e9934975b34d714a60fefb524c24d8d42a617863 Merge parents e3d6014 0bb5fe7 dschmelt Wed Mar 16 11:35:35 2022 -0700 Resolving merge refs #29100 diff --cc src/hg/makeDb/trackDb/human/panelApp.html index 8a2f1f4,66fc8ad..46affa4 --- src/hg/makeDb/trackDb/human/panelApp.html +++ src/hg/makeDb/trackDb/human/panelApp.html @@@ -1,91 -1,92 +1,92 @@@ <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 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> - Genes and genomic entities (short tandem repeats/STRs and copy number variants/CNVs) + <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"--> <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> <p> -Mouseover on items shows the gene name, confidence level, mode of inheritance -(if known) and phenotypes related to the gene. supporting evidence of -dosage sensitivity. Tracks can be filtered according to the confidence +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 -<a target="_blank" href="https://panelapp.genomicsengland.co.uk/#!FAQs">PanelApp FAQs</a>. +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="https://genome.ucsc.edu/cgi-bin/hgTables">Table Browser</a> or the - <a target="_blank" href="https://genome.ucsc.edu/cgi-bin/hgIntegrator">Data Integrator</a>. + <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="https://genome.ucsc.edu/goldenPath/help/api.html">REST API</a>. + <a target="_blank" href="/goldenPath/help/api.html">REST API</a>. 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="https://genome.ucsc.edu/FAQ/FAQdownloads.html#downloads36"> + <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>Methods</h2> <p> PanelApp files were reformatted at UCSC to the <a target="_blank" - href="https://genome.ucsc.edu/goldenPath/help/bigBed.html">bigBed</a> format. + href="/goldenPath/help/bigBed.html">bigBed</a> format. </p> <h2>Credits</h2> <p> Thank you to Genomics England PanelApp, especially Catherine Snow for technical - coordination and consultation, and to Beagan Nguy, Christopher Lee, Daniel Schmelter - and Anna Benet-Pages of the Genome Browser team. + 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. </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>