Introduction
Methods
Study design
Ultrasonic aspirator tissue sample processing
Nanopore low-pass whole genome sequencing
CNS tumor classification
Copy number analysis
Methylation array processing
Statistical analysis
Data and code availability
Results
Patient characteristics
Patient ID | Age | Sex | Tumor location | Reference diagnosis | Type of lesion | Type of non-surgical pre-treatment | Microarray methylation class (MC) | Nanopore methylation class (MC) | Score MC | Nanopore methylation class family (MCF) | Score MCF | tSNE concordance |
---|---|---|---|---|---|---|---|---|---|---|---|---|
DX-BLN-025 | 8 | F | Parieto-occipital right | CNS neuroblastoma | Primary | None | CNS neuroblastoma with FOXR2 activation | CNS neuroblastoma with FOXR2 activation | 0.68 | CNS neuroblastoma with FOXR2 activation | 0.68 | + |
DX-BLN-027 | 17 | F | Right trigeminal nerve | Schwannoma | Primary | None | schwannoma | schwannoma | 0.85 | schwannoma | 0.85 | + |
DX-BLN-028 | 9 | F | Right cerebellar hemisphere | Pilocytic astrocytoma | Primary | None | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.44 | pilocytic astrocytoma | 0.58 | + |
DX-BLN-029 | 1 | F | Fronto-temporo-parietal right | Ependymoma | Secondary | Cyclophosphamide/vincristine/methotrexate/carboplatin/etoposide | ependymoma, YAP fusion | ependymoma, YAP fusion | 0.07 | glioblastoma, IDH wildtype | 0.10 | + |
DX-BLN-037 | 5 | F | Right cerebellar hemisphere | Pilocytic astrocytoma | Secondary | Vincristine/carboplatin | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.33 | pilocytic astrocytoma | 0.54 | + |
DX-BLN-042 | 9 | F | Left cerebellar hemisphere | Pilocytic astrocytoma | Primary | None | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.46 | pilocytic astrocytoma | 0.56 | + |
DX-BLN-043 | 10 | M | Left frontal | Ependymoma, RELA fusion-positive | Primary | None | ependymoma, RELA fusion | ependymoma, RELA fusion | 0.43 | ependymoma, RELA fusion | 0.43 | + |
DX-BLN-044 | 9 | F | Left temporo-parieto-thalamic | High grade glioma, H3 K27M mutated | Secondary | None | Diffuse midline glioma, K27-mutant | Diffuse midline glioma, K27-mutant | 0.66 | Diffuse midline glioma, K27-mutant | 0.66 | + |
DX-BLN-047 | 8 | F | Left mesencephalic | Pilocytic astrocytoma | Secondary | Vincristine/carboplatin | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.34 | pilocytic astrocytoma | 0.50 | + |
DX-BLN-048 | 3 | M | IV. Ventricle | Anaplastic Ependymoma | Primary | None | ependymoma, posterior fossa group A | ependymoma, posterior fossa group A | 0.75 | ependymoma, posterior fossa group A | 0.75 | + |
DX-BLN-049 | 3 | F | Thoracic spine | Pilocytic astrocytoma | Primary | None | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass midline pilocytic astrocytoma | 0.07 | pilocytic astrocytoma | 0.12 | - |
DX-BLN-050 | 15 | F | Right lateral ventricle | Atypical central neurocytoma | Primary | None | central neurocytoma | central neurocytoma | 0.72 | central neurocytoma | 0.72 | + |
DX-BLN-054 | 16 | F | Left frontal | Diffuse astrocytoma, IDH-mutant | Primary | None | IDH glioma, subclass astrocytoma | control tissue, hemispheric cortex | 0.08 | pilocytic astrocytoma | 0.17 | - |
DX-BLN-064 | 6 | F | Foramen Monroi right | Subependymal giant cell astrocytoma | Primary | None | N/A | low grade glioma, subependymal giant cell astrocytoma | 0.15 | low grade glioma, subependymal giant cell astrocytoma | 0.15 | - |
DX-BLN-065 | 6 | M | Right mesencephalic | Pilocytic astrocytoma | Secondary | Vincristine/carboplatin | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.24 | pilocytic astrocytoma | 0.47 | + |
DX-BLN-071 | 7 | F | Optic pathway | Pilocytic astrocytoma | Secondary | Vincristine/carboplatin, vinblastine, MEK inhibitor | N/A | low grade glioma, subclass midline pilocytic astrocytoma | 0.37 | pilocytic astrocytoma | 0.48 | + |
DX-BLN-073 | 7 | M | Sella turcica | Craniopharyngioma | Primary | None | craniopharyngioma, adamantinomatous | craniopharyngioma, adamantinomatous | 0.56 | craniopharyngioma, adamantinomatous | 0.56 | + |
DX-BLN-074 | 6 | M | Right cerebellar hemisphere | Pilocytic astrocytoma | Primary | None | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.58 | pilocytic astrocytoma | 0.69 | + |
DX-BLN-075 | 9 | M | Right cerebellar hemisphere | Pilocytic astrocytoma | Secondary | None | low grade glioma, subclass posterior fossa pilocytic astrocytoma | low grade glioma, subclass posterior fossa pilocytic astrocytoma | 0.32 | pilocytic astrocytoma | 0.40 | + |