The HEAP project is made up of 12 Work Packages
Lead partner: Karolinska Institutet
Successfully delivering HEAP
The objective of the Management Work Package (WP1) is to successfully deliver the HEAP project on schedule and within budget. Another important outcome is to support the development of collaborative networks, or Project Clusters, between the institutions and individuals delivering HEAP and other European Human Exposome Network projects.
To deliver the project objectives, the Project Coordinator, Professor Joakim Dillner, based at Karolinska Institutet, will lead and oversee a series of workstreams, including Strategic, Financial and Legal, Innovation, Work Package Coordination, Quality, and Risk Management.
Ethical, legally compliant handling of patient data
The Ethics and Regulations Work Package (WP2) will develop the HEAP ethical and governance framework to ensure that data are handled legally and in line with the expectations of patients and the public. This will allow data to be shared under controlled and ethical conditions and in compliance with all regulations, including GDPR.
Lygature will work with other European institutions to share best practices and lessons learned about the legal and ethical challenges associated with big data projects. The aim is to reach a pan-European consensus on big data processing for better health care.
Lead partner: Pirkanmaa Hospital District
Populating the HEAP Information Commons with data
The focus of this Work Package is to populate the HEAP Information Commons with data from large sample cohorts. This will provide a comprehensive, reliable and customizable infrastructure for assessing the impacts of the exposome. The data encompass both environmental and healthcare-related exposures.
This Work Package will harmonize biospecimen (serum or cell sample) data from the world’s largest population-based cohorts and integrate this within HEAP.
Lead partner: Statens Serum Institut
New insights into the exposome of everyday purchases
Lead partner: Karolinska Institutet
A pioneering approach to gathering and assessing exposome data from wearable sensors
The Exposome Monitoring and Metabolomics Profiling Work Package will develop a framework for data acquisition from wearable sensors and the Internet of Things. It will investigate the impacts of the exposome on the metabolomic profiles of a group of pregnant volunteers, who will wear sensors to provide continuous monitoring of their environmental exposures. These data will be processed using metabolomic profiling, a technique that provides a point-in-time snapshot of an organism’s physiological state.
The technology that powers HEAP
The informatics platform, developed by Hopsworks, will deliver the technology that powers HEAP, offering analytics, machine learning and knowledge management capabilities, and the ability to interpret chronological and causal relationships from big data.
The informatics platform will feature:
- Horizontally scalable data analytics with Spark;
- Stream processing with Kafka and Flink/Spark;
- Deep learning with TensorFlow/PyTorch;
- Developer-friendly tooling (Jupyter/Python/Conda/R) and operations support;
- Back-end Platform as a Service (PaaS) featuring a scalable file system, Hopsworks.
Lead partner: The Medical University of Graz
Cultivating and curating the HEAP Information Commons
In close collaboration with the Ethics and Regulations Work Package (WP2), the Data Interoperability and Sharing Work Package (WP7) will make the data in the HEAP Information Commons Findable, Accessible, Interoperable and Reusable (FAIR).
WP7 will also help to connect, link and integrate data sets, both within HEAP and to external sources, to ensure sustainability of data formats, identifiers and data access procedures.
Lead partner: University of Innsbruck
Exploring the link between the exposome and epigenetics
The Epigenomic Analysis Work Package (WP8) will use the data collected as part of the data cohort studies (WP3) to analyse the epigenome to identify alterations triggered by environmental exposures. The study will consider length of exposure and age, using:
- samples collected as part of the H2020 Foresee project;
- samples from the Karolinska Institutet Clinical Cytology Biobank;
- samples from a cohort both during exposure (i.e. smoking, high body mass index) and a minimum of 6 months after stopping exposure.
Unlocking new insights from metagenomic data
The Metagenomics Analysis Work Package (WP9) will develop a high-performance workflow to analyse metagenomic sequencing datasets. These datasets will be generated from human biospecimens using next-generation sequencing (NGS) technologies. Further outputs of WP9 are:
- algorithms for taxonomic classification of metagenomic sequencing datasets;
- tools, metadata, and ontology for storage and retrieval of patient NGS datasets;
- microbiomic profiles for the HEAP Information Commons;
- an assessment of the risks of developing specific diseases according to microbiomic profiles, genetics and environmental exposures.
Lead partner: CSC – IT Center for Science
Secure management and storage for big data
The Secure Infrastructure for Big Data Work Package (WP10) will develop an Infrastructure as a Service (IaaS) platform for the HEAP Information Commons, to manage and store sensitive data. The platform will provide secure data storage in a cloud environment and allow streaming of remote data for processing through a secure data access mechanism.
Lead partner: The International Agency for Research on Cancer (IARC)
A legacy for HEAP through training and communication
The Education and Dissemination Work Package (WP11) will produce and disseminate knowledge and information about HEAP to project partners and the wider scientific community.
Using best practices from previous EU projects, in particular the B3Africa biobanking project, the IARC Education and Training Group (ETR) will plan and implement training activities (tutorials and online and on-site training sessions) to support data providers within the consortium to effectively upload data to HEAP, in compliance with the HEAP data model and the ethical and legal framework.
Another objective is to produce and disseminate learning and communications material to encourage and support European scientists beyond the consortium to use HEAP for research. This will promote the benefits of using HEAP, and build trust among policy-makers, civil society, and ethical and legal stakeholders, helping to secure a legacy for HEAP as a scientific resource.
Lead partner: Karolinska Institutet
A framework for collaboration and action
The Cluster Activities Work Package (WP12) will establish the European Human Exposome Network, linking HEAP and the other 8 projects funded by EU Horizon. This will serve as a framework for long-term, collaborative working relationships and knowledge sharing between project partners. Over the life of the project, WP12 will launch:
- an external Network Advisory Board (NAB) to support the development and implementation of a communication and dissemination strategy for the European Human Exposome Network;
- a joint strategy on translating scientific evidence to policy and action;
- a series of European Human Exposome Network conferences.