Data sharing will be done within the Working group for data sharing of the genetic laboratory society VKGL. This group consists of laboratory specialists and bioinformaticians of each centre. Of note, part of the implementation and deployment of the databases to be used is already financed by BBMRI and the centres themselves.
To efficiently interpret the clinical relevance of the enormous amount of variants generated by WGS in this project, it is necessary to have easy access to information about previous observations of variants and their frequencies. The first step in diagnostics interpretation is filtering the variants observed in the patient with known variants from, e.g. 1000Genomes, ExAC and dbSNP. From experience it is known that these databases do not contain sufficient information to efficiently filter population specific benign variants. Moreover, the time to do a diagnose will be considerably shortened by sharing rare potentially pathogenic variants; if a clinically similar patient with a variant in the same gene is identified it will be more likely this variant is indeed the cause of the disorder. This WP will deliver infrastructure for storage and data sharing by using bioinformatics tools like VARDA and MOLGENIS for storing frequency data (VCF) and by making high quality clinical classification accessible (Figure 4). To minimize cost, we will however not implement centralized variant calling, potentially sacrificing the opportunity to standardize this aspect between all Dutch genetic laboratories. The ultimate goal is to make all anonymized data publicly accessible.