An Affordable and Efficient In-House Approach for Detecting Gene Fusions in Bone and Soft Tissue Tumors Using a...

Area of Science:

• Oncology
• Genomics
• Molecular Diagnostics

Background:

• Accurate gene fusion detection is vital for diagnosing bone and soft tissue tumors.
• Conventional gene panel testing is expensive and inefficient for small sample batches.

Purpose of the Study:

• To develop a cost-effective and scalable in-house workflow for gene fusion detection.
• To utilize nanopore sequencing and custom capture panels for analyzing sarcoma samples.

Main Methods:

• A custom capture panel and TEQUILA-based probe synthesis were combined with nanopore sequencing.
• Analyzed 24 sarcoma samples (frozen and FFPE) for gene fusions.
• Performed gene expression quantification and down-sampling analysis.

Main Results:

• Successfully detected expected gene fusions in all 7 frozen and 16 of 17 FFPE samples.
• Long-read sequencing provided full-length transcript information.
• Gene expression quantification showed high concordance with short-read sequencing (Spearman r = 0.770-0.976).
• 100-200 Mb sequencing data per sample was sufficient for reliable fusion detection.

Conclusions:

• The developed workflow is practical, scalable, and cost-effective for in-house gene fusion detection.
• This approach enhances the accessibility of molecular diagnostics for rare cancers.
• Nanopore sequencing offers structural insights beyond fusion junctions.