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| Home > Publications database > M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors. |
| Home > Publications database > M-PACT leverages cell-free DNA methylomes to achieve robust classification of pediatric brain tumors. |
| Journal Article | DKFZ-2026-00373 |
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2026
Nature Research
London
Abstract: Cerebrospinal fluid (CSF) liquid biopsies serve as a rich source of tumor-derived cell-free DNA (cfDNA) for evaluating persons with central nervous system (CNS) tumors. However, challenges stemming from trace cfDNA yields and low mutational burden have hindered sensitivity, whereas first-generation clinical assays have relied on genetic alterations as biomarkers. Leveraging the diagnostic utility of DNA methylation classification in CNS tumors, we developed M-PACT (methylation-based predictive algorithm for CNS tumors), a robust deep neural network that accurately classifies tumors from subnanogram-input cfDNA methylomes. Across embryonal CNS tumor benchmarking (n = 79) and validation (n = 58) cohorts, M-PACT achieved 92% and 88% accuracy, respectively. We further showcase M-PACT utility in nonembryonal CNS tumors, balanced tumor genomes and nonmalignant CSF. Beyond classification, this workflow enables methylation-based cellular deconvolution and sensitive copy-number variation detection. Altogether, we provide a blueprint for CNS tumor classification from low-input cfDNA methylomes, motivating prospective validation for future clinical implementation.
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