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000306869 1001_ $$00000-0002-2544-5888$$aTaylor, Aaron Michael$$b0
000306869 245__ $$aA feasibility study of enzymatic methylation sequencing of cell-free DNA from cerebrospinal fluid of pediatric central nervous system tumor patients for molecular classification.
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000306869 520__ $$aArray-based DNA methylation profiling is the gold standard for central nervous system (CNS) tumor molecular classification, but requires over 100 ng input DNA from surgical tissue. Cell-free tumor DNA (cfDNA) in cerebrospinal fluid (CSF) offers an alternative for diagnosis and disease monitoring. This study aimed to test the utilization of enzymatic DNA methylation sequencing (EM-seq) methods to overcome input DNA limitations.We used the NEBNext EM-seq v2 kit on various amounts of cfDNA, as low as 0.1 ng, extracted from archival CSF samples of 10 patients with CNS tumors. Tumor classification was performed via MNP-Flex using CpG sites overlapping those on the MethylationEPIC array.EM-seq provided sufficient genomic coverage for 10 and 1 ng input DNA samples to generate global DNA methylation profiles. Samples with 0.1 ng input showed lower coverage due to read duplication. Methylation levels for CpG sites with at least 5× coverage were highly correlated across various input DNA amounts, indicating that lower input cfDNA can still be used for tumor classification. The MNP-Flex classifier, trained on tissue DNA methylation data, successfully predicted CNS tumor types for 7 out of 10 CSF samples using EM-seq methylation data with only 1 ng of input cfDNA, consistent with diagnoses based on tissue MethylationEPIC classification and/or histopathology. Additionally, we detected focal and arm-level copy number alterations previously identified via clinical cytogenetics of tumor tissue.This study demonstrated the feasibility of CNS tumor molecular classification based on CSF using the EM-seq approach, and establishes potential sample quality limitations for future studies.
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000306869 650_7 $$2Other$$aCNS tumor classification
000306869 650_7 $$2Other$$aMNP-flex
000306869 650_7 $$2Other$$acell-free DNA
000306869 650_7 $$2Other$$aenzymatic methylation sequencing
000306869 650_7 $$2Other$$amolecular diagnosis
000306869 7001_ $$aLombardi, Jody T$$b1
000306869 7001_ $$0P:(DE-He78)79506056c05e539af84edf040f0a93ad$$aPatel, Areeba Jamilkhan$$b2$$udkfz
000306869 7001_ $$aTamariz, Ariella$$b3
000306869 7001_ $$00000-0003-3180-2084$$aMartin, Jonathan$$b4
000306869 7001_ $$00000-0003-4422-8376$$aBookland, Markus J$$b5
000306869 7001_ $$00000-0003-1177-2201$$aHersh, David S$$b6
000306869 7001_ $$00000-0001-7302-9734$$aCantor, Evan$$b7
000306869 7001_ $$aSong, Xianyuan$$b8
000306869 7001_ $$0P:(DE-He78)a1f4b408b9155beb2a8f7cba4d04fe88$$aSahm, Felix$$b9$$udkfz
000306869 7001_ $$00000-0003-0364-7443$$aNg, Patrick Kwok-Shing$$b10
000306869 7001_ $$aGell, Joanna J$$b11
000306869 7001_ $$00000-0001-9173-8366$$aLau, Ching C$$b12
000306869 773__ $$0PERI:(DE-600)3009682-0$$a10.1093/noajnl/vdaf159$$gVol. 7, no. 1, p. vdaf159$$n1$$pvdaf159$$tNeuro-oncology advances$$v7$$x2632-2498$$y2025
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