Abstract Background Analysis of cell-free DNA (cfDNA) from cerebrospinal fluid (CSF) holds great potential as a diagnostic tool and surrogate marker for minimal residual disease in patients with medulloblastoma. Low-coverage Nanopore sequencing is a cost-efficient technique with clinically actionable turn-around time yielding both global DNA methylation patterns and copy number variations (CNV). Methods CSF supernatants were obtained during routine clinical care from patients with medulloblastoma enrolled in HIT trials/registries or treated at our center. DNA methylation patterns and CNV were analyzed in cfDNA from CSF using Nanopore sequencing. Molecular findings were correlated with clinical characteristics and disease course. Results In total, 129 CSF samples from 62 patients were analyzed, including serial samples from 19 patients (2-16 samples/patient). All medulloblastoma groups were represented (WNT, 6/62; SHH 16/62; Group 3, 14/62; Group 4, 26/62). Circulating tumor DNA (ctDNA) was detected in 58/129 samples (45.0%, “molecular M1”) by CNV (n = 55/58) and/or DNA methylation profiling (n = 47/58; both positive in 44/58), of which only nine corresponding CSF cytologies were positive (15.5%, M1). Detection of ctDNA was most frequent pre- or intraoperatively (6/10), at initial staging (17/38), and at radiological progression (16/21). In one patient with suspected medulloblastoma relapse, liquid biopsy revealed a radiation-induced glioma. The only patient with detectable ctDNA at end of therapy developed metastatic relapse three months later despite complete remission on MRI. ctDNA detection (“molecular M1”) at initial staging (n = 11/30 patients) was not associated with inferior survival (2-y-PFS/-OS 59%/69% vs. 80%/93%, p = 0.24/0.41). After initial staging, ctDNA detection (n = 16/33 patients) was not associated with differences in PFS or OS (2-y-PFS/-OS 45%/93% vs. 72%/100%, p = 0.12/0.31). Conclusion Nanopore-based cfDNA analysis from CSF enables sensitive ctDNA detection and early molecular diagnosis. Prospective evaluation at standardized time points in future clinical trials is warranted to validate the clinical relevance of positive liquid biopsy results.
Sönksen et al. (Tue,) studied this question.