Enhancing precision in sarcoma diagnosis: nCounter fusion panel implementation in a middle-income country.

Abstract

Background: Sarcoma diagnosis is challenging due to numerous subtypes with similar histopathological features and the high cost of fusion detection methods, particularly in middle-income countries.

Objectives: To implement a cost-effective custom-based nCounter approach previously validated for fusion analysis of suspected sarcoma in Brazil.

Design and methods: RNA isolated from 56 routine sarcomas, which were formalin-fixed and paraffin-embedded, was analyzed using a custom nCounter assay that detects 174 common sarcoma gene fusions. The results were compared to fluorescence in situ hybridization (FISH)/next-generation sequencing (NGS) and clinicopathological data.

Results: The nCounter assay was conclusive in 98.2% of cases, identifying 25 gene fusions with 82.5% accuracy, 76.6% sensitivity, and 100% specificity compared to FISH/NGS.

Conclusion: Although it does not identify all sarcoma fusions, especially for rare subtypes, the present nCounter assay is a rapid, affordable, and accurate tool for sarcoma diagnosis in resource-limited settings.