| Modality | What it detects | Typical use case | Key limitations | Recent evidence/examples with year + URL |
|---|---|---|---|---|
| MRI (standard structural MRI; advanced MRI adjuncts) | Tumor location, size, contrast enhancement, edema, mass effect; supports response/progression assessment | First-line detection, surgical planning, longitudinal monitoring, distinguishing enhancing vs non-enhancing disease | Limited specificity for molecular subtype; may not reliably distinguish progression from treatment effect/pseudoprogression | Standard imaging remains central in WHO-era glioma workup; radiologists integrate imaging with molecular classification (2022, https://doi.org/10.3174/ajnr.45-12.s15) (pqac-00000003) |
| Histopathology + immunohistochemistry (IHC) | Morphology plus surrogate protein markers such as IDH1 R132H, ATRX loss, p53 overexpression, H3K27M, BRAF V600E | Core tissue diagnosis after biopsy/resection; rapid subtype orientation and grading support | Sampling bias, interobserver variability, limited sensitivity for non-canonical mutations/fusions; cannot alone resolve all integrated diagnoses | WHO CNS5 layered diagnosis still relies on histology/IHC alongside molecular data (2022, https://doi.org/10.3174/ajnr.45-12.s15) (pqac-00000003) |
| FISH | 1p/19q codeletion, EGFR amplification, CDKN2A/B deletion and other copy-number events | Confirm oligodendroglioma-defining 1p/19q status; support glioblastoma-defining alterations when needed | Target-limited assay; may miss genome-wide context or complex chromosomal architecture | FISH remains part of the molecular toolbox for diffuse glioma classification in WHO CNS5 practice (2022, https://doi.org/10.3174/ajnr.45-12.s15) (pqac-00000003) |
| DNA NGS panels | SNVs/indels in genes such as IDH1/2, TP53, ATRX, TERT promoter, H3 genes; some copy-number calls depending on panel | Practical routine molecular workup for adult and pediatric gliomas; diagnosis, prognostication, and actionable target finding | Panel content constrains discovery; may miss fusions/structural events; lower utility for epigenetic subgrouping | Targeted DNA sequencing is described as the most practical routine approach and can detect diagnostically relevant alterations in >50% of CNS tumors (2024, https://doi.org/10.1007/s00428-023-03632-4) (pqac-00000033, pqac-00000035) |
| RNA-seq | Gene fusions, splice variants, expressed rearrangements; can reveal hidden drivers such as FGFR1 ITD and rare kinase fusions | Especially valuable in pediatric low-grade glioma and fusion-driven tumors when panel/IHC are unrevealing | Requires high-quality nucleic acid/bioinformatics; less commonly informative in adult diffuse glioma; tissue handling constraints | In LOGGIC pLGG, adding RNA-seq raised driver detection from 75% to 97%; 27/125 cases had drivers found only by RNA-seq and 22 were actionable (2023, https://doi.org/10.1093/neuonc/noad078) (pqac-00000031, pqac-00000032) |
| DNA methylation profiling (classifier) | Tumor-class methylome signature plus genome-wide copy-number profile; can refine subtype, resolve ambiguous cases, and support grading/class assignment | Difficult/ambiguous cases, novel entities, subclassification, integrated diagnosis under WHO CNS5 | Not all samples achieve high-confidence match; specialized platforms/classifiers required; interpretation expertise needed | Described as a critical/most impactful diagnostic tool; match scores ≥0.9 in ~50-65% of samples with diagnostic impact in ~10-20% of cases (2024, https://doi.org/10.1007/s00428-023-03632-4); DKFZ classifier v12.5 added >10 novel methylation classes (2023, https://doi.org/10.1007/s10014-022-00446-1) (pqac-00000033, pqac-00000035, pqac-00000037) |
| CSF ctDNA liquid biopsy | Tumor-derived mutations/copy-number alterations in CSF cfDNA; can reflect IDH1, TERT, TP53, PTEN and other glioma alterations | Adjunct when biopsy is risky, deep/brainstem lesions, postoperative monitoring, molecular follow-up | Blood-brain barrier limits blood sensitivity; CSF acquisition is invasive; no standardization; not a replacement for tissue diagnosis | Reviews emphasize ctDNA/CTCs/miRNA/EVs as promising but limited by BBB and lack of standardized workflows (2024, https://doi.org/10.3390/ijms25147974; 2024, https://doi.org/10.3390/cancers16051009). Reported CSF cfDNA mutation detection includes 70% in gliomas, 82.5% in brainstem glioma, and 97.3% concordance when tumor alterations are present (2024, https://doi.org/10.3390/cancers16051009) (pqac-00000039, pqac-00000040, pqac-00000041, pqac-00000042) |


*Table: This table summarizes the main current diagnostic modalities used in glioma care, what each modality detects, where it is most useful, and key limitations. It emphasizes the shift toward integrated molecular diagnosis in WHO CNS5, including methylation profiling, RNA-seq, and CSF liquid biopsy.*