European HPC cloud infrastructure for managing SARS-CoV-2 data in compliance with GDPR

 

The Connecting European SARS-CoV-2 Cohorts to Increase Common and Effective Response to SARS-CoV-2 Pandemic (ORCHESTRA) consortium, led by University of Verona (Italy), brings together key European academic experts and research institutions in infectious diseases, data management and High Performance Computing (HPC) from 26 organizations (extending to 37 partners) from 15 countries. The project aims to create a new pan-European cohort built on existing and new large-scale population cohorts in European and non-European countries to significantly impact on the responsiveness to SARS-CoV-2. The integration and analysis of the very heterogeneous characteristics of SARS-CoV-2 data coming from many different sources such as EHR, retrospective and prospective patient registries, and related ‘omics’ data (incl. genomics, proteomics and transcriptomics) can benefit of data analytics enabled by HPC, where both high compute performance and fast storage capabilities are immensely important. During the first year of the project, a dedicated HPC cloud infrastructure have been designed and partially deployed to fulfill the functional requirements for data management ensuring healthcare data confidentiality/privacy, integrity and security in compliance with the European GDPR regulations. The result is an infrastructure for Data Management composed by three main layers: National Data Providers; National Hubs (one for each HPC center involved: CINECA - Italy, CINES - France and HLRS - Germany), to centralize data at national level and to support data storage, sharing and analysis on data ingested from the National Data Providers; ORCHESTRA Data Portal: the pan-European portal for sharing aggregated data and results. Currently data collection is on going; at the end of the project, clinical centers are expected to have enrolled more than 10.000 patients with about 50.000 samples for the prospective studies.

Key messages

• The SARS-CoV-2 crisis made evident the need to manage and analyse very heterogeneous health data coming from many different resources across different countries.

• The HPC cloud infrastructure released for the Orchestra project can act as a model to manage future public health threats.

The 'Survivorship Passport' for childhood cancer survivors

BACKGROUND

Currently, there are between 300,000 and 500,000 childhood cancer survivors (CCSs) in Europe. A significant proportion is at high risk, and at least 60% of them develop adverse health-related outcomes that can appear several years after treatment completion. Many survivors are unaware of their personal risk, and there seems to be a general lack of information among healthcare providers about pathophysiology and natural history of treatment-related complications. This can generate incorrect or delayed diagnosis and treatments.

METHOD

The Survivorship Passport (SurPass) consists of electronic documents, which summarise the clinical history of the childhood or adolescent cancer survivor. It was developed by paediatric oncologists of the PanCare and SIOPE networks and IT experts of Cineca, together with parents, patients, and survivors' organisations within the European Union-funded European Network for Cancer research in Children and Adolescents. It consists of a template of a web-based, simply written document, translatable in all European languages, to be given to each CCS. The SurPass provides a summary of each survivor's clinical history, with detailed information about the original cancer and of treatments received, together with personalised follow-up and screening recommendations based on guidelines published by the International Guidelines Harmonization Group and PanCareSurFup.

RESULTS

The SurPass data schema contains a maximum of 168 variables and uses internationally approved nomenclature, except for radiotherapy fields, where a new classification was defined by radiotherapy experts. The survivor-specific screening recommendations are mainly based on treatment received and are automatically suggested, thanks to built-in algorithms. These may be adapted and further individualised by the treating physician in case of special disease and survivor circumstances. The SurPass was tested at the Istituto Giannina Gaslini, Italy, and received positive feedback. It is now being integrated at the institutional, regional and national level.

CONCLUSIONS

The SurPass is potentially an essential tool for improved and more harmonised follow-up of CCS. It also has the potential to be a useful tool for empowering CCSs to be responsible for their own well-being and preventing adverse events whenever possible. With sufficient commitment on the European level, this solution should increase the capacity to respond more effectively to the needs of European CCS.