Primary Brain Tumors – Brain Tumor Molecular Markers

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

What is the role of pangenomic testing in brain cancer?

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.

Which tumor types must be distinguished from primary brain tumors?

Some cancers, especially breast cancer, lung cancer, or melanoma, may metastasize to the brain. For more information on testing for these cancers, see the Breast Cancer Biomarkers, Melanoma, and Non-Small Cell Lung Cancer – NSCLC Molecular Markers ARUP Consult topics.

What is the role of cerebrospinal fluid testing in brain cancers?

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.

Tumor Classification

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.

Overview of the 2016 WHO Classification of Tumors of the Central Nervous System
Classification	Examples
Diffuse astrocytic and oligodendroglial tumors^a	Diffuse astrocytoma Glioblastoma Oligodendroglioma
Other astrocytic tumors	Pilocytic astrocytoma
Ependymal tumors^b	Ependymoma
Other gliomas	Astroblastoma Chordoid glioma Angiocentric glioma
Choroid plexus tumors	Choroid plexus carcinoma
Neuronal and mixed neuronal-glial tumors	Ganglioglioma Paraganglioma Central neurocytoma
Tumors of the pineal region	Pineoblastoma
Embryonal tumors	Medulloblastoma^c
Tumors of the cranial and paraspinal nerves	Schwannoma Neurofibroma
Meningiomas	Anaplastic meningioma
Mesenchymal, nonmeningothelial tumors	Ewing sarcoma/PNET Lipoma
Melanocytic tumors	Meningeal melanoma
Lymphomas	Diffuse large B-cell lymphoma of the central nervous system
Histiocytic tumors	Histiocytic sarcoma
Germ cell tumors	Embryonal carcinoma Teratoma
Tumors of the sellar region	Craniopharyngioma Pituicytoma
Metastatic tumors	Breast cancer metastases Lung cancer metastases Melanoma metastases
Tumors of the cranial and paraspinal nerves	Schwannoma Neurofibroma Perineurioma
^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 Source: WHO, 2016

Laboratory Testing

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.

Histology

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 Markers

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.

Brain Tumor Molecular Markers
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: MGMT promoter methylation Relatively favorable prognosis Survival benefit for patients treated with radiation or alkylating chemotherapy Wild type is often associated with: Increased risk of aggressive disease in grade II or III infiltrative gliomas 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	Codeletion suggests: Favorable prognosis Response to alkylating chemotherapy and combination radiation/alkylating chemotherapy
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
ATRX variants	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
TERT variants	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	Sequencing	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 variants	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 Source: NCCN, 2019

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.

Other Tests

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.