Molecular Approaches to Diagnosis in Ewing Sarcoma: Targeted RNA Sequencing

Molecular testing for pathognomonic gene fusions is mandatory for the diagnosis of small round cell tumors. In particular, in Ewing sarcoma, the identification of specific chimeric fusion genes is critical to distinguish it from other histologically similar subtypes. As the clinical relevance of gene fusion detection continues to grow, many laboratories have adopted targeted next-generation sequencing approaches to overcome the limitations of conventional singleplex assays. We were among the early adopters of targeted RNA sequencing using anchored multiplex PCR, a technique that enables the simultaneous detection of multiple fusion transcripts with prior knowledge of only one fusion partner. In this chapter, we provide a detailed description of our workflow, including recommendations for nucleic acid extraction, library preparation, sequencing, and interpretation of gene fusion results.