Introduction
Morphologic Classification of pLGG
Histological Diagnosis | Common Molecular Events |
---|---|
Glial Tumors | |
Pilocytic Astrocytoma | KIAA1549-BRAF (70-80%) FGFR1-TACC1 (3-5%) FGFR1 SNV (3-5%) BRAF p.V600E (3-5%) Other BRAF Fusions (2-5%) CRAF Fusions (2-5%) PTPN11 SNV (2-5%) KRAS/HRAS SNV (2-5%) |
Subependymal Giant Cell Astrocytoma | TSC1/2 SNV (85-95%) |
Diffuse Astrocytoma | BRAF p.V600E (20-40%) MYBL1 alteration (5-10%) KIAA1549-BRAF (5-10%) FGFR1 SNV (2-5%) H3.3 p.K27M (2-5%) IDH1 p.R132H (2-5%) Other RTK SNV/Fusions (2-3%) |
Pleomorphic Xanthoastrocytoma | BRAF p.V600E (80-90%) |
Oligodendroglioma | FGFR1-TKD duplication (10-20%) FGFR1 SNV (10-20%) BRAF p.V600E (5-10%) FGFR1-TACC1 (3-5%) IDH1 p.R132H (3-5%) 1p/19q co-deletion (3-5%) |
Mixed Glioneuronal Tumors | |
Ganglioglioma | BRAF p.V600E (40-50%) KIAA1549-BRAF (10-15%) |
Desmoplastic Infantile Astrocytoma and Ganglioglioma | BRAF pV600E/D (40-60%) FGFR1 SNV (5-10%) KIAA1549-BRAF (2-5%) |
Dysembryoplastic Neuroepithelial Tumor | FGFR1-TKD duplication (20-30%) FGFR1 SNV (20-30%) FGFR1-TACC1 (10-15%) Other RTK SNV/Fusions (5-10%) BRAF p.V600E (5-10) |
Papillary Glioneuronal Tumor | SLC44A1-PRKCA (80-90%) |
Rosette-forming Glioneuronal Tumor | PIK3CA SNV (20-30%) KIAA1549-BRAF (20-30%) FGFR1 SNV (20-30%) |
Angiocentric Glioma | MYB (80-90%) |
Chordoid Glioma of Third Ventricle | PRKCA SNV (80-90%) |
Polymorphous Low-Grade Neuroepithelial tumor of the Young (PLNTY) | BRAF p.V600E (30-40%) FGFR2/3 Fusions (30-40%) |
Multinodular and vacuolating neuronal tumor (MVNT) | MAP2K1 SNV/Indel (50-60%) BRAF p.V600E (5-10%) Other BRAF SNV (5-10%) FGFR2 Fusions (3-5%) |
The Molecular Landscape of pLGG
Up-regulation of the RAS/MAPK Pathway
Neurofibromatosis Type 1
KIAA1549-BRAF
Other BRAF Fusions
BRAF p.V600E
FGFR1
CRAF Fusions
NTRK Fusions
KRAS Mutations
PTPN11 Mutations
ALK Fusions
ROS1 Fusions
MAP2K1 Alterations
Other Rare RAS/MAPK Alterations
Non-RAS/MAPK Related Alterations in pLGG
MYB alterations
MYBL1 alterations
IDH1 Mutations
H3F3A Mutations
Secondary Alterations in pLGG
CDKN2A Deletion
Molecular Tests and Platforms for profiling pLGG
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 |