Plasma Cell-Free DNA-Based Next-Generation Sequencing for Molecular Profiling of Diffuse Gliomas
Swati Singh, Jyotsna Singh, Supriya Bhardwaj, Aanchal Verma, Ashwinee Kumar, Swati Mahajan, Ashish Suri, Chitra Sarkar, Mohammed Faruq, Vaishali SuriAbstract
Purpose
To evaluate the utility of plasma-derived cell-free DNA (cfDNA) using targeted next-generation sequencing (NGS) for molecular profiling of diffuse gliomas (DG) by assessing concordance with matched tumor tissue DNA, mutation profiles, variant allele frequencies, therapeutically actionable alterations, and survival associations.
Materials And Methods
A total of 30 DG cases were included and 10 healthy control were included. Paired plasma cfDNA and formalin-fixed paraffin-embedded tumor tissue DNA were analyzed using targeted next-generation sequencing (NGS).
Results
Plasma cfDNA concentrations were higher in patients with DG (n = 30) than in healthy controls (P = .0002), though this comparison was limited by the small, unmatched control cohort (n = 10). Targeted sequencing predominantly identified single nucleotide variants (81%). Gene-level concordance between plasma cfDNA and tumor tissue DNA was 90.0%, whereas ≥1 matched variant was identified in 76.7% of cases. Plasma cfDNA detectability and concordance varied across diffuse glioma subtypes, and multiple therapeutically actionable alterations involving receptor tyrosine kinase, MAPK, PI3K/AKT/mTOR, and mismatch repair pathways were identified. Higher plasma cfDNA concentrations were associated with shorter survival, whereas cases with matched plasma and tissue variants demonstrated longer survival; however, these associations were not statistically significant.
Conclusion
Plasma cfDNA-based liquid biopsy may serve as a minimally invasive approach for molecular profiling of diffuse gliomas, demonstrating high gene-level concordance with tumor tissue DNA and detection of clinically relevant, potentially actionable genomic alterations. Although variant-level concordance and detectability varied across glioma subtypes, these findings support a complementary role for plasma cfDNA analysis in diffuse gliomas. Further prospective studies, including serial sampling and matched leukocyte controls, are needed to improve analytical sensitivity and define its clinical utility.