Ultrasensitive detection of neuronal DNA using genome-wide non-CG methylation patterns

Methylation-based liquid biopsies can identify the tissue origins of circulating cell-free DNA (cfDNA). A major constraint on the sensitivity of these assays is the limited number of cell-type-specific CpG markers. Here we exploit the high abundance of non-CpG (CpH) methylation in neurons to enable ultrasensitive detection of neuronal DNA. We show that neurons carry 100-fold higher CpH methylation than other tissues, in which apparent CpH methylation largely reflects experimental artifacts. Using a computational criterion to identify cfDNA molecules carrying clusters of methylated CpA sites, we detect neuronal DNA at proportions as low as 20 parts per million. Analysis of 231 samples from 163 individuals revealed minimal neuronal cfDNA in the plasma of healthy subjects; elevated levels in patients with measles or acute neurological conditions; strikingly high levels in brain-dead donors, indicating extensive ongoing neuronal death; and the highest levels in the cerebrospinal fluid of patients in a neurological intensive care unit. These findings establish genome-wide, fragment-level analysis of non-CpG methylation as an ultrasensitive approach for blood-based monitoring of brain injury and disease.