Detection of Structural Variants in Circulating Cell-Free DNA from Sarcoma Patients Using Next Generation Sequencing

Area of Science:

• Oncology
• Genomics
• Molecular Diagnostics

Background:

• Circulating tumor DNA (ctDNA) analysis via next-generation sequencing (NGS) is increasingly used for cancer treatment stratification and monitoring.
• Detecting structural variants (SVs) in ctDNA is challenging, particularly for sarcomas where SVs are common.

Purpose of the Study:

• To evaluate the efficacy of a sarcoma-specific targeted NGS panel for identifying translocations and copy number variants in ctDNA.
• To assess the concordance of SV detection between tumor tissue and cell-free DNA (cfDNA) in soft tissue sarcoma patients.

Main Methods:

• A targeted NGS panel was developed and applied to 12 soft tissue sarcoma tissue specimens and matched plasma cfDNA samples.
• Analysis focused on identifying translocations and copy number variants (CNVs) in both tissue and cfDNA.
• Variant allele frequencies (VAFs) and sequencing depth were optimized for cfDNA analysis.

Main Results:

• Structural variants were identified in 91.6% of tissue samples and 50% of plasma cfDNA samples.
• SVs were detectable in cfDNA at VAFs >0.2% with an average sequencing depth of 1026×.
• The study included a diverse cohort of sarcoma subtypes, such as alveolar rhabdomyosarcoma, Ewing's Sarcoma, and synovial sarcoma.

Conclusions:

• NGS-based ctDNA analysis demonstrates clinical potential for aiding sarcoma diagnosis and monitoring.
• Further studies with larger cohorts are warranted to validate these findings.
• ctDNA analysis offers a minimally invasive approach for detecting genomic alterations in sarcomas.