Table 2 Common testing techniques utilized to molecularly characterize pLGG including their associated cost, input requirements, limitations and time requirements
From: Pediatric low-grade glioma in the era of molecular diagnostics
Technique | Time (hours) | Cost (per sample) | Input | Utility | Clinical Limitations |
|---|---|---|---|---|---|
Immunohistochemistry | + | + | 1 FFPE slide | 1 target/slide | • Subject to antibody availability |
Fluorescent in situ hybridization | ++ | ++ | 1 FFPR slide | 1 target/slide | • Subject to probe design/ availability |
Droplet digital PCR | + | + | 10-50ng DNA/target | 1 target per reaction | • Requires access to expensive equipment |
NanoString nCounter | ++ | ++ | 200-500ng RNA | Up to 800 targets per reaction | • Requires RNA <10 years old • Requires access to expensive equipment |
SNP Array | +++ | +++ | 100-200ng of DNA | Dependent on probe frequency | • Limited to copy number alterations • Subject to batch effect |
Next Generation Sequencing Panels | +++ | +++ | 20-100ng DNA/RNA | Design dependent | • Requires RNA <10 years old • Requires access to expensive equipment • Requires significant downstream analysis |
Methylation Array | +++ | +++ | 20-50ng of bisulphite converted DNA | Methylation-based diagnosis [20] | • Requires access to expensive equipment • Subject to batch effect |