cab14fa3bf11dc42ebf6250ee322c9c5e86bcc14 max Thu May 22 03:45:22 2025 -0700 docing panelApp AU, refs #35758 diff --git src/hg/makeDb/trackDb/human/panelApp.html src/hg/makeDb/trackDb/human/panelApp.html index 93cf20b9f2f..1a8b5b0f5e0 100644 --- src/hg/makeDb/trackDb/human/panelApp.html +++ src/hg/makeDb/trackDb/human/panelApp.html @@ -1,63 +1,73 @@ <h2>Description</h2> <p> -The -<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!">Genomics England PanelApp</a> -tracks show gene panels that are related to human disorders. Originally 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>, PanelApp is now also 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>. -As panels in PanelApp are publicly available, they can also be used by other groups -and projects. Panels are maintained and updated by -<a target="_blank" href="https://www.genomicsengland.co.uk/">Genomics England</a> curators. +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 +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" + 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> (short tandem repeats/STRs and copy number variants/CNVs) +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> -The available data tracks are: -</p> +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>Genomics England PanelApp Genes (PanelApp Genes):</b> + <b>PanelApp Genes (PanelApp Genes):</b> <br> shows genes with evidence supporting a gene-disease relationship. <p style="color:red">NOTE: Due to a bug in the PanelApp gene API, between 5 and 20% of gene entries are missing as of 11/2/22.</p> </li> <br> <li> - <b>Genomics England PanelApp STRs (PanelApp STRs):</b> + <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> <li> - <b>Only on hg38: Genomics England PanelApp Regions (PanelApp CNV Regions):</b> + <b>Only on hg38: PanelApp Regions (PanelApp CNV Regions):</b> <br> shows copy-number variants (region-loss and region-gain) with evidence supporting a gene-disease relationship.</li> </ul> + <h2>Display Conventions</h2> <p> The individual tracks are colored by <b>confidence level:</b> <ul> <li><b><font color="#32CD32">Score 3 (lime green)</font></b> - <b>High level of evidence</b> for this gene-disease association. Demonstrates confidence that this gene should be used for genome interpretation.</li> <li><b><font color="#FFBF00">Score 2 (amber)</font></b> - <b>Moderate evidence</b> for this gene-disease association. This gene should not be used for genomic interpretation.</li> <li><b><font color="red">Score 0 or 1 (red)</font></b> - <b>Not enough evidence</b> for this gene-disease association. This gene should not be used for genomic interpretation. </li> </ul> @@ -88,47 +98,50 @@ 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/$db/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p> <p> Please refer to our <a target="_blank" href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome"> mailing list archives</a> for questions, or our <a target="_blank" href="/FAQ/FAQdownloads.html#downloads36"> Data Access FAQ</a> for more information. </p> <p> Data is also freely available on the -<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!API">PanelApp API</a>. +<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!API">Genomics England PanelApp API</a> +and the <a target=_blank href="https://panelapp-aus.org/api/docs/">Australia PanelApp API</a>. </p> <h2>Updates and archiving of old releases</h2> <p> This track is updated automatically every week. If you need to access older releases of the data, you can download them from our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$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". </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>. </p> <h2>Credits</h2> <p> Thank you to Genomics England PanelApp, especially Catherine Snow for technical -coordination and consultation. Thank you to Beagan Nguy, Christopher Lee, Daniel Schmelter, -Ana Benet-Pagès and Maximilian Haeussler of the Genome Browser team for the creation of the tracks. +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>. <a href="https://www.ncbi.nlm.nih.gov/pubmed/31676867" target="_blank"> PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels</a>. <em>Nat Genet</em>. 2019 Nov;51(11):1560-1565. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/31676867" target="_blank">31676867</a> </p>