4f1745372c2a56d52df86f6c4f65013ea84ca04e brianlee Tue Feb 22 10:48:05 2022 -0800 Making edits to Track Sets paper announcement after feedback from b0b. diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 3f43a68..2dc11e1 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -45,79 +45,84 @@ <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 +The paper, <a href="https://doi.org/10.1002/humu.24335" +target="_blank">Variant interpretation: UCSC Genome Browser Recommended Track Sets</a>, 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 +Track Sets allow a user to quickly swap out the on-screen annotations they may be looking at +for a different set of tracks 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 +To access Recommended Track Sets, currently available only 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 +one view to another view without changing the current position. Please note this figure does not +include a fourth Track Set, Problematic Regions, we added since the release of the paper. Problematic +Regions help users evaluate if annotations in the Browser are located in areas of the genome of low +confidence due to high homology or other reported concerns. Once displayed, Recommended Track Sets 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> +The paper gives an example 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 +This figure from the paper shows a vertical blue highlight for NM_172107.4(KCNQ2):c.635A>G (p.Asp212Gly), +the Human Genome Variation Society (HGVS) nomenclature to describe this variant. +Located in the KCNQ2 gene, this variant is 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> +change of the Asp residue. The SNV Track Set also includes (discussed in another figure in the paper) +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.</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 +view from dense data on specified 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> +We would like to thank Ana Benet-Pagès and Robert Kuhn for their work publishing the paper, +and Kate Rosenbloom, Ana Benet-Pagès and Lou Nassar for implementation of the feature.</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>