ArticleActa neuropathologica communications2025
Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort.
Article in Acta neuropathologica communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Beyond variant detection: Mismatch repair gene alterations in plasma cell-free DNA from 1,226 glioma samples, and plasma-confirmed functional deficiency in an unbiopsied pontine glioma.The journal of liquid biopsy · 2026Article
- Early experience with cerebrospinal fluid cell-free DNA molecular profiling in a neuro-oncology practice.Journal of neuro-oncology · 2026Article
- Cerebrospinal fluid cell-free DNA sequencing in pediatric CNS tumors: towards liquid molecular neuropathology.Acta neuropathologica · 2026Review
- Circulating tumor DNA precision oncology enables effective and sensitive molecular diagnostics and actionable target detection in pediatric solid tumors - the INFORM experience.Genome medicine · 2026Article
- Platelet transcriptomic signatures in pediatric brain tumors distinguish cancer from cancer-free control.Acta neuropathologica communications · 2026Article
- Liquid Biopsy in Primary CNS Tumors: Bridging Biology, Technology, and Clinical Care.Molecular diagnosis & therapy · 2026Review
- Cerebrospinal Fluid in Pediatric Neuro-Oncology: Molecular Diagnosis, Disease Monitoring, and Clinical Translation.International journal of molecular sciences · 2026Review
- M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors.Nature cancer · 2026Article
- Decoding pediatric brain tumors via CSF-derived methylomes.Nature cancer · 2026Article
- Review
- Atypical Teratoid Rhabdoid Tumor: How Tumor Diagnostic Methods in the Laboratory Have Evolved over the Past 40 Years.Cancers · 2025Article
- Advances of nanopore direct sequencing technology and bioinformatics analysis for cell-free DNA detection and its clinical applications in cancer liquid biopsy.Frontiers in molecular biosciences · 2025Review
- Cerebrospinal fluid liquid biopsy guides differential diagnosis of relapsed medulloblastoma versus secondary glioma: A case report of a pediatric patient enrolled on aNeuro-oncology advancesArticle
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Authors and funding
22 authors.
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Abstract
Molecular profiling of pediatric central nervous system (CNS) tumors has important clinical utility for guiding diagnostic and therapeutic strategies. Cell-free DNA (cfDNA) from liquid biopsies has been used for minimally invasive tumor profiling and longitudinal disease assessment in adult oncology and pediatric hematology. However, in pediatric neuro-oncology, low cfDNA yields pose a major barrier to translating these assays from bench to bedside. Here, we implemented a low-coverage whole genome sequencing (lcWGS) assay for picogram-level cfDNA inputs and applied it to liquid biopsies from a sizeable, population-based, cross-entity pediatric CNS tumor cohort (n = 56 patients). Applying this protocol, cfDNA whole genome profiles were successfully acquired from all liquid biopsy samples (n = 61/61 serum, n = 56/56 CSF, 100%). Based on copy number variations (CNVs), circulating-tumor DNA (ctDNA) was detected in 2/61 serum (3%) and in 25/56 CSF (45%) samples across various brain tumor entities. The integration of cfDNA results with clinical data demonstrated the utility of CSF lcWGS as a biomarker assay at diagnosis to distinguish cancerous from non-cancerous pineal region lesions (n = 6 patients). Additionally, serial CSF assessment in n = 9 patients (n = 29 CSF samples) enabled minimally invasive disease monitoring, with the added value of molecular profile availability in n = 4/6 (67%) patients at relapse. Proof-of-concept data show the feasibility of serial CSF lcWGS to reveal tumor evolution, tumor heterogeneity and potential therapeutic vulnerabilities in a case of medulloblastoma and germ cell tumor. Our study underscores the clinical utility of a robust lcWGS-based liquid biopsy assay optimized for low-input samples. We identify use-cases for implementing liquid biopsies in the clinical management of pediatric CNS tumor patients and provide a strong rationale for integration into future trials.
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