f94190412d16ea558ace1ec9ea175db39aaa104b
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Fri Sep 30 08:40:43 2022 -0700
panelApp otto job, refs #25568
diff --git src/hg/makeDb/trackDb/human/panelApp.html src/hg/makeDb/trackDb/human/panelApp.html
index 46affa4..9508b66 100644
--- src/hg/makeDb/trackDb/human/panelApp.html
+++ src/hg/makeDb/trackDb/human/panelApp.html
@@ -1,42 +1,59 @@
<h2>Description</h2>
<p>
The
<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!">Genomics England PanelApp</a>
-tracks show virtual gene panels related to human disorders. Originally developed to
+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.
<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)
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>
-<!--#insert file="$db/panelAppTracks.html"-->
+<ul>
+ <li>
+ <b>Genomics England PanelApp Genes (PanelApp Genes):</b>
+ <br>
+ shows genes with evidence supporting a gene-disease relationship.</li>
+ <br>
+ <li>
+ <b>Genomics England 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>
+ <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>
@@ -45,48 +62,70 @@
Mouseover on items shows the gene name, panel associated, mode of inheritance
(if known), phenotypes related to the gene, and confidence level. Tracks can
be filtered according to the confidence
level of disease association evidence. For more information on
the use of this data, see the PanelApp
<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>
+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/$db/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout</tt></p>
+
+<p>
Please refer to our
<a target="_blank" href="https://groups.google.com/a/soe.ucsc.edu/forum/#!forum/genome">
mailing list archives</a> for questions, or our
<a target="_blank" href="/FAQ/FAQdownloads.html#downloads36">
Data Access FAQ</a> for more information.
</p>
<p>
Data is also freely available on the
<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!API">PanelApp API</a>.
</p>
+<h2>Updates and archiving of old releases</h2>
+<p>
+This track is updated automatically every week. If you need to access older releases of the data,
+you can download them from our <a href="https://hgdownload.soe.ucsc.edu/goldenPath/archive/$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.
+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,
-and Ana Benet-Pagès of the Genome Browser team for the creation of the tracks.
+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>