An Affordable and Efficient In-House Approach for Detecting Gene Fusions in Bone and Soft Tissue Tumors Using a Custom Capture Panel and Nanopore Sequencing.
Summary
This study introduces an innovative and cost-effective method for detecting gene fusions in bone and soft tissue tumors, particularly sarcomas. The protocol integrates a custom capture panel with Nanopore sequencing and TEQUILA-based probe synthesis. Validated on 24 samples, including FFPE tissues, it demonstrated reliable fusion detection and gene expression quantification concordant with short-read sequencing. This approach promises to enhance the accessibility of molecular diagnostics for rare cancers due to its flexibility and reduced cost.
Analysis
🔴 CLINIQUE: This novel approach provides a more affordable and practical solution for gene fusion detection in sarcomas, a group of rare cancers where accurate fusion diagnosis is critical. Its ability to process small sample numbers and FFPE specimens, commonly available in clinical settings, makes this method directly applicable. Clinical impact could be seen in the medium term (3-5 years) by improving access to molecular diagnostics. 🟢 BIOMOL: The method relies on a custom capture panel and Nanopore sequencing, utilizing TEQUILA-based probe synthesis. It successfully detected fusions in 16 out of 17 FFPE samples and all 7 frozen samples, demonstrating good analytical validity. Gene expression quantification showed strong concordance (r = 0.770-0.976) with short-read sequencing, supporting its quantitative reliability. 🔵 BIOINFO: The approach describes an in-house workflow utilizing Nanopore sequencing. Down-sampling analysis indicated that 100-200 Mb of sequencing data per sample is sufficient for reliable fusion detection, a crucial metric for optimizing computational resources and costs. This extensible framework could be clinically deployed to streamline gene fusion diagnostics.