dc8dfaf0aa08855d2f8351b872797527f03480a5 gperez2 Wed Aug 6 17:27:19 2025 -0700 Updating the panelApp description page, refs #35758 diff --git src/hg/makeDb/trackDb/human/panelApp.html src/hg/makeDb/trackDb/human/panelApp.html index 5ba168529d3..cfc2936b7dd 100644 --- src/hg/makeDb/trackDb/human/panelApp.html +++ src/hg/makeDb/trackDb/human/panelApp.html @@ -1,49 +1,49 @@ <h2>Description</h2> <p> The PanelApp tracks show regions that are related to human disorders. These can be either -genes, short tandem repeats or copy number variants. The regions were curated by groups of +genes, short tandem repeats, or copy number variants. The regions were curated by groups of specialists collaborating using the PanelApp web tool. The primary website is <a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!">Genomics England PanelApp</a>. Another deployment of the website, with different data, is <a target=_blank href="https://panelapp-aus.org/">PanelApp Australia</a>. </p> <p> Originally, PanelApp was developed to aid interpretation of participant genomes in the <a href="https://www.genomicsengland.co.uk/initiatives/100000-genomes-project" target="_blank"> -100,000 Genomes Project</a>, -<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!">Genomics England PanelApp</a> now being used as the platform for -achieving consensus on gene panels in the <a target="_blank" +100,000 Genomes Project</a>. +<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!">Genomics England PanelApp</a> +is now being used as the platform for achieving consensus on gene panels in the <a target="_blank" href="https://www.england.nhs.uk/genomics/nhs-genomic-med-service/"> NHS Genomic Medicine Service (GMS)</a>. Later, the same platform was also deployed by <a target=_blank href="https://www.australiangenomics.org.au/tools-and-resources/panelapp-australia/">Australian Genomics</a>. </p> <p> <a href="https://panelapp.genomicsengland.co.uk/panels/entities/" target="_blank">Genes and genomic entities</a>, so short tandem repeats/STRs and copy number variants/CNVs, have been reviewed by experts to enable a community consensus to be reached on which genes and genomic entities should appear on a <b>diagnostics grade panel</b> for each disorder. A <b>rating system</b> (confidence level 0 - 3) is used to classify the level of evidence supporting association with phenotypes covered by the gene panel in question. </p> <p> -There are six subtracks in total: Three different types (genes, STRs and CNVs) and these +There are six subtracks in total: Three different types (genes, STRs, and CNVs), and these three exist for both countries, England and Australia. The three types of tracks are:</p> <ul> <li> <b>PanelApp Genes (PanelApp Genes):</b> <br> shows genes with evidence supporting a gene-disease relationship. </li> <br> <li> <b>PanelApp STRs (PanelApp STRs):</b> <br> shows short tandem repeats that can be disease-causing when a particular number of repeats is present.</li> <br> @@ -99,63 +99,64 @@ <a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!FAQs">FAQs</a>. </p> <h2>Data Access</h2> <p> The raw data can be explored interactively with the <a target="_blank" href="/cgi-bin/hgTables">Table Browser</a> or the <a target="_blank" href="/cgi-bin/hgIntegrator">Data Integrator</a>. For automated analysis, the data may be queried from our <a target="_blank" href="/goldenPath/help/api.html">REST API</a>. </p> <p> For automated download and analysis, the genome annotation is stored in a bigBed file that can be downloaded from <a href="http://hgdownload.soe.ucsc.edu/gbdb/$db/panelApp/" target="_blank">our download server</a>. -The files for this track are called <tt>genes.bb</tt>, <tt>tandRep.bb</tt> and <tt>cnv.bb</tt>. Individual -regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt> +The files for this track are called <tt>genes.bb</tt>, <tt>tandRep.bb</tt>, and <tt>cnv.bb</tt>. Individual +regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads">here</a>. The tool can also be used to obtain only features within a given range, e.g. <tt>bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/$db/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p> <p> Please refer to our <a target="_blank" href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"> mailing list archives</a> for questions, or our <a target="_blank" href="/FAQ/FAQdownloads.html#downloads36"> Data Access FAQ</a> for more information. </p> <p> Data is also freely available on the <a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!API">Genomics England PanelApp API</a> and the <a target=_blank href="https://panelapp-aus.org/api/docs/">Australia PanelApp API</a>. </p> <h2>Updates and archiving of old releases</h2> <p> This track is updated automatically every week. If you need to access older releases of the data, -you can download them from our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/panelApp/">archive directory</a> on the download server. To load them into the browser, select a week on the archive directory, copy the link to a file, go to <a href="http://genome.ucsc.edu/cgi-bin/hgCustom">My Data > Custom Tracks</a>, click "Add custom track", paste the link into the box and click "Submit". +you can download them from our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$db/panelApp/">archive directory</a> on the download server. To load them into the browser, select a week on the archive directory, copy the link to a file, go to <a href="http://genome.ucsc.edu/cgi-bin/hgCustom">My Data > Custom Tracks</a>, click "Add custom track", paste the link into the box, and click "Submit". </p> <h2>Methods</h2> <p> PanelApp files were reformatted at UCSC to the <a target="_blank" href="/goldenPath/help/bigBed.html">bigBed</a> format. The script that updates the track is called -<tt>updatePanelApp</tt> and can be found in our <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/utils/otto/panelApp">Github repository</a>. +<tt>doPanelApp.py</tt> and can be found in our <a target="_blank" +href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/utils/otto/panelApp/doPanelApp.py">GitHub repository</a>. </p> <h2>Credits</h2> <p> Thank you to Genomics England PanelApp, especially Catherine Snow for technical coordination and consultation, and Zornitza Stark from Australia PanelApp. Thanks to Beagan Nguy, Lou Nassar, Christopher Lee, Daniel Schmelter, Ana Benet-Pagès and Maximilian Haeussler of the Genome Browser team for the creation of the tracks. </p> <h2>Reference</h2> <p> Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E <em>et al</em>.