Panel App Archives - Gen9 Genetics
Read our new publication in the American Journal of Human Genetics highlighting the benefits of using the PanelApp platform in harmonizing gene and panel curation efforts in collaborative healthcare systems.
We are pleased to announce the launch of the NHS Genomic Medicine Service (GMS) Panels Resource, which provides an overview of the 173 signed panels related to genomic testing listed in the NHS National Genomic Test Directory. This platform contains only 'Green' (diagnostic level of evidence) genes, STRs and regions (CNVs) approved for diagnostic testing in the NHS in England and is intended for use by NHS users and clinicians.
The main Genomics England PanelApp knowledge base here will be for use by the wider scientific community for visualization and assessment of genes/genomic entities on virtual gene panels and will be further updated by Genomics England curators.
For more information on the review and approval process of the content of GMS-signed panels, please refer to the update to the NHS National Genomic Test Directory webpage.
Click here to go to the NHS GMS Panels Resource
What is PanelApp?
Genomics England PanelApp is a publicly available knowledge base that enables the creation, storage and retrieval of virtual gene panels related to human disorders. It includes a crowdsourcing tool that allows genes and genomic entities (short tandem repeats/STRs and copy number variants/CNVs) to be added or reviewed by experts in the global scientific community, providing an opportunity for the standardization of gene panels and a consensus on which genes provide sufficient evidence have for disease association.
Diagnostic 'green' genes/genomic entities and their modes of inheritance are used in the interpretation of the genome. Originally developed to facilitate the interpretation of the genomes of participants in the 100,000 Genomes Project, PanelApp is now also used as a platform for consensus building on gene panels in the NHS Genomic Medicine Service (GMS). Because panels in PanelApp are publicly available, they can also be used by other groups and projects.
Types of PanelApp Gene Panels
A ‘Panel Type’ is assigned to each PanelApp panel that denotes what the gene panel is utilised for. Panels may have more than one panel type, for example when the panel was created for both the 100,000 Genomes Project and the NHS Genomic Medicine Service. Current panel types are:
Rare Disease 100K: a gene panel used for the Rare Disease programme of the 100,000 Genomes Project.
Cancer Germline 100K: a gene panel used for the Germline Cancer programme of the 100,000 Genomes Project.
GMS Rare Disease: a panel developed for the NHS Genomic Medicine Service; may be delivered by whole exome sequencing, whole genome sequencing, or as a ‘wet lab’ panel.
GMS Rare Disease Virtual: a panel developed for the NHS Genomic Medicine Service; will be used as a virtual panel for whole genome sequencing.
GMS Cancer Germline Virtual: a panel developed for the NHS Genomic Medicine Service for analysis of germline cancer susceptibility from whole genome sequencing (WGS).
Super Panel: A panel made up of two or more component panels. When the component panels are updated, the Super panel is automatically updated.
Component of Super Panel: A panel that is a constituent of a Super panel. Changes to this panel will automatically update the Super panel.
Actionable: A panel containing actionable information related to genes or genomic entities, such as clinical trial information.
Research: A panel from a research project.
External Diagnostic Lab: a gene panel from a diagnostic lab or other source, external to Genomics England and not directly used for genome analysis for the 100,000 Genomes Project or NHS Genomic Medicine Service.
How Gene Panels were Defined and Created for the 100,000 Genomes Project
For the 100,000 Genomes Project, gene panels are mapped to one or more recruitment categories, indicated by the gene panel name (Level 4 Title) and/or listed under ‘relevant disorders’ for each panel in PanelApp.
For the 100,000 Genomes Rare Disease programme, gene panels are created in the following steps:
An initial gene list is drawn up from established sources (UKGTN, Radboud UMC, Emory Genetic Laboratory and Illumina) and from disease area experts. The initial gene panel created is Version 0.
Expert review of each gene is crowdsourced.
Evaluation of the reviews, further curation and consultation with the Genomics England clinical team results in a finalised panel.
Promotion of the panel to Version 1 allows the panel to be used in the interpretation of participant genomes.
For the 100,000 Genomes Cancer Germline programme, gene panels are created in the following steps:
Initial gene lists with strong clinical evidence conferring susceptibility of clinically-relevant penetrance to the respective tumour type were submitted from the gene lists used in the interpretation pipeline. Initial gene panels are Version 0.
Review, Evaluation and Promotion of the panel as outlined in steps 2-4 for the Rare Disease programme, above.
Note that PanelApp gene panels are not used in interpretation until initial expert review and curation has been completed and the panel has been promoted to Version 1. Before this, panels are viewable and can be reviewed but the rating of genes has not been finalised.