Genetic Sequencing Panel for Medulloblastoma
For medulloblastoma genetic sequencing, you must include genes that identify the four molecular subgroups (WNT, SHH, Group 3, Group 4) and critical prognostic markers, specifically: CTNNB1, TP53, PTCH1, SUFU, SMO, MYC, MYCN, and genes detectable through comprehensive DNA methylation profiling with next-generation sequencing. 1, 2
Gold Standard Approach
Genome-wide DNA methylation with brain tumor classifier application combined with next-generation sequencing is the gold standard for medulloblastoma diagnosis and subgroup classification. 3, 2 This approach is superior to other methods because it:
- Reduces diagnostic error by 11% compared to classic histopathology alone 3
- Allows differential diagnosis with other posterior fossa tumors 3, 2
- Distinguishes between Group 3 and Group 4 tumors, which cannot be reliably differentiated by immunohistochemistry 3
- Provides reliable and reproducible subgroup assignment 3
Essential Genes by Molecular Subgroup
WNT-Activated Subgroup
- CTNNB1: Mutated in 90% of WNT tumors, the defining molecular feature 1
- Chromosome 6 monosomy detection 4
SHH-Activated Subgroup
- TP53: Critical for risk stratification due to prognostic importance; requires sequencing due to multiple hotspots 3, 1
- PTCH1, SUFU, SMO: Frequent mutations in SHH pathway genes 1, 5
- MYCN: Amplification indicates high-risk disease 1, 4
- MLL1, LDB1, GLI1: Additional recurrent alterations 1
Group 3 Medulloblastoma
- MYC: Amplification is a defining feature and indicates worst prognosis 1, 4
- OTX2: Amplification patterns 4
- Isochromosome 17q alterations 1
Group 4 Medulloblastoma
- MYCN: Amplification for risk stratification 1
- KDM6A: Recurrent mutations 5, 4
- Chromosome 17 copy number alterations 1
- CDK6: Amplification patterns 4
Additional Critical Genes
Chromatin modifiers are frequently altered across all subgroups and should be included: 5
- MLL2 (KMT2D): Recurrent mutations across subgroups 5
- SMARCA4: Recurrent alterations 5
- KDM6A: Mutations particularly in Group 4 5, 4
- DDX3X: Novel recurrent mutations identified 5
- CTDNEP1, TBR1: Additional genes linked to medulloblastoma 5
Practical Implementation
The NCCN guidelines recommend molecular profiling to identify clinically relevant subtypes, with testing referred to academic tertiary centers with expertise. 3 The testing panel should include:
- DNA methylation profiling for subgroup classification 3, 2
- Next-generation sequencing for mutation detection 3, 2
- FISH or array-CGH for MYC and MYCN amplification 1, 6
- Copy number analysis for chromosome 17q and other alterations 1, 4
Critical Pitfalls to Avoid
Do not rely solely on immunohistochemistry for subgroup assignment. While IHC panels (β-catenin, GAB1, YAP1) provide rapid screening, they result in misclassification in approximately 17% of cases. 6 Specifically:
- Nuclear β-catenin expression in adults does not carry the same favorable prognosis as in children 3
- IHC interpretation can be operator-dependent and challenging 3
- YAP1 testing may not be available at smaller practices 3
- Molecular changes may not result in corresponding protein-level changes 3
Germline testing should be performed in all medulloblastoma cases, particularly for SHH-activated tumors associated with hereditary cancer syndromes like Gorlin syndrome. 1, 2
Risk Stratification Impact
Metastatic disease, subtotal resection, or MYC amplification automatically classify patients into high-risk groups irrespective of molecular subgroup. 1 The genetic sequencing results directly determine: