Classification of pediatric soft and bone sarcomas using DNA methylation-based profiling

Pediatric sarcomas present heterogeneous morphology, genetics and clinical behavior posing a challenge for an accurate diagnosis. DNA methylation is an epigenetic modification that coordinates chromatin structure and regulates gene expression, determining cell type and function. DNA methylation-based tumor profiling classifier for sarcomas (known as sarcoma classifier) from the German Cancer Research Center (Deutsches Krebsforschungszentrum) was applied to 122 pediatric sarcomas referred to a reference pediatric oncology hospital. The classifiers reported 88.5% of agreement between histopathological and molecular classification confirming the initial diagnosis of all osteosarcomas and Ewing sarcomas. Transcriptome raw data quality was verified with FASTQC. We used STAR-fusion to identify and annotate fusion transcripts based on discordant read alignments with default configurations. ChimeraViz was used to plot fusion-genes.