Molecular features unique to circulating tumor DNA enable the tumor-naïve liquid biopsy of glioblastoma

Glioblastoma is the most common and deadly brain cancer in adults. Although the disease disrupts the blood-brain barrier and exposes the tumor to the systemic circulation, using circulating cell-free DNA as a non-invasive biomarker for diagnosing glioblastoma remains elusive. The main obstacles are the confounding effects from artifactual variants in cell-free DNA caused by errors during next-generation sequencing and real variants in cell-free DNA originating from white blood cells that acquired somatic mutations during normal aging. Here, we developed and validated TrueR sequencing to overcome next-generation sequencing-related false positives in cell-free DNA. Subsequently, TrueR identified molecular features unique to tumor-derived cell-free DNA (i.e., circulating tumor DNA) that are detectable in blood during a tumor-naïve search. Specifically, variants associated with glioblastoma circulating tumor DNA were exclusively present in cell-free DNA (i.e., absent in white blood cell DNA) and showed gene-specific subclones. These features were uncommon in low-grade glioma, stroke, and age-related somatic mosaicism of white blood cells. We also detail a variant-agnostic method, demonstrating that copy number gains and losses in short cell-free DNA fragments (