FutureTech: Project update Gene-ius project to help rare disease diagnosis An innovative project with the potential to help identify, diagnose and treat people with rare diseases in the UK won a £400,000 grant earlier this year. Now almost halfway through the project, Mark Avery, Director of Health Informatics for Eastern AHSN and Cambridge University Health Partners, explains more “I think that this is a really exciting project that will make it much easier for researchers to help other people like me with rare diseases. I am also reassured that there is a really strong emphasis on keeping our information secure and to prevent individuals from”being identifiable Debbie, a rare disease patient from London patients, an average difference of £7,000 more per patient per year. At the end of last year, we led a piece of work with the NIHR BioResource – a national resource of volunteers who have provided consent for information retrieved from their health records to be used for medical research – to apply for funding to develop a proof of concept project that would link NHS care pathway data to genetic data. Debbie, from London, who is affected by a rare disease, explains: ‘To really understand a rare disease – what causes it and how to diagnose, treat or prevent it – researchers need access to as much relevant information on as many patients as possible.’ So, in January, we were delighted to be told we had won our bid for £400,000. All we had to do was deliver it. We are now five months into the Rare Diseases Sprint Exemplar Innovation Project and we have been designing and building the architecture to process 1,600 patients’ records across three rare disease areas and five NHS Trusts in Cambridge, Liverpool, Leeds and Newcastle. We have tested each step with small volumes of dummy data, and are now in the process of transferring the NHS data to a secure environment within the NHS firewall provided by AIMES and managed by the informatics team at the BioResource. Professor John Bradley , Director of NIHR Cambridge Biomedical Research Centre and Co-chair of NIHR BioResource, explains: ‘Recent advances in clinical imaging, pathology, and genomic technologies have led to remarkable progress One in 17 people will be affected by a rare disease in their lifetime, but because they are rare, they can be extremely difficult to diagnose – a process that sometimes takes years. At least 80 per cent of rare diseases have a genetic component, but for many this has not yet been defined and the disease mechanism remains unknown. This means rare diseases are still often not being diagnosed, treated or supported effectively. The delay, uncertainty and deterioration while waiting for an effective treatment to be identified has an untold impact on patients and their families. In addition to the human impact, this also represents a significant financial burden on the NHS. The cost of an undiagnosed rare disease patient is more than twice that of other in understanding disease – particularly rare diseases. However, the power of these technologies cannot be fully realised until the immense volume of data generated can be integrated with NHS data, then analysed by researchers in a secure environment that protects the privacy of individuals.’ Over the next few months, we will show how the data can be transformed to get it into a common format and then merged. Specific use case datasets will be de-identified using a tool developed by specialist data privacy engineering company Privitar and transferred to a secure cloud platform provided by Microsoft Azure. There they will be matched to the patient’s genetic data, demonstrating the capability to deliver an immensely rich research resource with the potential to transform our understanding of rare genetic disorders, drive improvements in diagnosis and management and provide proof of principle for use in other diseases. Debbie adds: ‘I think that this is a really exciting project that will make it much easier for researchers to help other patients like me with rare diseases. I am also reassured that there is a really strong emphasis on keeping our information secure and preventing individuals from being identifiable.’ Our first use case, a combined dataset focusing on blood count and genetic signatures for patients with bleeding and blood platelet disorders, is on track for delivery in autumn 2019. Building on our rare diseases project, we are now applying for further funding to apply these methods and data architecture to a large-scale common disease area – inflammatory bowel disease (IBD). Crohn’s Disease and ulcerative colitis are the main forms of IBD. They cause debilitating symptoms affecting 0.78 per cent of the UK population (500,000 people), and cost UK health budgets approximately £1.5 billion each year. Treatment is with steroids, immunosuppressants and antibody therapies, but results are variable. More than 70 per cent of patients with Crohn’s and 15 per cent with colitis require major surgery. There is an urgent need to better understand why patients respond differently to treatments in order to improve outcomes and reduce costs. This proof of concept project, from initial development and funding application, through to project delivery is being led by Mark Avery, Director of Health Informatics for Cambridge University Health Partners and Eastern AHSN. The rare diseases sprint project is funded through the UK Research and Innovation Industrial Strategy Challenge Fund (ISCF) as part of the Health Data Research UK (HDR UK) led Digital Innovation Hub programme. An innovative project with the potential to help identify, diagnose and treat people with rare diseases in the UK won a £400,000 grant earlier this year. Now almost halfway through the project, Mark Avery, Director of Health Informatics for Eastern AHSN and Cambridge University Health Partners, explains more “I think that this is a really exciting project that will make it much easier for researchers to help other people like me with rare diseases. I am also reassured that there is a really strong emphasis on keeping our information secure and to prevent individuals from”being identifiable Debbie, a rare disease patient from London patients, an average difference of £7,000 more per patient per year. At the end of last year, we led a piece of work with the NIHR BioResource – a national resource of volunteers who have provided consent for information retrieved from their health records to be used for medical research – to apply for funding to develop a proof of concept project that would link NHS care pathway data to genetic data. Debbie, from London, who is affected by a rare disease, explains: ‘To really understand a rare disease – what causes it and how to diagnose, treat or prevent it – researchers need access to as much relevant information on as many patients as possible.’ So, in January, we were delighted to be told we had won our bid for £400,000. All we had to do was deliver it. We are now five months into the Rare Diseases Sprint Exemplar Innovation Project and we have been designing and building the architecture to process 1,600 patients’ records across three rare disease areas and five NHS Trusts in Cambridge, Liverpool, Leeds and Newcastle. We have tested each step with small volumes of dummy data, and are now in the process of transferring the NHS data to a secure environment within the NHS firewall provided by AIMES and managed by the informatics team at the BioResource. Professor John Bradley , Director of NIHR Cambridge Biomedical Research Centre and Co-chair of NIHR BioResource, explains: ‘Recent advances in clinical imaging, pathology, and genomic technologies have led to remarkable progress One in 17 people will be affected by a rare disease in their lifetime, but because they are rare, they can be extremely difficult to diagnose – a process that sometimes takes years. At least 80 per cent of rare diseases have a genetic component, but for many this has not yet been defined and the disease mechanism remains unknown. This means rare diseases are still often not being diagnosed, treated or supported effectively. The delay, uncertainty and deterioration while waiting for an effective treatment to be identified has an untold impact on patients and their families. In addition to the human impact, this also represents a significant financial burden on the NHS. The cost of an undiagnosed rare disease patient is more than twice that of other in understanding disease – particularly rare diseases. However, the power of these technologies cannot be fully realised until the immense volume of data generated can be integrated with NHS data, then analysed by researchers in a secure environment that protects the privacy of individuals.’ Over the next few months, we will show how the data can be transformed to get it into a common format and then merged. Specific use case datasets will be de-identified using a tool developed by specialist data privacy engineering company Privitar and transferred to a secure cloud platform provided by Microsoft Azure. There they will be matched to the patient’s genetic data, demonstrating the capability to deliver an immensely rich research resource with the potential to transform our understanding of rare genetic disorders, drive improvements in diagnosis and management and provide proof of principle for use in other diseases. Debbie adds: ‘I think that this is a really exciting project that will make it much easier for researchers to help other patients like me with rare diseases. I am also reassured that there is a really strong emphasis on keeping our information secure and preventing individuals from being identifiable.’ Our first use case, a combined dataset focusing on blood count and genetic signatures for patients with bleeding and blood platelet disorders, is on track for delivery in autumn 2019. Building on our rare diseases project, we are now applying for further funding to apply these methods and data architecture to a large-scale common disease area – inflammatory bowel disease (IBD). Crohn’s Disease and ulcerative colitis are the main forms of IBD. They cause debilitating symptoms affecting 0.78 per cent of the UK population (500,000 people), and cost UK health budgets approximately £1.5 billion each year. Treatment is with steroids, immunosuppressants and antibody therapies, but results are variable. More than 70 per cent of patients with Crohn’s and 15 per cent with colitis require major surgery. There is an urgent need to better understand why patients respond differently to treatments in order to improve outcomes and reduce costs. This proof of concept project, from initial development and funding application, through to project delivery is being led by Mark Avery, Director of Health Informatics for Cambridge University Health Partners and Eastern AHSN. The rare diseases sprint project is funded through the UK Research and Innovation Industrial Strategy Challenge Fund (ISCF) as part of the Health Data Research UK (HDR UK) led Digital Innovation Hub programme. Gene-ius project to help rare disease diagnosis