Brain tumor detection based on transcription regulation features identified from public cerebrospinal fluid cell-free DNA sequencing data

Background: Characterization of the molecular features of a brain tumor is a critical step for patient treatment. Tissue-based detection methods are limited by the location of brain tumors and high intratumor heterogeneity, which also preclude repeat sampling to monitor tumor progression. Cerebrospinal fluid (CSF)-based noninvasive methods may provide an opportunity to solve these problems, but efficient markers are lacking. This study aims to develop and validate a CSF-based liquid biopsy approach to investigate the molecular characterization and transcriptional regulation features of brain tumors. Methods: In this study, we conducted genome wide analysis of CSF cell free DNA (cfDNA) data collected from Sonic hedgehog (SHH) pathway-activated medulloblastoma (MB) patients sourced from gene expression omnibus (GEO) database, to identify genome features that differed significantly between patients with MB and those with hydrocephalus (P