分子脑肿瘤诊断通常依赖于组织活检或手术切除。这可能存在与麻醉或神经外科手术相关的几个风险，尤其是对于脑干或其他难以达到的解剖部位的病变。除了初步诊断外，肿瘤进展、复发或新的基因变异的获得只能通过重新活检来证实。我们应用纳米孔测序技术对脑脊液中的细胞游离DNA（cfDNA）进行分析，使用随机森林分类器分析拷贝数变异（CNV）和全基因组DNA甲基化。我们测序了129个具有足够DNA的样本，这些样本来自99名患者，涵盖了22种实体瘤。结果与临床诊断和肿瘤组织的分子分析结果进行了比较。其中110个样本的技术成功，其中50个样本通过CNV或甲基化谱分析检测到循环肿瘤DNA（ctDNA）。ctDNA在进展性疾病患者的样本中被检测到，但也在没有明确残留疾病的患者的样本中被检测到。CNV图显示了诊断和预后的变异，如多层玫瑰胶状胚状肿瘤中的C19MC扩增，以及后颅窝A组室管膜瘤中的Chr.1q增益和Chr.6q损失。大多数CNV谱与相应肿瘤组织的谱相一致。DNA甲基化可准确分类110例中的22例肿瘤，并导致2例分类错误。只有5例在显微镜下检测到了可见的肿瘤细胞的样本中检测到的ctDNA。我们的结果表明，从脑脊液样本中获得的cfDNA的纳米孔测序数据可能是脑肿瘤初步诊断的有希望的方法，也是疾病监测的重要工具。© American Association for Clinical Chemistry 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Molecular brain tumor diagnosis is usually dependent on tissue biopsies or resections. This can pose several risks associated with anesthesia or neurosurgery, especially for lesions in the brain stem or other difficult-to-reach anatomical sites. Apart from initial diagnosis, tumor progression, recurrence, or the acquisition of novel genetic alterations can only be proven by re-biopsies.We employed Nanopore sequencing on cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) and analyzed copy number variations (CNV) and global DNA methylation using a random forest classifier. We sequenced 129 samples with sufficient DNA. These samples came from 99 patients and encompassed 22 entities. Results were compared to clinical diagnosis and molecular analysis of tumor tissue, if available.110/129 samples were technically successful, and 50 of these contained detectable circulating tumor DNA (ctDNA) by CNV or methylation profiling. ctDNA was detected in samples from patients with progressive disease but also from patients without known residual disease. CNV plots showed diagnostic and prognostic alterations, such as C19MC amplifications in embryonal tumors with multilayered rosettes or Chr.1q gains and Chr.6q losses in posterior fossa group A ependymoma, respectively. Most CNV profiles mirrored the profiles of the respective tumor tissue. DNA methylation allowed exact classification of the tumor in 22/110 cases and led to incorrect classification in 2/110 cases. Only 5/50 samples with detected ctDNA contained tumor cells detectable through microscopy.Our results suggest that Nanopore sequencing data of cfDNA from CSF samples may be a promising approach for initial brain tumor diagnostics and an important tool for disease monitoring.© American Association for Clinical Chemistry 2023. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.