Primary Brain Tumors – Brain Tumor Molecular Markers

Last Literature Review: May 2021 Last Update:

Medical Experts




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

Brain tumors comprise a heterogeneous group of abnormal collections of benign or malignant cells that may present with a variety of symptoms, including cognitive dysfunction, psychiatric disorders, and seizures. Brain tumors are diagnosed and classified using a combination of histology and molecular markers (eg, IDH1/2 variants and 1p/19q codeletion).   Molecular tests may also be used for prognosis/risk stratification, treatment decision-making (eg, MGMT promoter methylation), and to determine clinical trial eligibility. 

Quick Answers for Clinicians

What is the role of targeted and whole exome testing in brain cancer?

Targeted and whole exome genomic 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 pangenomic tests is currently low. However, targeted testing for specific, well-validated variants is more frequently utilized in routine patient care.

Which tumor types must be distinguished from primary brain tumors?

Some cancers, particularly breast cancerlung cancer, or melanoma, may metastasize to the brain. For more information on testing for these cancers, see the ARUP Consult Breast Cancer BiomarkersMelanoma, and Non-Small Cell Lung Cancer 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, to investigate for metastases, and in monitoring.  CSF should be obtained via lumbar puncture when possible, safe, and not contraindicated.  Lumbar puncture should not be performed before imaging studies or within 2 weeks after surgery due to the possibility of false-positive results.  CSF analysis should include a cell count with differential, as well as glucose and protein analysis. For solid tumors, cytology is recommended. 

Should molecular marker testing be performed in glioblastoma?

Although there are no targeted treatments for glioblastoma, molecular testing in glioblastoma is encouraged by the National Comprehensive Cancer Network.  Molecular testing may inform treatment as part of a clinical trial or for compassionate use. 

Indications for Testing

After thorough physical and neurologic examinations, imaging, and cerebrospinal fluid (CSF) analysis (if appropriate), individuals with brain tumors should undergo biopsy and/or resection 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
Diffuse astrocytic and oligodendroglial tumorsa

Diffuse astrocytoma



Other astrocytic tumorsPilocytic astrocytoma
Ependymal tumorsbEpendymoma
Other gliomas

Angiocentric glioma


Chordoid glioma

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

Central neurocytoma



Tumors of the pineal regionPineoblastoma
Embryonal tumorsMedulloblastomac
Tumors of the cranial and paraspinal nerves



MeningiomasAnaplastic meningioma
Mesenchymal, nonmeningothelial tumors

Ewing sarcoma/PNET


Melanocytic tumorsMeningeal melanoma
LymphomasDiffuse large B-cell lymphoma of the central nervous system
Histiocytic tumorsHistiocytic sarcoma
Germ cell tumors

Embryonal carcinoma


Tumors of the sellar region



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.  Enough tissue should be obtained from biopsy or resection for both histology and molecular testing. 


Specimens obtained via needle biopsy may not be suitable for histology, given that 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, provided that the appropriate caveats are noted.   For example, tumors cannot be classified as oligoastrocytomas 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. 

Brain Tumor Molecular Markers
MarkerUse of Laboratory TestingAnalysis TechniquesClinical Implications
1p/19q codeletionRecommended in oligodendrogliomas

Array-based testing


Massively parallel sequencing


Codeletion associated with:

  • Favorable prognosis
  • Response to alkylating chemotherapy
  • Response to combination therapy

Codeletion mutually exclusive with wild-type IDH and not usually found with ATRX variants

Presence of both codeletion and IDH variant defines oligodendroglioma

ATRX variants (decreased ATRX expression)Strongly recommended for gliomas



ATRX variants associated with:

  • IDH variants
  • Astrocytoma (if IDH variant present)

ATRX variants rarely found with 1p/19q codeletion

IDH sequencing is recommended if ATRX expression is absent and IDH1 R132H is negative by IHC

BRAF fusion/variantsRecommended if clinically appropriate

PCR (fusions)

RNA sequencing (fusions)

Sequencing (V600E and other variants)

Fusions associated with:

  • Indolent tumors
  • Pilocytic astrocytomas

V600E variant:

  • May be associated with increased response to BRAF inhibitors
  • Must be interpreted in conjunction with histology and other prognostic factors
H3F3A and HIST1H3B variantsRecommended if clinically appropriateAntibody testing (H3K27M variant)

K27M variant associated with poor prognosis

Histone variants suggest infiltrative glioma

IDH1 and IDH2 variants

Recommended in all gliomas

Sequencing recommended if IDH1 R132H negative by IHC

IHC (R132H variant)


Presence of both variant and 1p/19q codeletion defines oligodendroglioma

Variants associated with:

  • Favorable prognosis
  • Increased survival with alkylating chemotherapy or radiation
  • Lower probability of aggressive disease in grade 2 or 3 infiltrative gliomas
  • MGMT promoter methylation

Variants define:

  • Grade 2 and 3 astrocytomas
  • Grade 2 and 3 oligodendrogliomas
  • Secondary grade 4 glioblastomas

Variants not present in:

  • Grade1 noninfiltrative gliomas
  • Primary glioblastomas

Wild type is mutually exclusive with 1p/19q codeletion

MGMT promoter methylationRecommended for all grade 3 and 4 gliomas

Array-based testing

PCR (methylation specific)


Methylation associated with:

  • Epigenetic changes across the genome
  • IDH variants
  • Increased survival in glioblastoma
  • Sensitivity to alkylating chemotherapy
RELA fusionsRecommended if clinically appropriate


RNA sequencing

Fusions associated with:

  • Ependymomas
  • Increased tumor aggressiveness
TERT variantsRecommended for gliomasSequencing

TERT variant in the presence of 1p/19q codeletion and IDH variant is typical of oligodendroglioma

Variants associated with:

  • 1p/19q codeletions
  • Favorable prognosis (if IDH variant present)
  • Glioblastomas
  • Less favorable prognosis in diffusely infiltrative glioma (if no IDH variant present)
  • Oligodendrogliomas

Wild-type TERT in the presence of an IDH variant is characteristic of astrocytoma

FISH, fluorescence in situ hybridization; IHC, immunohistochemistry; PCR, polymerase chain reaction

Source: NCCN, 2020 

Other Molecular Markers

Molecular markers, including SHH activation, TP53 variants, and WNT activation, are used in the classification of medulloblastomas.  These markers are not specific to, or diagnostic of, medulloblastoma.  WNT-activated tumors have a better prognosis than non-WNT/non-SHH, SHH-activated/TP53 variant, and SHH-activated/TP53 wild-type tumors.  The National Comprehensive Cancer Network (NCCN) recommends that testing for these markers be performed by a center with specialized expertise. 

Many other potential molecular markers are currently being investigated for use in the classification, diagnosis, and prognosis of gliomas (eg, CDKN2A/B loss or deletion, EGFR amplification, PTEN loss or promoter methylation). 

Molecular markers may also be useful in patients with brain metastases from breast cancer, melanoma, or non-small cell lung cancer. 

Familial Genetic Testing

A number of genetic syndromes have been associated with brain tumors (particularly pediatric brain cancer), including tuberous sclerosis complex.  Genetic 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, but are not limited to, 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 both astrocytoma and melanoma in the individual or in 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 commonly occur in patients with brain tumors, and such disorders may be affected by treatment.  Evaluation of adrenal, hypothalamic, pituitary, and thyroid function is recommended for patients who report decreased quality of life.  Long-term monitoring of the hypothalamic-pituitary-adrenal axis may be appropriate in patients who were treated with radiation.  Monitoring of the effects of steroid therapy, including monitoring for adrenal insufficiency if a patient is being weaned off of long-term steroid therapy, is recommended. 

ARUP Laboratory Tests


See ARUP Immunohistochemistry Stain Offerings for a complete list of stains

Molecular Markers

Familial Genetic Testing

For additional test information, refer to the Hereditary Central Nervous System Cancer Panel, Sequencing and Deletion/Duplication Test Fact Sheet