Brain tumors are a heterogeneous group of abnormal collections of benign or malignant cells that may present with a variety of symptoms, including seizures, psychiatric disorders, and cognitive dysfunction. Brain tumors are diagnosed and classified using a combination of histology and molecular markers (eg, IDH1 and IDH2, 1p/19q codeletion, MGMT promoter methylation). Molecular tests may also be used for prognosis/risk stratification, treatment decision-making, and to determine clinical trial eligibility.
Quick Answers for Clinicians
Pangenomic tests are promoted as tools for identifying clinically relevant genomic variants that can inform targeted therapy, immunotherapy, and clinical trial enrollment. These tests may be marketed by private companies and used for drug development purposes. The yield of useful clinical information from these tests is currently low; more targeted testing for specific, well-validated variants may be more appropriate in patient care.
Analysis of cerebrospinal fluid (CSF) may be useful to rule out other causes of symptoms in an initial evaluation or to investigate for metastases (including postoperatively); CSF should be obtained via lumbar puncture when possible and safe. CSF analysis should include a cell count with differential, as well as glucose and protein analysis. For solid tumors, cytology is recommended, and analysis for gene rearrangements may be appropriate. Lumbar puncture should not be performed before imaging studies or within 2 weeks after surgery due to the possibility of false-positive results. Lumbar puncture is contraindicated in certain cases, such as in patients with a posterior fossa mass.
Indications for Testing
After thorough physical and neurologic examinations, imaging, and cerebrospinal fluid (CSF) analysis, individuals with brain tumors should undergo biopsy for histology and molecular marker testing.
Brain tumors are often classified according to the 2016 World Health Organization (WHO) Classification of Tumors of the Central Nervous System. Classification involves histology and molecular marker testing and is important for diagnosis, prognosis, and treatment decision-making.
|Diffuse astrocytic and oligodendroglial tumorsa||
|Other astrocytic tumors||Pilocytic astrocytoma|
|Choroid plexus tumors||Choroid plexus carcinoma|
|Neuronal and mixed neuronal-glial tumors||
|Tumors of the pineal region||Pineoblastoma|
|Tumors of the cranial and paraspinal nerves||
|Mesenchymal, nonmeningothelial tumors||
|Melanocytic tumors||Meningeal melanoma|
|Lymphomas||Diffuse large B-cell lymphoma of the central nervous system|
|Histiocytic tumors||Histiocytic sarcoma|
|Germ cell tumors||
|Tumors of the sellar region||
Breast cancer metastases
Lung cancer metastases
|Tumors of the cranial and paraspinal nerves||
aTesting for molecular markers, including IDH variants and 1p/19q codeletion, is required for the classification of diffuse astrocytic and oligodendroglial tumors.
bRELA fusion testing is recommended in the classification of gliomas.
cWNT activation, SHH activation, and TP53 variant testing is used in the classification of genetically defined medulloblastomas.
PNET, pancreatic neuroendocrine tumor
For most brain tumors, diagnosis and classification are based on a combination of histology and molecular findings ; sufficient tissue should be obtained from biopsy or resection to allow for both histology and molecular analysis.
Specimens obtained via needle biopsy may not be suitable for histology, as brain tumors (particularly gliomas) may exhibit differences in cellularity, mitoses, or necrosis across regions. According to the 2016 WHO classification system, if molecular data are unavailable, classification of tumors can be based on histology with appropriate caveats. For example, oligoastrocytoma is not a valid classification unless molecular data cannot be obtained, in which case a tumor may be designated an “oligoastrocytoma, not otherwise specified.”
Molecular tests on tumor samples are recommended as a complement to histology in diagnosis, for prognosis/risk stratification, and in treatment decision-making. Molecular markers are also useful in determining clinical trial eligibility. Although there are no targeted therapies for glioblastoma, molecular testing is encouraged because targeted therapies may be tried for compassionate use or as part of a clinical trial.
|Marker||Use in Diagnosis and Classification||Analysis Techniques||Clinical Implications|
|IDH1 and IDH2 variants||
Recommended in the evaluation of gliomas
Variants define WHO grade II and III astrocytomas, oligodendrogliomas, and secondary grade IV glioblastomas
May provide evidence of a diffusely infiltrative glioma
Primary glioblastomas and grade I noninfiltrative gliomas (eg, pilocytic astrocytomas and gangliogliomas) are IDH wild type
IHC for most common variant (R132H)
Sequencing (Sanger, pyro, or massively parallel) of both IDH1 and IDH2 for less common variants
Variants often associated with:
Wild type is often associated with:
Variant status may inform the most appropriate surgical approach
|1p and 19q codeletion||
Used to diagnose oligodendroglioma
Testing should be considered in gliomas with an IDH variant that do not show loss of ATRX
If a glioma is IDH wild type, it cannot be 1p/19q codeleted, and 1p/19q testing is unnecessary
Diagnosis of anaplastic oligodendroglioma is only possible if both IDH variant and 1p/19q codeletion are present
|FISH, PCR, array-based genomic copy number testing, or massively parallel sequencing||
|MGMT promoter methylation||
Useful in all grade III and IV gliomas
Associated with IDH variants and genome-wide epigenetic changes (G-CIMP phenotype)
|Methylation-specific PCR, pyrosequencing, or array-based technology||
Patients with MGMT promoter-methylated glioblastoma have survival advantage
Methylated MGMT promoter suggests sensitivity to treatment with alkylating agents
Patients with a non-MGMT promoter-methylated glioma are less likely to benefit from treatment with temozolomide
Variant analysis is strongly recommended for gliomas
ATRX variants are strongly associated with IDH variants and are generally not found with 1p/19q codeletion
Combination of ATRX deficiency and an IDH variant is typical for astrocytoma
If glioblastoma exhibits loss of ATRX expression and is negative for IDH1 R132H immunostaining, IDH1 and IDH2 sequencing is recommended
|Loss of wild-type ATRX can be detected by IHC or sequencing|
Variant analysis is recommended for gliomas
Variants are nearly always found in conjunction with 1p/19q deletions in oligodendrogliomas
Variants are found in most glioblastomas
Combination of TERT variant, 1p/19q deletion, and IDH variant is characteristic of oligodendroglioma
An IDH variant in the absence of a TERT variant is characteristic of astrocytoma
Variants in the absence of an IDH variant in a diffusely infiltrative glioma are associated with reduced survival
Combined TERT and IDH variants in the absence of a 1p/19q deletion are associated with a more favorable prognosis
|H3F3A and HIST1H3B variants||
H3F3A and HIST1H3B variant analysis (including testing for the most common histone variant in brain tumors, H3K27M, and the G34 variant more commonly present in pediatric cortical gliomas) is recommended in the appropriate clinical context
Variants in H3F3A and HIST1H3B provide evidence for an infiltrative glioma
Antibody testing for the H3K27M variant is possible
Sequencing of H3F3A and HIST1H3B is preferred
|K27M variant suggests a poor prognosis in adults and children|
BRAF fusion and variant testing is recommended in the appropriate clinical context
Presence of a BRAF fusion provides evidence of a pilocytic astrocytoma
BRAF V600E must be interpreted in the context of histology for appropriate diagnosis
BRAF V600E variant can be detected by sequencing
BRAF fusions can be detected by RNA sequencing or PCR-based breakpoint analysis
FISH should not be used for BRAF testing
Tumors with BRAF fusions are usually indolent
Prognosis of tumors with BRAF V600E variants requires consideration of other prognostic factors
Tumors with BRAF V600E variant may be more likely to respond to BRAF inhibitors (eg, vemurafenib)
|RELA fusions||RELA activating fusion testing is recommended in the appropriate clinical context, such as in certain ependymomas||Fusions can be detected with RNA sequencing or FISH||Ependymomas that contain RELA fusions tend to be more aggressive than other ependymoma|
|WNT activation, SHH activation, and TP53 variants||Associated with subtypes of medulloblastoma (nonspecific)||
WNT-activated tumors have a better prognosis than SHH-activated/TP53 variant, SHH-activated/TP53 wild-type, and non-WNT/non-SHH medulloblastomas
Molecular profiling may be useful for clinical trial enrollment
FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; PCR, polymerase chain reaction
Other Molecular Markers
NOTCH1, CIC, and FUBP1 variants, TP53 variants or overexpression, PTEN loss or promoter methylation, CDKN2A/B loss or deletion, EGFR amplification, chromosome 7 gain, and chromosome 10 loss are all currently being researched as potential molecular markers in the classification of gliomas. Molecular markers may also be useful for treatment planning in patients with brain metastases from melanoma (associated with BRAF variants), non-small cell lung cancer (associated with ALK or EGFR variants), and breast cancer (HER2-positive form).
Familial Genetic Testing
A number of genetic syndromes have been associated with brain tumors (particularly pediatric brain cancer), including Cowden syndrome, Turcot syndrome, neurofibromatosis types 1 and 2, and tuberous sclerosis complex. Familial testing for tuberous sclerosis and referral to genetic counseling should be considered in patients diagnosed with a subependymal giant cell astrocytoma. Other indications for referral to genetic counseling include pediatric diagnosis of a brain tumor with signs of a related genetic disorder, a brain tumor in the presence of additional Lynch syndrome-associated cancers in the individual or family, and astrocytoma and melanoma in the same person or two first-degree relatives. Several other indications should prompt referral to genetic counseling, and the list of indications continues to expand. For more details, see the American College of Medical Genetics (ACMG) guidelines.
Endocrine disorders are common in patients with brain tumors, and such disorders may be affected by treatment. Evaluation of hypothalamic, pituitary, adrenal, and thyroid function is recommended for patients who report decreased well-being or quality of life. Long-term monitoring of the hypothalamic-pituitary-adrenal axis may be considered if a patient received radiation therapy. Careful monitoring of the effects of steroid therapy, including monitoring for adrenal insufficiency for patients being weaned off of long-term steroid therapy, is recommended.
ARUP Lab Tests
Aids in diagnosis and classification of brain tumors
Aids in diagnosis, classification, prognosis, and treatment decision-making in oligodendrogliomas
Aids in diagnosis, classification, prognosis, and treatment decision-making in gliomas
Polymerase Chain Reaction/Sequencing
Aids in prognosis and treatment decision-making in high-grade gliomas
Aids in diagnosis and classification of gliomas
Aids in classification, prognosis, and treatment decision-making in some brain tumors
Polymerase Chain Reaction/Pyrosequencing
May be useful in diagnosis and prognosis in solid tumors
Includes BRAF, IDH1, IDH2, TERT promoter, TP53, NOTCH1, PTEN, and EGFR
For additional test information, including genes tested, refer to the Solid Tumor Mutation Panel by Next Generation Sequencing Test Fact Sheet
Test Fact Sheet(s)
National Comprehensive Cancer Network. NCCN Clinical Practice Guidelines in Oncology, Central Nervous System Cancers, Version 3.2019. [Updated: Oct 2019; Accessed: Feb 2020]Online
Louis DN, Perry A, Reifenberger G, et al. The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary. Acta Neuropathol. 2016; 131 (6): 803-20.PubMed
PDQ Pediatric Treatment Editorial Board. PDQ Childhood Brain and Spinal Cord Tumors Treatment Overview. Bethesda, MD: National Cancer Institute (US); 2002-2019 Sep 9.PubMed
Hampel H, Bennett RL, Buchanan A, Pearlman R, Wiesner GL; Guideline Development Group, American College of Medical Genetics and Genomics Professional Practice and Guidelines Committee and National Society of Genetic Counselors Practice Guidelines Committee. A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. Genet Med. 2015;17(1):70–87. Reaffirmed with Addendum: Genetics in Medicine (2019) 21:2844.PubMed
Cohen A, Sato M, Aldape K, et al. DNA copy number analysis of Grade II-III and Grade IV gliomas reveals differences in molecular ontogeny including chromothripsis associated with IDH mutation status. Acta Neuropathol Commun. 2015;3:34.
Lloyd IE, Clement PW, Salzman KL, et al. An unusual and challenging case of HIV-associated primary CNS Lymphoma with Hodgkin-like morphology and HIV encephalitis. Diagn Pathol. 2015;10:152.
Paxton CN, Rowe LR, South ST. Observations of the genomic landscape beyond 1p19q deletions and EGFR amplification in glioma. Mol Cytogenet. 2015;8:60.
Philip B, Yu DX, Silvis MR, et al. Mutant IDH1 Promotes Glioma Formation In Vivo. Cell Rep. 2018;23(5):1553-1564.
Tiburcio PDB, Xiao B, Chai Y, et al. IDH1R132H is intrinsically tumor-suppressive but functionally attenuated by the glutamate-rich cerebral environment. Oncotarget. 2018;9(80):35100–35113. Published 2018 Oct 12.