Genomics England launches tool to crowdsource rare disease gene panels

9 September 2015

A new tool from Genomics England offers a crowdsourcing resource for sharing rare disease genomics knowledge – in the form of an app.

The newly launched PanelApp is publicly available and allows all users to view gene panels (sets of genetic variants that have previously been linked with specific rare conditions). Experts in clinical genomics can also register as a reviewer to provide evaluations of those gene panels.

Genomics England is the NHS-owned company charged with leading and delivery of the 100,000 Genomes Project (100KGP). Their Lead Scientific Curator Dr Ellen McDonagh called for experts to contribute their knowledge via the PanelApp, saying

“We’ve developed the PanelApp to crowd source knowledge of genetic testing for rare diseases and provide a tool for experts to utilise. We are encouraging those with an expertise in rare disease genetics to register to be a reviewer. We’d like experts to help finalise the list of genes that can be used to help diagnose a rare disease”. 

Rare diseases are one of two main areas of focus for the 100kGP, along with cancer. Patients are being recruited to the project with over 120 different rare diseases, the underlying causes of which remain unknown or uncertain. It is hoped that an underlying genetic cause will be pinpointed in some cases, but all of them will contribute to wider research into the genetic basis of rare diseases. Making a formal genetic diagnosis can help inform patients, families and their doctors about treatment and management choices.

The 100kGP gene panels comprise lists of genetic variants potentially associated with each different clinical condition. They were created using publicly available resources from the UK Genetic Testing Network (UKGTN), as well as the Illumina TruGenome Predisposition Screen, the Emory Genetic Laboratory and the Radboud University Medical Center. Now expert input is sought to review them and supply evidence that variants are (or are not) linked with the disease.

Using evidence to improve genetic testing is an important part of clinical genomics, where so much remains to be discovered about genetics and disease. Whilst some genetic variants are agreed by experts to be definitely disease causative (known pathogenic) or not (known benign), many others would fall into interim categories as probably or possibly pathogenic or benign. As more evidence emerges it will become possible to move some of these uncertain genetic variants into known categories as likely to be linked with disease or not. Genomics England’s new PanelApp will allow existing and new evidence for these ‘research grade’ (uncertain) gene variants to be collected and assessed.

It is also intended to be easy to use and to encourage movement in the clinical research community towards increased and ongoing standardisation of gene panels, something that professionals have themselves worked to develop. The app seeks ratings to identify those genes for which there is strong evidence of association with a disease, sufficient to justify a diagnostic report being returned to clinicians and patients.