WP1: Clinical network and biobanking
The main objective of the EUCLIDS international clinical network is to maintain, conduct, and regulate the clinical network and biobank. The consortium already holds the most important meningococcal disease (MD) biobank in the world, with more than 2,800 DNA samples and clinical records of children with MD; 2,500 of these samples have already been genotyped. Five thousand new patients will be recruited with the inclusion criteria – patients 0 to 18 years old presenting with a severe bacterial infection- and using the latest state-of-the-art rapid diagnostic facilities .
WP2: Genome-Wide Association Studies of Meningococcal disease
2. To select significant SNPs from the single SNP analysis in each of the cohorts for cross validation among them.
4. To select top hits for each of the GWAS analyses for fine mapping and sequencing of candidate genes, and validation in the prospective meningococcal cohort and in other cohorts with invasive bacterial infections.
5. To undertake fine mapping and validation of hits from Vaccine GWAS performed in WP3.
WP3: Genetic control of the immune response to meningococcal vaccines
The Oxford Vaccine group headed by Professor Pollard carried out initial UK trials of the Men C vaccines. DNA from this large cohort of vaccine recipients, and serum to characterise their responses is maintained in an existing biobank, which will be used for the proposed genetic and functional analyses. The Oxford Vaccine group has also undertaken the immunogenicity studies of candidate serogroup B vaccines under trial, and the DNA and serum from participants in these studies is available. On-going Vaccine study recruitment in months 0-36 will provide the prospective cohorts for RNA expression studies and extreme phenotype studies.
WP4: Identifying functional variation in the DfH region by sequencing
We recently identified the complement factor H (CfH) and CFH-related (CfHR) gene region as strongly associated with meningococcal disease (MD) susceptibility (Davila, Wright et al. Nature Genetics 2010); however the functional variation(s) causing the association remains unknown. In this work package our goal is to identify the causative variants in this region through deep re-sequencing and to predict functional changes for population based follow-up. The approach outlined will be used for other hits identified in severity and pathway analyses.
WP5: Functional analysis of the influence of CfH and CfHR1-5 on meningococcal interactions with complement
To define the mechanistic basis for the genetic association of the CfH/CfH1-5 locus with meningococcal disease in our recent GWAS, we will generate reagents to analyse the interaction between N. meningitidis and these complement regulators at a biochemical level, to examine samples from our unique cohort of patients, and determine the influence of these complement factors, alone and in combination, to enable N. meningitis to avoid complement mediated lysis.
WP6: Animal models to resolve CfH function in meningococcal and pneumococcal infection
The animal work package has focused on exploring the fH finding from the initial meningococcal GWAS and extending this from meningococcal disease to pneumococcal disease.
The proposed work has focused on the existing genetic association with fH and what appeared realistic within the timeframes of the proposal. However, as other hits are observed within the severity and pathway analysis and extreme phenotype cohort, these may be taken forward in additional animal experiments. As the identity of these genomic hits will not be known until year 3 of the project, no clear description of the precise models to be used or work plan is set out. However, the animal work package has the capability to select appropriate animal models and explore other key hits in the last year of this work package. A proportion of the funded resource will be used for exploration of novel hits in addition to the work on fH.
WP7: Extreme phenotype cohort genomic analysis for clinical biomarker discovery
To elucidate genetic differences between the extreme phenotype cohort of at least 100 patients, each group with severe meningococcal disease, staphylococcal disease, pneumococcal disease and salmonella infection, and vaccine extreme phenotypes and controls. The goal being to find genomic differences including severe single Mendelian genes or major genes, and epigenetic modifications which explain severity, and can be used for the development of diagnostic test/s for the early identification of patients who are at high risk once infected. The severe phenotype cohort samples will be studied using microarrays (including methylation and miRNA and Next Gen Sequencing) to see which of the following either singularly or in combination can be used to identify those patients with an increased risk from each bacterial infection.
WP8: Bioinformatics and data management work package
This package will support and co-ordinate the bioinformatics analyses of each of the other work packages, and also carry out integrated analyses on the full dataset. Our aims in this work package are:
1. Develop an efficient, integrated data infrastructure which enables sharing, storage and integrated querying of the large amount of clinical, genetic, gene-expression, epigenetic, proteomic and functional data that will be generated throughout the project.
2. Liaise with the different work packages with regard to data generation in order to ensure uniformity in the way the data are being collected and stored.
3. Co-ordinate the bioinformatics analyses carried out within the different work-packages in order to ensure consistency of approach.
4. Perform bioinformatics analyses on the integrated dataset.
5. Development of novel algorithms for integrated analysis of genomic, epigenomic, transcriptomic and proteomic data.
6. Improved understanding of the racial / ethnic differences in population substructure and comparison of disease causing variants in African and European populations.
WP9: Consortium Management
In close co-operation with the Coordinator (Prof Michael Levin), consortium management will be the responsibility of Imperial Consultants, which is a wholly owned subsidiary of Imperial College London. Imperial Consultants has previous experience of participating in and managing large multidisciplinary consortia across the EU.
The overall aim of this work-package is to:
1. Deliver a successful and effective project.
2. Ensure effective communication with the EU Commission.
3. Ensure efficient communication across the project on financial, administrative, exploitation, training, and dissemination issues.
4. Organise meetings and teleconferences of the Project Steering Group (PSG).
5. Collate and produce the periodic reports - progress report, management report and financial report, assist all partners in providing timely financial and administrative documents and in compliance with EC rules.
6. Prepare the final reports.
7. Overall (non-scientific) coordination
WP10: Dissemination, training, and translation of results into clinical benefits
The programme of work undertaken will lead to major scientific advances in our understanding of the genetic basis of life threatening bacterial infection, improved understanding of disease mechanisms, and methods to predict susceptibility, outcome and response to immunisation.
The objectives of this work package will be:
1. To disseminate the findings to the scientific community and the public
2. To train scientists on all aspects of the project
3. To translate the finding into clinical use and public health benefit.