Description
The
Genomics England PanelApp
tracks show gene panels that are related to human disorders. Originally developed to
aid interpretation of participant genomes in the
100,000 Genomes Project, PanelApp is now also being used as the platform for
achieving consensus on gene panels in the
NHS Genomic Medicine Service (GMS).
As panels in PanelApp are publicly available, they can also be used by other groups
and projects. Panels are maintained and updated by
Genomics England curators.
Genes and genomic
entities (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 diagnostics grade panel for each disorder.
A rating system (confidence level 0 - 3) is used to classify the level of evidence
supporting association with phenotypes covered by the gene panel in question.
The available data tracks are:
Display Conventions
The individual tracks are colored by confidence level:
- Score 3 (lime green) - High level of evidence
for this gene-disease association. Demonstrates confidence that this gene should be
used for genome interpretation.
- Score 2 (amber) - Moderate evidence
for this gene-disease association. This gene should not be used for genomic
interpretation.
- Score 0 or 1 (red) - Not enough evidence
for this gene-disease association. This gene should not be used for
genomic interpretation.
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
FAQs.
Data Access
The raw data can be explored interactively with the
Table Browser or the
Data Integrator.
For automated analysis, the data may be queried from our
REST API.
For automated download and analysis, the genome annotation is stored in a bigBed file that
can be downloaded from
our download server.
The files for this track are called genes.bb, tandRep.bb and cnv.bb. Individual
regions or the whole genome annotation can be obtained using our tool bigBedToBed
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
here.
The tool
can also be used to obtain only features within a given range, e.g.
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg38/panelApp/genes.bb -chrom=chr21 -start=0 -end=100000000 stdout
Please refer to our
mailing list archives for questions, or our
Data Access FAQ for more information.
Data is also freely available on the
PanelApp API.
Updates and archiving of old releases
This track is updated automatically every week. If you need to access older releases of the data,
you can download them from our archive directory 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 My Data > Custom Tracks, click "Add custom track", paste the link into the box and click "Submit".
Methods
PanelApp files were reformatted at UCSC to the bigBed format. The script that updates the track is called
updatePanelApp and can be found in our Github repository.
Credits
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.
Reference
Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR,
Gerasimenko O, Haraldsdottir E et al.
PanelApp crowdsources expert knowledge to establish consensus diagnostic gene panels.
Nat Genet. 2019 Nov;51(11):1560-1565.
PMID: 31676867
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