6a60cdb51e2832102b71d7b88c6740825720929f gperez2 Tue Mar 26 12:19:53 2024 -0700 Announcing the release of the gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/hg38) tracks, refs #33084 #32916 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index e544b82..d90f2d5 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -51,52 +51,65 @@ </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> +<a name="032624"></a> +<h2>Mar. 26, 2024 New gnomAD v4 Constraint Metrics (hg38) and gnomAD Non-cancer filter (hg19/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> +We are pleased to announce the release of the +<a href="/cgi-bin/hgTrackUi?&db=hg38&g=gnomadPLI">gnomAD v4 constraint metrics</a> for human +assembly hg38/GRCh38 and the addition of a non-cancer filter for the +<a href="/cgi-bin/hgTrackUi?db=hg19&g=gnomadExomes">GRCh37/hg19 Exome Variants v2.1.1</a> and the +<a href="/cgi-bin/hgTrackUi?db=hg38&g=gnomadGenomesVariantsV3_1_1"> +hg38/GRCh38 Genome Variants v3.1.1</a> tracks.</p> +<p> +The gnomAD v4 constraint metrics 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. +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. The release of +the gnomAD v4 constraint metrics consists of two new subtracks in the gnomAD Constraint Metrics +composite track:</p> <ol> <li><b>Transcript LoF Constraint track</b>: Predicted constraint metrics at the whole transcript level 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> +The GRCh37/hg19 Exome Variants v2.1.1 and the hg38/GRCh38 Genome Variants v3.1.1 tracks now have a +non-cancer filter that allows the option to exclude/include variants from samples of individuals +who were not ascertained for having cancer in a cancer study. These non-cancer subsets follow the +new guidelines for clinical variant testing of BRCA1 and BRCA2 genes and are used for the +assessment of breast cancer patients.</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 and Jairo Navarro for the creation and release of these tracks.</p> ---> +Chris Lee, Ana Benet-Pagès, Gerardo Perez, and Jairo Navarro for the creation and release of thee +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>