TY  - JOUR
AU  - Fischer, Tom
AU  - Maass, Kendra
AU  - Puranachot, Pitithat
AU  - Mieskolainen, Markus
AU  - Sill, Martin
AU  - Schad, Paulina
AU  - Volz, Stefanie
AU  - Rosing, Fabian
AU  - Wedig, Tatjana
AU  - Schwarz, Nathalie
AU  - Finster, Agnes
AU  - Iser, Florian
AU  - Meyer, Jochen
AU  - Sahm, Felix
AU  - Lohi, Olli
AU  - Damaty, Ahmed El
AU  - Brors, Benedikt
AU  - Haapasalo, Hannu
AU  - Pfister, Stefan
AU  - Haapasalo, Joonas
AU  - Pajtler, Kristian
AU  - Nordfors, Kristiina
TI  - Ultra-low-input cell-free DNA sequencing for tumor detection and characterization in a real-world pediatric brain tumor cohort.
JO  - Acta Neuropathologica Communications
VL  - 13
IS  - 1
SN  - 2051-5960
CY  - London
PB  - Biomed Central
M1  - DKFZ-2025-01317
SP  - 134
PY  - 2025
N1  - #EA:B062#LA:B062#
AB  - 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
KW  - Humans
KW  - Child
KW  - Male
KW  - Brain Neoplasms: genetics
KW  - Brain Neoplasms: diagnosis
KW  - Brain Neoplasms: cerebrospinal fluid
KW  - Brain Neoplasms: blood
KW  - Female
KW  - Child, Preschool
KW  - Adolescent
KW  - Cohort Studies
KW  - Whole Genome Sequencing: methods
KW  - Biomarkers, Tumor: cerebrospinal fluid
KW  - Biomarkers, Tumor: genetics
KW  - Biomarkers, Tumor: blood
KW  - Liquid Biopsy
KW  - Circulating Tumor DNA: cerebrospinal fluid
KW  - Circulating Tumor DNA: genetics
KW  - Circulating Tumor DNA: blood
KW  - Cell-Free Nucleic Acids
KW  - Infant
KW  - DNA Copy Number Variations
KW  - Cell-free DNA (Other)
KW  - Cerebrospinal fluid liquid biopsies (Other)
KW  - Circulating-tumor DNA (Other)
KW  - Copy number variation profiling (Other)
KW  - Longitudinal molecular biomarkers (Other)
KW  - Low-coverage whole genome sequencing (Other)
KW  - Low-input samples (Other)
KW  - Minimally-invasive disease monitoring (Other)
KW  - Pediatric neuro-oncology (Other)
KW  - Tumor evolution (Other)
KW  - Biomarkers, Tumor (NLM Chemicals)
KW  - Circulating Tumor DNA (NLM Chemicals)
KW  - Cell-Free Nucleic Acids (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:40579709
DO  - DOI:10.1186/s40478-025-02024-w
UR  - https://inrepo02.dkfz.de/record/302322
ER  -