8627f085aa0d1397dea24329d08cd243a13e39ef lrnassar Tue Oct 20 16:05:44 2020 -0700 4th coronavirus release announcement refs #26280 diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 326d47a..4428c77 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -40,30 +40,177 @@ <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> <!-- ============= 2020 archived news ============= --> <a name="2020"></a> +<a name="102120"></a> +<h2>Oct. 21, 2020 October 21st release for SARS-CoV-2 genome browser</h2> +<p> +We are pleased to announce our fourth 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>, and <a href="#080720">third</a> +releases)</p> +<p> +In line with our previous releases, these tracks include diverse data such as gene +models, immunology, pathogenicity, and conservation. We would also like to bring +attention to our <a href="#092520">recently released</a> COVID-19 GWAS +tracks for the <a href="/cgi-bin/hgTrackUi?db=hg19&g=covidHgiGwas&position=lastDbPos" +target="_blank">GRCh37/hg19</a> and <a +href="/cgi-bin/hgTrackUi?db=hg38&g=covidHgiGwas&position=lastDbPos" +target="_blank">GRCh38/hg38</a> human assemblies. The COVID-19 GWAS track displays data +which aims to identify genetic determinants of SARS-CoV-2 infection susceptibility +and disease severity.</p> +<p> +Clicking on any of the track titles below will lead to the track description +page, which includes additional information and allows for configuration of +various display options.<br><br>This release includes the following tracks:</p><br> + +<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=phyloGenes"> +PhyloCSF Genes - Curated conserved genes</a> - This composite includes two tracks +displaying curated SARS-CoV-2 protein-coding genes conserved within the +<em>Sarbecovirus</em> subgenus as determined using PhyloCSF, FRESCo, and other +comparative genomics methods, consistent with experimental evidence in SARS-CoV-2. +<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=phyloGenes"> +PhyloCSF Genes</a> - This track shows the conserved protein-coding genes, namely +ORF1a, ORF1ab, S, ORF3a, ORF3c (a.k.a. ORF3h, ORF3a*, and 3a.iORF1), E, M, +ORF6, ORF7a, ORF7b, ORF8, N, and ORF9b (a.k.a. ORF9a).</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=phyloGenes"> +PhyloCSF Rejected Genes</a> - This track shows other genes that have been proposed +that do not show the signature of conserved protein-coding genes or persuasive +experimental evidence, and are thus unlikely to be actual protein-coding genes, +namely ORF3d, ORF3b, ORF14 (a.k.a. ORF9b, ORF9c), and ORF10.</li></ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=weizmanOrfs"> +New ORFs based on RNA-seq and Ribo-seq by the Weizman Institute tracks</a> - The +Weizman ORFs (Open Reading Frames) track shows previously unannotated ORF predictions +based on Ribo-Seq and RNA-seq data. It contains four tracks comprised of the +predicted gene models, and data supporting them.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=icshape"> +icSHAPE RNA Structure</a> - This track shows normalized icSHAPE reactivity data of +in vivo and in vitro SARS-CoV-2 experiments.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=icshape"> +Validated epitopes from IEDB</a> - This track shows epitope sequences displayed by +various class I MHC alleles as annotated by National Institute for Allergy and +Infectious Diseases (NIAID) <a href="https://www.iedb.org/" target="_blank"> +Immune Epitope Database (IEDB)</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=potPathoIndel"> +Potential pathogenic insertions and deletions from Gussow <em>et al</em>, PNAS 2020</a> +- This track shows genomic features that differentiate SARS-CoV-2 and the viruses +behind the two previous deadly coronavirus outbreaks, SARS-CoV and Middle East +respiratory syndrome coronavirus (MERS-CoV), from less pathogenic coronaviruses.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=pond"> +Natural selection analysis from Sergei Pond's research group</a> - This track shows +data from Pond <em>et al</em>, 2020 "Natural selection analysis of +SARS-CoV-2/COVID-19" where authors used several statistical techniques to +identify selection sites of interest in SARS-CoV-2 data from <a +href="https://www.gisaid.org/about-us/mission/" target="_blank">GISAID</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=sarsCov2PhyloPub"> +Phylogenetic Tree and Variants from High-coverage Sequences in Public Databases</a> +- This track displays a phylogenetic tree inferred from SARS-CoV-2 genome sequences +from <a +href="https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=SARS-CoV-2,%20taxid:2697049" +target="_blank">GenBank</a>, <a href="https://www.cogconsortium.uk/data/" +target="_blank">COG-UK</a> and the <a href="https://bigd.big.ac.cn/ncov/release_genome" +target="_blank">China National Center for Bioinformation</a>, and variants found +in the sequences. It uses the phylogenetic tree from the <a +href="https://github.com/roblanf/sarscov2phylo/releases/tag/28-08-20" +target="_blank">sarscov2phylo 28-08-20</a> release, pruned to include only public +sequences. Since the public sequences are unrestricted, we can offer VCF files with +sequence variants for <a href="https://hgdownload.soe.ucsc.edu/gbdb/wuhCor1/sarsCov2PhyloPub/" +target="_blank">download</a>.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_antibody"> +Spike protein receptor-binding domain (S RBD) Deep Mutational Scanning</a> - Tracks created +from this data include:<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_antibody"> +S RBD Deep Mutational Scanning: Antibody Escape</a> - This track shows deep mutational +scanning data measuring the effect of the mutations to the Spike RBD to binding of antibodies +using a yeast surface display system.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom_bind"> +S RBD Deep Mutational Scanning: ACE2 Binding</a> - This track shows deep mutational scanning +data measuring effect of all possible point (amino acid) RBD mutations on ACE2 binding +affinity using a yeast surface display system.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=Starr_Bloom"> +S RBD Deep Mutational Scanning: Expression</a> - This track shows deep mutational scanning +data measuring effect of all possible point (amino acid) RBD mutations on protein expression +using a yeast surface display system.</li></ul></li></ul> +<ul> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=problematicSites"> +Updated - Problematic sites where masking or caution are recommended for analysis</a> +- This track shows locations in the SARS-CoV-2 genome that have been identified as +problematic for analysis for various reasons. The data was updated to the most recent +release from July 29th.</li> +<li> +<a target="_blank" href="/cgi-bin/hgTrackUi?db=wuhCor1&c=NC_045512v2&g=sarsCov2Phylo"> +Updated - Phylogenetic Tree and Variants from High-coverage Sequences in GISAID EpiCoV TM</a> +- This track displays a phylogenetic tree inferred from SARS-CoV-2 genome sequences +collected by GISAID, and variants found in the sequences. It has now been updated to +sarscov2phylo 28-08-20 release.</li></ul><br> + +<p> +We would like to thank the publication authors <a +href="https://virological.org/t/issues-with-sars-cov-2-sequencing-data/473" +target="_blank">De Maio <em>et al</em></a>, <a href="https://www.pnas.org/content/117/26/15193" +target="_blank">Gussow <em>et al</em></a>, <a +href="https://observablehq.com/@spond/natural-selection-analysis-of-sars-cov-2-covid-19" +target="_blank">Pond <em>et al</em></a>, <a href="https://pubmed.ncbi.nlm.nih.gov/32841599/" +target="_blank">Starr <em>et al</em></a>, <a href="https://www.biorxiv.org/content/10.1101/2020.07.07.192732v1" +target="_blank">Sun <em>et al</em></a>, and <a href="https://www.biorxiv.org/content/10.1101/2020.06.08.141127v1" +target="_blank">Turakhia <em>et al</em></a> for making these data available. +We would also like to thank <a href="http://www.robertlanfear.com/" target="_blank"> +Rob Lanfear</a>, <a href="https://www.biorxiv.org/content/10.1101/2020.06.02.130955v1" +target="_blank">Irwin Jungreis</a>, <a href="http://zhanglab.net/" target="_blank"> +Qiangfeng Cliff Zhang</a>, <a href="http://public.gi.ucsc.edu/~jferna10/" target="_blank"> +Jason Fernandes</a>, <a href="https://snerli.wordpress.com/about/" target="_blank"> +Santrupti Nerli</a>, <a href="https://www.lji.org/faculty-research/labs/peters/#overview" +target="_blank">Bjoern Peters</a>, +the <a href="https://research.fhcrc.org/bloom/en.html" +target="_blank">Bloom Lab</a>, the <a href="https://www.weizmann.ac.il/pages/" +target="_blank">Weizmann Institute of Science</a> and the <a href="https://gisaid.org/" +target="_blank">GISAID Initiative</a>.</p> +<p> +These tracks are made possible due to the worldwide efforts of scientists, including the +<a href="/staff.html" target="_blank">Genome Browser team</a>. Will will continue to +provide SARS-COVID-2 resources as they become available. For the latest data, see our +<a href="http://genome-preview.soe.ucsc.edu/cgi-bin/hgTracks?db=wuhCor1&position=lastDbPos" +target="_blank">development site</a>. Note that content on our preview server has not +undergone our QA process, and is subject to change at any time.</p> + <a name="101520"></a> <h2>Oct. 15, 2020 Updated Ensembl gene tracks for 47 assemblies (v101)</h2> <p> We are pleased to announce an update to the <a href="http://uswest.ensembl.org/info/genome/genebuild/index.html" target="_blank"> Ensembl gene annotation</a> tracks to <strong>v101</strong> for the following assemblies:</p><br> <div class="container"> <div class="row"> <div class="col-sm-4"> <ul> <li>Armadillo <a href="../cgi-bin/hgTrackUi?db=dasNov3&g=ensGene" target=_blank>(dasNov3)</a></li> <li>Baboon <a href="../cgi-bin/hgTrackUi?db=papAnu4&g=ensGene" target=_blank>(papAnu4)</a></li>