Peer-reviewed article
DIPG-47. TSO500ctDNA sequencing reveals oncogenic mutations and copy number variations in the liquid biome of children with diffuse midline glioma
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Summary
Written by AI, not yet AICS's view · claude-haiku-4-5-20251001This is a medical research paper about a laboratory technique for detecting tumor DNA in blood and cerebrospinal fluid samples from children with a type of brain cancer called diffuse midline glioma. The study validated a sequencing method to identify genetic mutations and copy number variations that could help with diagnosis and monitoring. While the work involves children as patients, it is a technical methods paper focused on molecular profiling rather than child well-being outcomes.
Key points
- TSO500ctDNA sequencing successfully detected DMG-associated mutations including H3-3A, H3C2, TP53, and ACVR1 in circulating tumor DNA
- H3K27M mutations were detected in 89% of CSF samples but only 33% of plasma/serum samples compared to tumor tissue
- Copy number variations including PDGFRA, KIT, and MDM4 gains were identified in both CSF and paired tumor samples
- Some mutations were found in CSF but absent from paired tumor, suggesting tumor genomic heterogeneity
- The method enables longitudinal monitoring of tumor evolution without repeated invasive biopsies
Limitations
This is a technical validation study (n=10) focused on the feasibility and accuracy of a laboratory sequencing method. It does not evaluate clinical outcomes, treatment effectiveness, or impact on child health and well-being, and the small sample size limits generalizability.
Abstract
Abstract BACKGROUND: Molecular profiling of childhood CNS tumors is critical for diagnosis and clinical management, yet tissue access is restricted due to sensitive neuroanatomical locations. Moreover, CNS tumors including diffuse midline glioma (DMG) exhibit mutational heterogeneity and clonal evolution, which cannot be captured by upfront diagnostic biopsy alone. To address the lack of tumor visibility, and tprovide opportunity for longitudinal sampling, we validated and optimized a commercially available deep sequencing platform for analysis of circulating tumor DNA (TSO500ctDNATM). METHODS: In a proof-of-concept study, we defined the sensitivity, specificity, and clinical relevance of our novel ctDNA platform via analysis of paired tissue, CSF, and blood from children with DMG (n=10). Paired samples were assessed for concordance and sequencing results were compared to digital droplet PCR (ddPCR) detection of prognostic H3K27M mutation. RESULTS: DMG associated mutations in genes including H3-3A, H3C2, TP53, and ACVR1 were detected in ctDNA, including in CSF samples with low (<5ng) starting DNA input. Of 9 H3K27M mutations identified in tumor, 8 were present in CSF and 3 in plasma/serum, for a positive percent agreement with tumor results of 89% and 33%, respectively. Among CSF samples, H3.3K27M was detected in 6/6 cases, and H3.1K27M in 2/3 cases, with variant allele frequencies comparable to ddPCR results. CNVs including PDGFRA, KIT, and MDM4 gains were detected in CSF and paired tumor. Low frequency events including ACVR1, PIK3CA activating mutations and KRAS amplification were detected in CSF but absent from paired tumor, indicating tissue heterogeneity. Strategies to optimize ctDNA detection, including optimization of ctDNA isolation and adjustment of library QC metrics, were identified. CONCLUSION: Targeted ctDNA deep sequencing is feasible, can inform on clinically relevant tumor mutation and CNV profiling, and provides an opportunity for longitudinal monitoring of tumor genomic evolution in the liquid biome of children with CNS tumors.