Implementing nf-core/rnafusion in a clinical setting: Key insights and lessons learned

nf-core/rnafusion is designed for detecting gene fusions, which are increasingly observed across various cancer types. Identifying these fusions can significantly impact cancer diagnoses and therapy selection. The pipeline emphasizes reproducibility, robustness, and ease of operation. For approximately a year, Clinical Genomics Stockholm has used this pipeline to provide crucial data to geneticists at Karolinska University Hospital, aiding in clinical decision-making. Although still in its early days in the clinic, the standard of care for specific cancer types, such as sarcomas, is being updated to include gene fusion analysis. This presentation will focus on pipeline development strategies that facilitate clinical implementation, technical setups, and insights gained from our use of nf-core and the Seqera Platform frameworks. Importantly, steps towards obtaining an accredited and IVDR-compliant community-based pipeline will be described.