Bioinformatics Core
The Bioinformatics/Genomics core will integrate, disseminate, store and archive sequencing data generated by different GEoPD sites.
Part of our objective is to develop a standardized analytical pipeline to seamlessly perform downstream genomic analyses, to use either next-generation sequencing data (exome, genome, resequencing) or candidate SNP data generated via different genotyping platforms. However, the Bioinformatics/Genomics core also serves to integrate data generated by different cores (i.e. Epidemiology core, Clinical core, Biology core) with raw genomic data. As such the Core will be responsible for developing and managing a “GEoPD database”, containing genomic data accessible to GEoPD members.
The Bioinformatics/Genomics broader mission is to help GEoPD investigators perform novel, multi-dimensional, clinico-genetic-epidemiological studies.
Core Leaders: Manu Sharma , Lars Bertram
Biology Core
The Biology core is to compile a resource of expertise, resources and reagents within the GEoPD Consortium. Its objectives are to facilitate research by members of the GEoPD Consortium and to encourage multi-site collaborations.
The descriptors expertise, resources and reagents may be subdivided into sub-categories. Some examples: Expertise may include key professionals with major interests in atypical parkinsonism, neuroimaging (PET, MRI), genetics, etc. Resources might include longitudinal clinical data, high-throughput sequence or genotype information, etc. Reagents might include inducible pluripotent cell lines (iPSCs), plasmid constructs, or mouse models for genes implicated in Parkinson’s disease.
Although there will be some overlap with other cores e.g. with the Communications core on who is a current/active GEoPD member, with the Clinical core on number of patients and control subjects for whom clinical data and DNA is available, with the Bioinformatics core on genotype/sequence information etc. It will be the Biology’s core’s responsibility to create and maintain an indexed, searchable database of biologic ‘meta-data’ for the GEoPD Consortium.
Core Leaders: Matthew Farrer , Nobutaka Hattori , Jan Aasly
Communications Core
The Communications core is to maintain a list of active members and their contact details. It is to explicitly enable effective correspondence between sites/individuals and Cores, by whatever means is most effective, currently email, list serves and more recently via shared folders on dropbox.
Website development is a Core activity to enable direct communication between members to facilitate projects and the exchange of information and resources. The Communications core will aim to provide an archive of past dialogues within projects and cores. It will also seek to archive data from past meetings, including their program and event photographs.
Core Leaders: Matthew Farrer , Christine Klein , Rejko Krüger
Epidemiology & Statistics Core
The Epidemiology and Statistics core is to maintain a list of epidemiologic data available at different GEoPD sites. It will serve to facilitate data harmonization across sites.
It will monitor the epidemiological literature, with a particular interest in gene-environment interactions, and will regularly provide updates on recent findings. It will also monitor the statistical literature for relevant methods that can be used within the Consortium.
Members of the consortium will also be able to consult the core for questions on study design, analysis, and presentation of results.
Core Leaders: Alexis Elbaz , George Mellick , Karin Wirdefeldt , Christina Lill
Clinical Core
The Clinical Core will establish a basic clinical database for all patients/controls in the Consortium in an advanced database built using REDCap software. It integrates our long term project the LONG-PD study (PI: Katerina Markopoulou) that includes data from longitudinal follow-up of patients with parkinsonism.
The objectives of the Clinical Core are also to provide a standard dataset of basic clinical assessments that can be used by each site, using site-specific access, in a web-based REDCap system. This will facilitate future data sharing in upcoming projects within the Consortium.
The clinical database will not only comprise data on idiopathic Parkinson’s disease but also other forms of neurodegenerative parkinsonism, i.e. PSP, MSA, CBS. The database will also be built to capture and allow analyses of therapeutic outcomes, to integrate information on pharmacological treatment and device-based interventions i.e. deep brain stimulation (DBS) or pumps (LCIG, apomorphine).
It will be the Clinical Core’s responsibility (i) to create a basic dataset, that is harmonized based on current state-of-the-art diagnostic criteria and clinical scores, and (ii) to maintain a comprehensive, regularly updated searchable database of clinical data for the Consortium in collaboration with the Bioinformatics Core.
Core Leaders: Jan Aasly , Rejko Krüger , Beom Jeon , Katerina Markopoulou