The IBD-BIOM Workpackages

The following are summaries of the ten workpackages in the IBD-BIOM research programme. These are from the IBD-BIOM DOW (Description of Work for the European FP7 programme).

WP 1: Project Management

Main workpackage participants: UEDIN, Genos

The main objective of this work-package is to set up an effective management framework for IBD-BIOM which will ensure:

Good governance of administrative tasks, integration of the science across work packages in order to reach optimal translation of results, and sound financial management;
Timely and adequate reporting to the European Commission and within the consortium;
Effective and efficient communication within IBD-BIOM and with the stakeholders and the society as a whole;
The facilitation of the research programme by active troubleshooting (“anticipating things that might go wrong and prevent them from going wrong”);
Proper attention to research governance

WP 2: Collection and organization of samples

Main workpackage participants: UEDIN, UHCF, CS-MC

To organize, coordinate and distribute the existing clinical samples and data between centres.

WP 3: Genetic and epigenetic predisposing (risk) and prognostic factors in IBD

Main workpackage participants: UNI-ZG, UEDIN, UHCF, Genos

To define the genome-wide methylation profiles characteristic of newly-diagnosed Crohn’s disease and ulcerative colitis, in peripheral blood, and to define the relative contribution of different leucocyte subsets.
To investigate the relationship between DNA-methylation profile and disease progression, phenotype, behaviour and medication.
To define the relationship between genome wide methylation profile and germline variation in patients with Crohn’s disease and ulcerative colitis.
To integrate genome-wide methylation profiling and phenotypic data, to develop a predictive model of susceptibility, progression and response to therapy.
To validate this model using the clinical datasets available in the collaborators’ teams.

WP 4: Plasma and IgG N-glycome in IBD

Main workpackage participants: Genos, UNI-ZG, UEDIN, CS-MC, UHCF, LUMC

To analyse plasma glycome in IBD patients and controls
To isolate IgG and analyse its glycosylation in IBD patients and controls
To develops assays and analyse epigenetic regulation of key regulatory genes for IgG glycosylation

WP 5: Glycoproteomic biomarkers for early diagnosis and prognosis of IBD

Main workpackage participants: MPI, LUMC, UHCF, UEDIN

To describe IBD-associated O-glycosylation and N-glycosylation of the inflamed tissue
To detect plasma proxies of tissue inflammation in IBD and evaluate them for their diagnostic and prognostic potential

WP 6: Activomics approach to early diagnosis and prognosis of IBD

Main workpackage participants: IPRC, Genos, UHCF, UEDIN

To identify and validate a panel of activomics biomarkers in a prospective study of IBD.
To provide insight into the molecular pathology of IBD and chronically inflamed tissue.

WP 7: Integrated models for identification of biomarkers and potential new therapeutic targets

Main workpackage participants: CS-MC, Genos, UHCF, UNI-ZG, UEDIN

To perform integrated analysis of genomic, epigenetic, immunological, biochemical, glycomic and glycoproteomic data to develop the best predictive model for the classification of IBD patients into subgroups, including CD versus UC, Severe UC vs mild UC, complicated CD vs non-complicated CD, and responder vs non-responders to anti-TNF therapy.
The significant predictors so identified may serve as potential new therapeutic targets.

WP 8: Validation of biomarkers in a prospective cohort

Main workpackage participants: UEDIN, Genos, UHCF, MPI, CS-MC, IPRC, LUMC, UM

To bring together an adequately-sized cohort of newly-diagnosed parients with Crohn’s disease and ulcerative colitis, and to follow the clinical couse of these patients over a median of 24 months,
To allow validation of the value of biomakers identified elsewhere within the programme in predicting susceptibility, progression, response to therapy, and complications

WP 9: Development of simple and robust assays for new individual and combined biomarkers

Main workpackage participants: Ludger, CS-MC,Genos,UEDIN, IPRC, LUMC

To establish an appropriate Quality Management System (QMS) for the IBD biomarker discovery and assay system (IBD-BDAS)
To establish standard operating procedures (SOPs) and performance specifications for key processes in the IBD-BDAS and validate them
To develop an integrated, commercial grade IBD-BDAS for clinical diagnostics
To develop tools to help rapid adoption of the IBD-BDAS by clinicians

WP 10: Dissemination and exploitation

Main workpackage participants: Ludger, UEDIN, Genos, LUMC

To disseminate information on the project to the scientific community
Dissemination of IBD-BIOM goal and achievements to the general public
To support application of developed methods for the benefit of patients and clinicians in Europe and European industry