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 tumorsa

Diffuse astrocytoma



Other astrocytic tumors Pilocytic astrocytoma
Ependymal tumorsb Ependymoma
Other gliomas


Chordoid glioma

Angiocentric glioma

Choroid plexus tumors Choroid plexus carcinoma
Neuronal and mixed neuronal-glial tumors



Central neurocytoma

Tumors of the pineal region Pineoblastoma
Embryonal tumors Medulloblastomac
Tumors of the cranial and paraspinal nerves



Meningiomas Anaplastic meningioma
Mesenchymal, nonmeningothelial tumors

Ewing sarcoma/PNET


Melanocytic tumors Meningeal melanoma
Lymphomas Diffuse large B-cell lymphoma of the central nervous system
Histiocytic tumors Histiocytic sarcoma
Germ cell tumors

Embryonal carcinoma


Tumors of the sellar region



Metastatic tumors

Breast cancer metastases

Lung cancer metastases

Melanoma 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

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. 


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


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.  (For more information, see the Tuberous Sclerosis Complex Test Fact Sheet.) 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. 

ARUP Laboratory Tests


Aids in diagnosis and classification of brain tumors

See ARUP Immunohistochemistry Stain Offerings for a complete list of stains

Molecular Markers

Aids in diagnosis, classification, prognosis, and treatment decision-making in oligodendrogliomas

Aids in diagnosis, classification, prognosis, and treatment decision-making in gliomas

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

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

Medical Experts




Joshua M. Klonoski, MD, PhD
Former Resident Physician, Department of Pathology, University of Utah
Former Assistant Medical Director of Informatics and Content Editor at ARUP Laboratories