Feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric brain tumors for classification

Array-based DNA methylation profiling is the gold standard for molecular classification of brain tumors. However, it relies on significant amount of input DNA extracted from surgical tissue, thus limiting its use for tumors where biopsy is challenging or limited in quantity. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) presents alternative opportunities for brain tumor diagnosis and disease monitoring following treatment. Novel enzymatic DNA methylation sequencing (EM-seq) methods may allow us to overcome input DNA limitations and accurately quantify methylation from cfDNA for tumor classification.

Type: Epigenetics
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 1 Publication

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001268	Enzymatic methylation sequencing data generated from cell-free tumor DNA extracted from cerebrospinal fluid (CSF). CSF was gathered from pediatric brain tumor patients of varying diagnoses treated at Connecticut Children's Medical Center, or from the Children's Brain Tumor Network. After DNA extraction, libraries were prepped using the Enzymatic Methyl-seq V2 kit (New England Biolabs).	Illumina NovaSeq X	17

Publications	Citations
A feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric central nervous system tumor patients for molecular classification. Taylor AM, Lombardi JT, Patel A, Tamariz A, Martin J, Bookland MJ, Hersh DS, Cantor E, Song X, Sahm F, Ng PK, Gell JJ, Lau CC. Neurooncol Adv 7: 2025 vdaf159	0