Short-read genome sequencing at population scale: diagnostic insights from 2317 patients

As part of the Danish National Genome Centre (DNGC) initiative, the Central Denmark Region has implemented short-read whole-genome sequencing (srWGS) as a first-tier diagnostic tool for suspected monogenetic disorders. Despite increasing adoption of genome sequencing, evidence from large-scale implementation across clinical specialties remains limited. Here, we evaluate the implementation from patient inclusion and srWGS scaling to diagnostic performance. From 2021 to 2024, we sequenced 2317 patients with suspected genetic diseases across a wide range of medical specialities. Following clinical evaluation and informed consent, Illumina srWGS was performed. Patients were categorised into clinical subgroups based on phenotype and age to support targeted variant filtration and germline variant reporting. The primary outcome was diagnostic yield across all disease groups/categories. The project is a public/private partnership co-funded by the Novo Nordisk Foundation. Diagnostic yield ranged from 6% in children with cancerto 60% in patients with skin disorders, with an overall yield of 20%. We observed substantial variation in the clinical use of srWGS as a first-tier diagnostic tool across patient categories. Regional implementation of srWGS within the DNGC framework demonstrates its scalability as a first-tier diagnostic tool for monogenic disorders. Importantly, the combination of expert-guided inclusion criteria for srWGS and mixed public/private funding has ensured equitable access to genetic diagnostics. We identify patient groups with high diagnostic returns well suited for srWGS, as well as groups where alternative strategies could also be applied.