Periodic Reporting for period 3 - SCREEN4CARE (Shortening the path to rare disease diagnosis by using newborn genetic screening and digital technologies)
Período documentado: 2023-10-01 hasta 2024-09-30
There are over 7000 rare diseases, resulting in 30 million Patients in Europe with Rare Diseases (RD), and globally, 250 million Patients are affected. Being 75% of Rare Diseases (RDs) of genetic origin, genetic diagnosis is compulsory so patients can enter into an appropriate and often personalised path of care. Consequently, less than 10% of persons living With a Rare Disease (PLWRD) receive treatment, and only 1% are managed using an approved treatment in Europe. Achieving early diagnosis and delivering effective treatments for PLWRD, where the prevalence is low, have been described as one of the major global health challenges for the 21st century. Screen4Care (S4C) project aims to accelerate the diagnosis of RDs using a multi-tier strategy based on genetic newborn screening (gNBS) and digital technologies.
WP1 tasks (completed) generated outstanding and comprehensive knowledge about business, regulatory , social, networking and stakeholders' engagement of RDs. The finalized overview of available symptom checkers and related platforms will now feed the symptom checker design in WP5. Twelve papers, 7 events, and 10 conferences were finalized. The forum meeting in Barcelona took place successfully. Chaired by Eurordis, theforum collected parents' experiences of genetic newborn screening pilots, results of the studies across various tasks within WPs.
WP2 aims at establishing a federated infrastructure dedicated to rare disease data by descriptive metadata from data sites which go to federated metadata repository (MDR). WP2 also adapts federated machine learning algorithms to process data related to RDs. During the 3rd year the above objectives were further refined, and the federated metadata repository infrastructure was finalized, while two novel algorithms (interface with WP4) were designed, for the concrete use-cases in WP4. Further, co-creation and adoptability efforts have been commenced to support the work in WP2, 4 and 5. Overall, the research tasks have provided the results expected, as described in detail in the deliverables. Main achievements in this reporting period are : i) the fully advanced metadata repository with technologies and visualization of the metadata tested; ii) the common data model (CDM) and special documentation for neuromuscular diseases; iii) needs identified for open innovation (OI) campaigns to increase the adoptability of the developed technologies.
WP3 has finalized first set of preference studies (paper published). A systematic literature review has been carried out to capture relevant attributes related to newborn screening for rare diseases (paper submitted). The standard operating procedure and the NBS pipeline for the TREAT panel and WGS analysis output were finalized (the TREAT panel gene selection manuscript has been submitted). 56 genes selected for inclusion in the ACT-panel were determined through a systematic process involving extensive consultation with experts, clinicians, patient organizations, Scientific Advisory Board. Ethical application will be submitted by the end of 2024. Technical aspects of the TREAT-panel design have been implemented, TREAT-panel data workflow is in place. The clinical NBS pipeline has been designed for the steps from recruitment to the communication of gNBS results and a pipeline for positive cases to be referred to the specific ERNs was designed. Designing and concept of cost-effectiveness evidence generation of NBS of rare diseases has started.
WP4, activities have ensured a possible repurposing of ML models and have provided insights into data to be used for the early identification of RDs, in neuromuscular diseases, through EHR monitoring by systematic landscape research analysis and by the diagnostic model of MSOT (published). WP4 worked on the implementation the EHR pilots to facilitate integration of recruited patients into the S4C ecosystem. A key issue has revealed to be the EHR-data model definition to be reused for the larger data sets of the German research portal but also to be adopted for other country EHRs. The definition of an agreement to share country-specific data is under development.
WP5 The work in this reporting period has led to the creation of the initial working prototypes of each part of the Screen4Care sustainable Platform, as a Meta-Symptom Checker that delivers value to the patient HCPs and the wider RD community by offering functionality not offered by other existing symptom checkers (as identified via horizon scanning). The meta-platform, the Screen4Care Platform (to be linked to the Screen4Care website in future), provides a first port of call and Best Practice page where patients, families, RD community members and HCPs can consult medically-validated information sources and find recommendations for educational materials in the RD space. Links to other resources, such as those of EURORDIS, will be featured, and lists of existing symptom checkers will be included. The second progress took inspiration from features of the original Screen4Care App developed by UCD, since it operates based on a novel Privacy by Design. Unlike all other existing symptom checkers for RD currently on the market, ours has been specifically designed to keep patient data private to the patient. The data is input by the patient and stored only on the patient’s smart device. Patients can control their symptom-checking journey with functionalities such as input on IOS or Android devices. The Screen4Care app also does not utilise non-medically validated data and offers secure, patient-friendly support tools for input and monitoring of symptoms and curates the symptoms with lay language-medical language translation. UCD also co-developed a new Co-creation Campaign and planned the third and final Focus Group with Eurordis to provide in-depth feedback on the app plans and demos to date.
WP2 aims at establishing a federated infrastructure dedicated to rare disease data by descriptive metadata from data sites which go to federated metadata repository (MDR). WP2 also adapts federated machine learning algorithms to process data related to RDs. During the 3rd year the above objectives were further refined, and the federated metadata repository infrastructure was finalized, while two novel algorithms (interface with WP4) were designed, for the concrete use-cases in WP4. Further, co-creation and adoptability efforts have been commenced to support the work in WP2, 4 and 5. Overall, the research tasks have provided the results expected, as described in detail in the deliverables. Main achievements in this reporting period are : i) the fully advanced metadata repository with technologies and visualization of the metadata tested; ii) the common data model (CDM) and special documentation for neuromuscular diseases; iii) needs identified for open innovation (OI) campaigns to increase the adoptability of the developed technologies.
WP3 has finalized first set of preference studies (paper published). A systematic literature review has been carried out to capture relevant attributes related to newborn screening for rare diseases (paper submitted). The standard operating procedure and the NBS pipeline for the TREAT panel and WGS analysis output were finalized (the TREAT panel gene selection manuscript has been submitted). 56 genes selected for inclusion in the ACT-panel were determined through a systematic process involving extensive consultation with experts, clinicians, patient organizations, Scientific Advisory Board. Ethical application will be submitted by the end of 2024. Technical aspects of the TREAT-panel design have been implemented, TREAT-panel data workflow is in place. The clinical NBS pipeline has been designed for the steps from recruitment to the communication of gNBS results and a pipeline for positive cases to be referred to the specific ERNs was designed. Designing and concept of cost-effectiveness evidence generation of NBS of rare diseases has started.
WP4, activities have ensured a possible repurposing of ML models and have provided insights into data to be used for the early identification of RDs, in neuromuscular diseases, through EHR monitoring by systematic landscape research analysis and by the diagnostic model of MSOT (published). WP4 worked on the implementation the EHR pilots to facilitate integration of recruited patients into the S4C ecosystem. A key issue has revealed to be the EHR-data model definition to be reused for the larger data sets of the German research portal but also to be adopted for other country EHRs. The definition of an agreement to share country-specific data is under development.
WP5 The work in this reporting period has led to the creation of the initial working prototypes of each part of the Screen4Care sustainable Platform, as a Meta-Symptom Checker that delivers value to the patient HCPs and the wider RD community by offering functionality not offered by other existing symptom checkers (as identified via horizon scanning). The meta-platform, the Screen4Care Platform (to be linked to the Screen4Care website in future), provides a first port of call and Best Practice page where patients, families, RD community members and HCPs can consult medically-validated information sources and find recommendations for educational materials in the RD space. Links to other resources, such as those of EURORDIS, will be featured, and lists of existing symptom checkers will be included. The second progress took inspiration from features of the original Screen4Care App developed by UCD, since it operates based on a novel Privacy by Design. Unlike all other existing symptom checkers for RD currently on the market, ours has been specifically designed to keep patient data private to the patient. The data is input by the patient and stored only on the patient’s smart device. Patients can control their symptom-checking journey with functionalities such as input on IOS or Android devices. The Screen4Care app also does not utilise non-medically validated data and offers secure, patient-friendly support tools for input and monitoring of symptoms and curates the symptoms with lay language-medical language translation. UCD also co-developed a new Co-creation Campaign and planned the third and final Focus Group with Eurordis to provide in-depth feedback on the app plans and demos to date.
Massive progress was made during the 3rd year of the S4C project. We have completed all WP1 activities, implemented international collaborations and delivered several S4C papers, abstracts, and contributes to conferences. We have fully established the RD newborn ecosystem landscape analysis, two algorithms were designed to analyze EHRs trained by neuromuscular phenotypes, S4C dataset platform has been fully designed and establishing agreements to maximize data sharing among S3C partners are ongoing. All ethical approvals for NBS are in place, the full NBS data output, clinical, and post-screening pipelines are fully established, the TREAT panel has been designed, synthesized and technically validated, and also symptom checker definition is progressing. S4C i ready to enroll babies (interventional clinical trial already registered on ClinicalTrial.gov) and recruiting will start by the end of 2024. The definition of the precise number of infants who gNBS will screen is 18.000. This is based on the budget available and on the EFPIA partners in-kind contribution. However, S4C is committed to explore other possibilities to increase the number of babies, and/or it has in place corrective actions to keep high/higher number of enrolled babies. During the following 4th year S4C will provide real-life results for NBS, EHRs interoperability and first pilot of symptom checker app, bringing an unprecedented amount of knowledge and consequently benefit to the RD community.