Genome-wide cell-free DNA methylation profiling via TAPS for moyamoya disease diagnosis and postoperative collateral formation prediction.

Moyamoya disease (MMD) lacks reliable biomarkers for distinguishing it from atherosclerotic cerebrovascular disease (ACVD) and predicting postoperative collateral formation (PCF). Here, we apply low-input, bisulfite-free TET-assisted pyridine borane sequencing to plasma cell-free DNA (cfDNA) from 39 MMD and 37 ACVD patients in the discovery cohort and 40 MMD and 16 ACVD patients in an external multicenter cohort. The same libraries enable the analysis of methylation, fragmentation, end-nucleotide composition, nucleosome positioning, and tissue-of-origin signals. Although global methylation and tissue-of-origin profiles are broadly similar, differentially methylated regions distinguish MMD from ACVD and associate with PCF. A cfDNA methylation model achieves areas under the curve (AUCs) of 0.923 and 0.822 in the discovery and external cohorts, respectively, while a separate model predicts PCF with AUCs of 0.907 and 0.854. These findings provide proof-of-concept evidence for cfDNA methylation profiling as a minimally invasive approach to MMD diagnosis and preoperative assessment, while establishing an epigenomic resource for future studies.