3093b11e9c0b496cbe59c362a6d64a0efd0001ca brianlee Thu Feb 17 14:53:22 2022 -0800 Adding a new announcement about the Track Sets paper by Ana and b0b diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 0b6f549..3f43a68 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -39,30 +39,86 @@ </div> <div class="col-sm-3"> <ul> <li><a href="#2006">2006 News</a></li> <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="#2001">2001</a>-<a href="#2002">2002 News</a></li> </ul> </div> </div> </div> <!-- ============= 2022 archived news ============= --> <a name="2022"></a> + +<a name="022222"></a> +<h2>Feb. 22, 2022 Recommended Track Sets paper</h2> +<p> +We are pleased to announce a new paper about our Recommended Tracks Set feature, available +on GRCh37/hg19, which collects related clinical tracks to help investigate variants. +The <a href="https://doi.org/10.1002/humu.24335" +target="_blank">Variant interpretation: UCSC Genome Browser Recommended Track Sets</a> paper +covers how this new feature can facilitate the interpretation of variants for clinicians.</p> +<p> +Track Sets quickly swap out the on-screen annotations a user may be looking at in current genomic +position for a different dataset relevant to specific medical scenarios: investigating single +nucleotide variants in coding regions (Clinical SNVs), structural copy number variants +(Clinical CNVs), and functional aspects of non-coding variants (Non-coding SNVs).</p> +<p class ="text-center"> + <a href="https://doi.org/10.1002/humu.24335"> + <img class="text-center" src="../images/newsArchImages/track_sets1.png" width="900px"> + </a> +</p> +<p> +To access Recommended Track Sets, only available currently on the hg19 assembly, go to the top blue bar +and under the "Genome Browser" menu click the "Recommended Track Sets" +option. This will launch a dialog box offering pre-configured track sets, enabling swapping from +one view to another view without changing the current position. The displayed tracks can then +be customized, where one can configure tracks in the browser by clicking the grey bar on the +left of a track. Or to see more information about displayed items, one can mouseover for an +informative pop-up summary, or click on the item to access a details page.</p> +<p> +The new paper gives examples of using the experimental data in the Clinical SNV Track Set to examine a variant.</p> +<p class ="text-center"> + <a href="https://doi.org/10.1002/humu.24335"> + <img class="text-center" src="../images/newsArchImages/track_sets2.png" width="900px"> + </a> +</p> +<p> +This image from the paper shows a vertical blue highlight for NM_172107.4(KCNQ2):c.635A>G (p.Asp212Gly). +This variant is located in the KCNQ2 gene, in a codon for Aspartic acid (D212), and the mutation +has been associated with early-onset epileptic encephalopathy, an autosomal dominant inherited +disease. The ClinVar Short Variants and SNVs tracks show that all three possible single nucleotide +substitutions have been described at this position with pathogenic or likely pathogenic +classifications with red blocks (A>C, A>T, A>G). Each described variant leads to a missense +change of the Asp residue. The SNV Track Set also includes computational and predictive components, +such as the Rare Exome Variant Ensemble Learner (REVEL) and Combined Annotation Dependent Depletion +(CADD) tracks, which calculate impacts of nucleotide changes, discussed in another figure in the paper.</p> +<p> +The paper also discusses many of the other features developed with the release of Track Sets, +including the ability to merge items that span a region to declutter the view of CNVs and the +addition of multiple configuration filters to allow users to dynamically generate a subset +view of dense data on categories of interest. Lastly, a far more informative mouseover +was created when viewing clinical data that could combine multiple fields. For instance, +in the ClinVar track, it is now possible to view a variant's HGVS annotation, molecular +consequence, clinical significance, population frequency, and associated phenotypes without +having to click into an item's details page.</p> +<p> +We would like to thank Ana Benet-Pagès and Robert Kuhn for their work publishing this new article.</p> + <a name="021022"></a> <h2>Feb. 10, 2022 GENCODE Genes v39 for human (hg38)</h2> <p> We are happy to announce the release of the <a href="/cgi-bin/hgTrackUi?db=hg38&g=knownGene&c=chrX">GENCODE Genes v39</a> track for the human (<a href="/cgi-bin/hgGateway?db=hg38">GRCh38/hg38</a>) genome assembly. The track includes protein-coding genes, non-coding RNA genes, and pseudo-genes, though pseudo-genes are not displayed by default. It contains annotations on the reference chromosomes as well as assembly patches and alternative loci (haplotypes). </p> <p> <table class="stdTbl"> <tr><th COLSPAN=4 style="text-align:center">GENCODE v39 Release Stats</th></tr> <tr align=left>