Table 1 Examples of what has been accomplished using digital droplet PCR, alone or in combination with BEAMing PCR or custom amplicon sequencing, with a focus on CNS cancers

From: Liquid biopsy for pediatric central nervous system tumors

Method

Cancer type

Input and source

Biomarkers detected

Sensitivity, specificity

Reference

Digital droplet PCR

DIPG and other pediatric midline gliomas

10.5 ng DNA from CSF

H3F3A and HIST1H3B K27M mutation

87.5% sensitivity, 100% specificity

38

150 bp DNA fragments via centrifugation

 

Glioblastoma

mRNA from extracellular vesicles in CSF (cisternal or LP)

EGFR(v)III amplification

61% sensitivity, 98% specificity

41

High-grade glioma

mRNA transcripts from exosomes; 2–3 mL serum

EGFR(v)III amplification

81.58% sensitivity, 79.31% specificity

40

High and low-grade gliomas

Cell free DNA from serum

Alu hypomethylation in high grade compared to low-grade gliomas

 

121

Digital droplet and BEAMing PCR

Adult glioma

mRNA isolated from extracellular vesicles in 1 mL CSF (cisterns and LP) and serum

IDH1 G395A mutant transcripts

 

92

Digital droplet PCR and custom amplicon sequencing

Adult diffuse glioma

2–5 ng cell free DNA from 2 mL CSF, obtained from cisterna magna tap during autopsy and LP

TERT promoter mutations (C228T, C250T), H3F3A and HIST1H3B (K27M), IDH1, IDH2, TP53 point mutations

 

37

Targeted exon sequencing of IDH1, IDH2, ATRX, and TP53

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