8fa6db788b44f96802b25ae1e8fb27524a90907f gperez2 Fri Jan 22 10:17:42 2021 -0800 Updating news for gnomAD track updates, refs #26449 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index f89d609..4926041 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,32 +40,65 @@ <div class="col-sm-3"> <ul> <li><a href="#2005">2005 News</a></li> <li><a href="#2004">2004 News</a></li> <li><a href="#2003">2003 News</a></li> <li><a href="#2002">2002 News</a></li> <li><a href="#2001">2001 News</a></li> </ul> </div> </div> </div> <!-- ============= 2021 archived news ============= --> <a name="2021"></a> +<a name="012221"></a> +<h2>Jan. 22, 2021 Updates to gnomAD variation track (GRCh37/hg19)(GRCh38/hg38)</h2> +<p> +We are pleased to announce updates to the +<a href="../../cgi-bin/hgTrackUi?db=hg38&c=chr22&g=gnomadVariants" +target="_blank">gnomAD Variants super-track</a> for the <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg19&c=chrX&g=gnomadSuper">hg19/GRCh37</a> +and <a target="_blank" +href="../../cgi-bin/hgTrackUi?db=hg38&c=chrX&g=gnomadVariants">hg38/GRCh38</a> +human assemblies.</p> +<ul> + <li>gnomAD v3.1 is now available and contains variants from 76,156 whole genomes (and no exomes), + all mapped to the GRCh38/hg38 reference sequence. 4,454 genomes were added to the number of + genomes in the previous v3 release. For more detailed information on gnomAD v3.1, see the related + <a href="https://gnomad.broadinstitute.org/blog/2020-10-gnomad-v3-1/"target="_blank">blog post</a>.</li> + <li>The latest release (gnomAD 2.1.1) is also available for GRCh37/hg19 genome assembly. This release + contains variant data for 125,748 exomes and 15,708 whole genomes.</li> + <li>Three filters are now available for our updated v2.1.1 (GRCh37/hg19) and gnomAD v3.1 (GRCh38/hg38) tracks, + by minor allele frequency (MAF), quality tags, annotation type, and variant type.</li> + <li>Mouse hover over now displays details about each variant, including the affected gene(s), the variant type, + and annotation.</li> + <li>Following the conventions on the gnomAD browser, items are shaded according to their Annotation type: pLoF + is red, Missense is orange, Synonymous is green, and Others are black.</li></ul> +<p class="text-center"> + <img class='text-center' src="../images/gnomadV3_1.jpg" width='100%' alt="The gnomAD v3.1 track display."> +</p> + +<p> +We would like to thank the <a target="_blank" href="http://gnomad.broadinstitute.org/">Genome Aggregation Database +(gnomAD)</a> team at the BROAD institute and the UCSC Genome Browser team members Christopher Lee, Anna Benet-Pages, +Daniel Schmelter, and Gerardo Perez for developing and releasing these tracks.</p> + + <a name="011321"></a> -<h2>Jan. 13, 2020 New GENCODE gene tracks: Human V35/V36 (hg19/hg38)</h2> +<h2>Jan. 13, 2021 New GENCODE gene tracks: Human V35/V36 (hg19/hg38)</h2> <p> We are pleased to announce new GENCODE Gene annotation tracks, which correspond to <a href="http://www.ensembl.info/2020/08/20/ensembl-101-has-been-released/" target="_blank">Ensembl 101</a> and <a target="_blank" href="https://www.ensembl.info/2020/11/30/ensembl-102-has-been-released/">Ensembl 102</a>, for the <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg19&c=chr21&g=wgEncodeGencodeV36lift37">hg19/GRCh37</a> and <a target="_blank" href="../../cgi-bin/hgTrackUi?db=hg38c=chr1&g=wgEncodeGencodeSuper">hg38/GRCh38</a> human assemblies. The annotations were mapped to hg38 and then back-mapped to the hg19 assembly. All gene sets contain the following tracks:</p> <ul> <li>Basic - a subset of the <em>Comprehensive set</em>.</li> <li>Comprehensive - all GENCODE coding and non-coding transcript annotations, including polymorphic pseudogenes. This includes both manual and automatic annotations.</li> <li>Pseudogenes - all annotations except polymorphic pseudogenes.</li></ul> @@ -76,31 +109,31 @@ <li>2-way Pseudogenes - pseudogenes predicted by both the Yale Pseudopipe and UCSC Retrofinder pipelines.</li> <li>PolyA - polyA signals and sites manually annotated on the genome based on transcribed evidence (ESTs and cDNAs) of 3' end of transcripts containing at least 3 A's not matching the genome.</li></ul> <p> Details on each release can be found on the <a target="_blank" href="https://www.gencodegenes.org/">GENCODE site</a>. This includes <a target="_blank" href="https://www.gencodegenes.org/human/stats.html">statistics on each release</a>. <p>We would like to thank the <a target="_blank" href="https://www.gencodegenes.org/pages/gencode.html">GENCODE project</a> for providing these annotations. We would also like to thank Mark Diekhans and Lou Nassar for the development and release of these data.</p> <a name="010821"></a> -<h2>Jan. 8, 2020 January 8th SARS-CoV-2 update</h2> +<h2>Jan. 8, 2021 January 8th SARS-CoV-2 update</h2> <p> We are pleased to start the year with our fifth data release for the <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank">coronavirus genome browser</a>. (See also our <a href="#040320">first</a>, <a href="#050420">second</a>, <a href="#080720">third</a>, and <a href="#102120">fourth</a> releases)</p> <p> This update includes an updated track as well as three new tracks for the <a href="/cgi-bin/hgTracks?db=wuhCor1" target="_blank">coronavirus genome browser</a>, and a track for the <a href="/cgi-bin/hgTracks?db=hg19" target="_blank">hg19/GRCh37</a> and <a href="/cgi-bin/hgTracks?db=hg38" target="_blank">hg38/GRCh38</a> human assemblies. Worth note is the <a href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=lineageB_1_1_7_US" target="_blank">B.1.1.7 in USA</a> track which shows substitution and deletion variants in the <b>B.1.1.7 lineage</b>, known for its