A novel next generation sequencing approach to improve sarcoma diagnosis

Area of Science:

• Oncology
• Genetics
• Molecular Diagnostics

Background:

• Sarcoma, a rare cancer of bone and connective tissue, presents diagnostic challenges due to over 100 subtypes.
• Current diagnostic methods like immunohistochemistry, FISH (fluorescence in situ hybridization), and RT-PCR (reverse transcription polymerase chain reaction) can yield inconclusive results.

Purpose of the Study:

• To design and validate a novel next-generation sequencing (NGS) tool for improved sarcoma diagnosis.
• To assess the feasibility and cost-effectiveness of targeted NGS for identifying genetic aberrations in sarcomas.

Main Methods:

• Development and optimization of an NGS DNA capture panel targeting 87 fusion genes and 7 genes with copy number variations.
• Validation using 113 DNA samples from formalin-fixed, paraffin-embedded (FFPE) soft-tissue and bone sarcomas with known FISH/RT-PCR results.
• Comparison of NGS results against FISH and RT-PCR as the gold standard for detecting translocations and gene amplifications.

Main Results:

• The NGS panel confirmed sarcoma-specific translocations or gene amplifications in 110 out of 113 cases (97% sensitivity).
• Identified MDM2/CDK4 amplification and 25 distinct fusion genes within the patient cohort.
• Achieved 100% specificity and a 0% failure rate, demonstrating high accuracy and reliability.

Conclusions:

• Targeted NGS is a feasible, cost-effective, and highly accurate method for improving sarcoma subtype diagnosis.
• The developed NGS panel effectively screens for a broad spectrum of genetic aberrations in a single test, aiding differential diagnosis.