Implementing WGS-based rare inherited disease diagnostics in the Stockholm healthcare region

Abstract

In healthcare clinical genetics is transitioning to clinical genomics and especially rare disease diagnostics is increasingly done through panel, exome and whole-genome sequencing. At Karolinska we have formed Genomic Medicine Center Karolinska Rare Diseases (GMCK-RD), a joint unit between healthcare and academia, enabling large-scale genome sequencing of patients. GMCK-RD brings together experts from various medical disciplines with clinical geneticists, bioinformaticians and researchers. Through GMCK-RD, over 10,000 individuals have been analysed by clinical genome sequencing (GS) with an overall yield of 33%, providing a genetic diagnosis to >2,543 individuals. By tight collaboration in 15 multidisciplinary expert teams thousands of patients with various rare diseases have been diagnosed. Our analysis covers detection and interpretation of SNVs, INDELs, uniparental disomy, CNVs, balanced structural variants, and short tandem repeat expansions. Visualisation of results for clinical interpretation is carried out in Scout- a custom-developed decision support system. To facilitate the discovery of new disease genes, GMCK-RD is reporting variants to ClinVar and has joined international data sharing initiatives, including UDNI, Beacon, and MatchMaker Exchange. Altogether, we at GMCK-RD have moved healthcare in our region towards precision diagnostics and precision medicine.