This demonstrator has two key focus areas. First, the interconnection of key technological infrastructures for handling sensitive human data. The European Genome-phenome Archive (EGA) and RD-Connect both ensure that genomic and phenotypic data, including metadata, can be used only by researchers who are allowed to do so. Second, the integration of different omics data, Whole Genome Sequencing (WGS) and RNA-Seq. This allows for the establishment of a protocol to prioritize genetic variants associated with the observed phenotype. The aim was to develop workflows to ensure different datasets were processed in the same way and thereby allow for good comparisons and meta-analysis.
The analysis pipelines developed in this demonstrator are designed to be used in a broad range of contexts, although the initial focus of the project is on the Congenital Myasthenic Syndrome (CMS) use case.
We expected to be able to prioritize a few genetic variants which explain the observed phenotype differences among CMS patients. However, initial findings indicate that personalized analyses are needed to identify the genetic origin of the disease and its associated level of severity. This illustrates that each case has its own complexity, which cannot always be tackled by standard pipelines. Thus, interconnection of high quality analysis pipelines and metadata allow application of personalized analyses leading to clinically relevant insights.
BSC (Salvador Capella, Alfonso Valencia)
CRG-EGA (Jordi Rambla)
CRG-CNAG (Sergi Beltran)
Publications
Our experience has been pretty great, for us it has been a way to contribute to EOSC-Life and work with some people we already knew [from participating organisations].
– Salvador Capella
