BED score representing the alignment confidence. The BED score is calculated by -10log10(E-value) and is reflected in the grayscale value. Scores >=100 are colored black. It is important to note that when a NuMT is a merged result, the score is taken as the highest score among all results.</p> <p> For more detailed information on the methods used for detecting NuMTs, please visit the following webpage:<br> <a href="https://github.com/Koumokuyou/NUMTs">https://github.com/Koumokuyou/NUMTs</a></p>