Table 2 Examples of liquid biopsy applications, including analysis of CTCs, cell free DNA and protein biomarkers, with a focus on CNS cancers

Exome sequencing

Neuroblastoma

100 μL–3.3 mL plasma

ALK alterations

100x coverage

⁹⁴

MAPK pathway alterations

MYCN amplification

1p and 11q chr deletions

17q chr gain

Targeted exon sequencing

Hepatocellular carcinoma

5-30 ng cell free DNA from 10 mL blood per patient

MET, TP53, EGFR, PIK3CA, BRAF, ARID1A, PTEN, CDKN2A, CTNNB1

15,000x average coverage depth, 0.1% limit of detection

⁹⁵

Targeted panel sequencing

Non-small cell lung cancer with leptomeningeal metastases

CTCs from 7.5 mL peripheral blood, and 5–7.5 mL CSF

MET amplification, ERBB2 and EGFR mutations

89.5% concordance of CTC DNA to matched tumor. 95.2% sensitivity for detecting metastasis

⁹⁶

Shotgun massively parallel bisulfite sequencing

Neuroendocrine tumor, hepatocellular and smooth muscle carcinomas, nasopharyngeal, breast, and lung cancers

cfDNA extracted from 4 mL plasma

Detecting global hypomethylation of cfDNA genome, and copy number alterations

68% sensitivity, 94% specificity at 10 million reads per sample

⁹⁷

CAPP-Seq

Lung cancer, lymphoma, leiomyosarcoma

cfDNA from 3–5 mL plasma

Indels, single nucleotide variants, rearrangements, copy number alterations

Variant detection as low as 0.01% frequency

^{112, 122,123,124,– 125}

32 ng cfDNA for library prep (range 18.3–32 ng)

LC-MS/MS, reverse phase protein array, Western blot, and ELISA

Pediatric CNS tumors including ATRT, ependymoma, malignant gliomas, medulloblastoma, PNET

Proteins isolated from CSF

Identification of candidate biomarkers predictive of metastasis

⁶¹