Development of a high throughput gene, environment and epigenetics database and analysis system for international ALS research

Our Research 

The project is embedded within the bioinformatics group (http://core.brc.iop.kcl.ac.uk/) at the NIHR Biomedical Research Centre for Mental Health (BRC-MH), Kings College London. From here, we are collaborating with ENCALS and NEALS through multiple consortia including STRENGTH, EuroMotor, Project MinE, SOPHIA and ALSGEN. The solution will be based on dedicated open source frameworks for the integration of genetics and related data for analysis, tailored to fit a set of specific user requirements set out by a stakeholder group. Since the EuroMotor and SOPHIA projects use an existing Progeny-based clinical database, a specific component will allow a direct two-way transfer of key data between the two systems allowing them to be compatible and avoiding duplication of effort.  We are implementing a solution that will enable the sharing of each of the 1-4 levels of omics and associated data: Level 1 data refers to the data in its raw, non-normalised form, levels 2 and 3 represent data at different stages of processing and level 4 represents summary results data (https://wiki.nci.nih.gov/display/TCGA/Data+level#Datalevel- DataLevelClassification). 

The data base system will be a combination of both a central data warehouse that can be accessed by users through a web browser, and a  federated system where multiple storage locations are used but accessed through a single portal. We are producing a set of standardised analysis pipelines for data processing and submission to the repository. For example, there will be a pipeline for ALS Genome Wide Association Study (GWAS) genotype imputation.  

Themes
Discovery Science
Public Health
Learning Health  Systems

Disease: Neurodegenerative Disorders

People: Prof Ammar Al-Chalabi, Dr Richard Dobson, Prof Leonard van den Berg, Dr Stephen J. Newhouse, Dr Alfredo Iacoangeli

Collaborators: Dr Jan H. Veldink, Prof Vincenzo Silani, Prof John Landers, Prof Adriano Chio, Prof Orla Hardiman

Impact in research