PhenoMeNal: The gateway to individually adapted medication
10 September 2015
The first of September is the start-up date for PhenoMeNal. This is an international research project which aims to establish a secure e-infrastructure for clinical metabolomics. One of the project’s work packages will be led by Uppsala University and SciLifeLab. Together, they will be responsible for setting up the cloud-based e-infrastructure to serve as the basis for the project work.
Metabolome is a concept which in principle includes all the smaller molecules to be found in an individual person, e.g. in the blood, at a certain time and in a certain situation. These molecules may comprise, for example, metabolic products and substances which control our metabolism. They may also include small molecule fats, various hormones and other substances which may be secreted during an inflammation or other medical condition. The study of metabolomes at the individual level is called metabolomics.
The consortium now starting up the PhenoMeNal project consists of 13 partners. It is being co-ordinated from EMBl-EBI in England and financed by ca. eight million euros from EU Horizon 2020. The e-infrastructure will make it possible to analyse large amounts of metabolomic and genetic data, thus improving our ability to discover, treat and manage illnesses.
A large number of EU citizens are expected to have their genomes sequenced and included in their medical records in the next decade. However, understanding environmental and genetic factors which affect people’s health is crucial to providing evidence-based treatment. Co-ordinating genetic and metabolomic data with other factors which affect a patient’s health is a way to gather a large amount of this very dynamic information at a relatively low cost. The amount of data generated, however, is so enormous that the existing e-infrastructure cannot cope with it.
'We are facing major challenges in standardising how researchers can access and analyse such great volumes of data,' says Ola Spjuth of the Department of Pharmaceutical Biosciences at Uppsala University who is leading one of the work packages within the project.
The main purpose of PhenoMeNal is to develop and distribute a portal and an e-infrastructure which allows researchers and care providers to process and analyse medical molecular phenotyping and genotyping data using powerful computers. This also requires developing and standardising data formats, software and data analysis flows with a major emphasis placed upon security and scalability.
Kim Kultima is leading a group of clinical metabolomics researchers at the Department of Medical Sciences at Akademiska sjukhuset (University Hospital). He is responsible for the newly started CARAMBA programme, run in close collaboration between Uppsala University and Akademiska sjukhuset. It is aimed at applying new research discoveries to routine analysis of patient samples in order to improve diagnostics.
'Clinical metabolomics has great potential for use in routine analysis. However, we are badly in need of a scalable e-infrastructure adapted to clinical applications. This will help us manage and analyse large amounts of data so that we can quickly provide clinically relevant results,' says Kim Kultima.
The work on the PhenoMeNal cloud-based e-infrastructure will be done in consultation with the European Grid and Cloud infrastructure as well as national, European and international initiatives. The aim is to put in place an end product which can be used on a global scale.
'We are strong both at Uppsala University and within SciLifeLab which has a world-leading position in the field of large-scale biological data analysis. We will be responsible for setting up the cloud-based e-infrastructure which will form the basis of the work on Phenomenal,' says Ola Spjuth.
Science for Life Laboratory (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource and a collaboration between four universities: Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University.