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 Genomics England PanelApp. Another deployment of the website, with different data, is PanelApp Australia.
Originally, PanelApp was developed to aid interpretation of participant genomes in the -100,000 Genomes Project, -Genomics England PanelApp now being used as the platform for -achieving consensus on gene panels in the . +Genomics England PanelApp +is now being used as the platform for achieving consensus on gene panels in the NHS Genomic Medicine Service (GMS). Later, the same platform was also deployed by Australian Genomics.
Genes and genomic entities, 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 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.
-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:
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 +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/$db/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 Genomics England PanelApp API and the Australia PanelApp API.
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". +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".
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. +doPanelApp.py and can be found in our GitHub repository.
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.
Martin AR, Williams E, Foulger RE, Leigh S, Daugherty LC, Niblock O, Leong IUS, Smith KR, Gerasimenko O, Haraldsdottir E et al.