How to use the Genome-Phenome Analysis Platform
The Platform is a rich source of sequencing data thanks to the initial collaboration with research projects NeurOmics and EURenOmics, which submitted hundreds of whole exomes and genomes of patients with rare neuromuscular, neurodegenerative and kidney diseases. The number of cases submitted by researchers is increasing, covering various disease areas.
What you need to know about Genome-Phenome Analysis Platform
All sequencing data are submitted as raw data in FASTQ (or BAM) format and are processed through the same standard pipeline. This ensures that data from different sequencing providers are comparable. The raw data are stored for long-term access at the European Genome-phenome Archive (EGA), a secure, controlled-access repository. The processed data are accessible online for real-time analysis in the RD-Connect Genome-Phenome Analysis Platform.
The European Genome-phenome Archive (EGA) is a repository for all types of sequencing and genotype experiments, including case control, population, and family studies. It includes genotypes regarding single nucleotide polymorphism (SNPs) and copy number variant (CNVs) from array based methods and genotyping done with re-sequencing methods.
The EGA serves as archive for publication as well as data on several levels, including the raw data (so they could be re-analysed in the future using other algorithms) and the genotype calls (information about pathogenic genetic variants) provided by the data submitters.
The EGA provides the necessary security required to control access to the data and maintain patient confidentiality. Data can be viewed only by authorised researchers and clinicians. In all cases, data access decisions are made not by the EGA but by an appropriate Data Access Committee.
RD-Connect pays much attention to the data quality and security and the data in the Platform meet high quality and safety standards.
Who can access the data? The data stored on the Genome-Phenome Analysis Platform can be accessed only by the authorised scientists and clinicians who underwent the registration and verification process. How to register >>
Embargo period The users can analyse and query their own data as well as data submitted by others. Data become accessible to other authorised users only after a predefined embargo period of six months which allows researchers priority to access to their own data.
Patient security and confidentiality To protect patient privacy, data of individual patients are linked to the unique RD-Connect IDs. Patients’ identity data are not stored on the Platform and cannot be accessed by Platform users. Only the researcher, who submitted the data, has the key to identify the IDs corresponding to his/her data. Read more about ethical, legal and social issues >>
No. RD-Connect only helps to analyse sequencing data, but does not provide sequencing services.
The Platform has been developed at the Centro Nacional de Análisis Genómico (CNAG) in Barcelona, Spain.