Diagnosis of childhood brain and spinal cord tumours

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Diagnosis is the process of finding out the cause of a health problem. Diagnosing cancer often means first ruling out other health conditions that share similar symptoms with cancer. It can be a very worrying time for you, your child and your loved ones. Sometimes this process is quick. Sometimes it can feel long and frustrating. But it's important for doctors to get all the information they need before making a diagnosis of cancer.

Diagnosing childhood brain and spinal cord tumours usually begins with a visit to your child's doctor. The doctor will ask about any symptoms your child has and do a physical exam. Based on this information, the doctor may refer your child to a specialist or order tests to check for childhood brain and spinal cord tumours or other health problems.

The following tests are usually used to diagnosis or rule out brain and spinal cord tumours. Many of the same tests used to diagnose cancer are used to find out the stage (how far the cancer has spread). The doctor may also order other tests to check general health and to help plan treatment.

Health history and physical exam

Your child's health history is a record of the symptoms, risks and all the medical events and problems that they have had in the past. The doctor will ask questions about your child’s health history, including their personal or family history of:

  • neurofibromatosis
  • von Hippel-Lindau (VHL) syndrome
  • Li-Fraumeni syndrome
  • tuberous sclerosis
  • Turcot syndrome
  • basal cell nevus syndrome
  • Cowden syndrome
  • Rubinstein-Taybi syndrome (RSTS)

A physical exam allows the doctor to look for any signs of childhood brain and spinal cord tumours. During a physical exam, the doctor will do a neurological exam to check how the child’s brain, spinal cord and nerves are working. It usually involves a series of questions and tests to measure mental status, cranial nerve function, coordination, movement and how well the muscles, senses and reflexes work. A visual field test will be done to measure central vision (how much a person can see when looking straight ahead) and peripheral vision (how far a person can see in all directions when looking straight ahead). Hearing tests may also be done.

Find out more about physical exams.


Magnetic resonance imaging (MRI) uses powerful magnetic forces and radiofrequency waves to make cross-sectional images of organs, tissues, bones and blood vessels. A computer turns the images into 3D pictures.

An MRI is considered the best way to look at tumours in the brain and spinal cord areas. It usually provides more detailed images of soft tissue than CT scans.

You need to lie still for long periods of time during an MRI. Young children may need a general anesthetic or sedative to help them stay still.

The following special types of MRIs might be done to rule out or diagnose a brain or spinal cord tumour.

A contrast MRI (MRI) involves injecting gadolinium (a contrast dye) into a vein to improve the quality of the image and make the blood vessels easier to see. It allows doctors to more easily identify brain tumours.

A magnetic resonance angiography (MRA) and magnetic resonance venography (MRV) are used to look at blood vessels in the brain. These tests are useful for planning surgery.

A magnetic resonance spectroscopy (MRS) shows some features of brain tumours that are not clearly seen with an MRI. It may help doctors determine the possible tumour type. An MRS is used after treatment to see if an abnormal area is a tumour or scar tissue.

A magnetic resonance perfusion (perfusion MRI) shows the amount of blood going through different parts of the brain. It can give doctors an idea of how fast a tumour is growing and help them determine the best place to take a biopsy. It is used after treatment to see if an abnormal area is a tumour or scar tissue. A contrast dye is injected into a vein or IV line for this test.

A functional MRI (fMRI) is a newer type of MRI that looks for tiny changes in blood flow to certain parts of the brain. It can be used to show the part of the brain that functions during a particular activity, such as speaking, thinking, touching or moving. Doctors can use an fMRI to help them plan surgery or radiation therapy. It shows them which areas are important to avoid. It involves asking the child to answer questions or move certain parts of the body while scans are being done.

Diffusion tensor imaging (DTI) is a type of MRI that can give an idea of how the white matter is organized in the brain. This can be helpful for doctors in planning surgery.

Find out more about MRIs.

CT scan

A computed tomography (CT) scan uses special x-ray equipment to make 3-D and cross-sectional images of organs, tissues, bones and blood vessels inside the body. A computer turns the images into detailed pictures.

CT scans are often the first imaging test done to see if there is an abnormality in the brain. If an abnormality is found, an MRI is done. CT scans are very fast and often the child doesn't need to be given a sedative. CT scans may also be used to provide better detail of the bones near the tumour or when an MRI is not an option (for example, for a child who is very sick, unable to stay still or afraid of enclosed spaces). Sometimes a contrast dye will be injected before the scan to get a better picture of any tumours present.

A CT angiography (CTA) shows the blood vessels in the brain and can be used to plan surgery. A contrast dye is injected into a vein or IV line for this test.

Find out more about CT scans.

PET scan

A positron emission tomography (PET) scan uses radioactive materials called radiopharmaceuticals to look for changes in the metabolic activity of body tissues. A computer analyzes the radioactive patterns and makes 3D colour images of the area being scanned.

A PET scan is used to see if abnormal areas seen on an MRI or a CT scan are likely to be cancerous. It may also be used after treatment to see if an abnormal area is a tumour or scar tissue.

PET scans may not be available in all cancer treatment centres. Find out more about PET scans.


During a biopsy, the doctor removes tissues or cells from the body so they can be tested in a lab. The report from a pathologist will confirm whether or not cancer cells are found in the sample.

The type of biopsy commonly used for brain and spinal cord tumours is either a surgical (open) biopsy or a stereotactic (closed) biopsy.

A surgical (open) biopsy is used for tumours that appear to be treatable with surgery based on the imaging tests. It involves taking a biopsy sample during surgery to remove the tumour. The type of surgery used to remove a brain tumour is called a craniotomy. During a craniotomy, part of the skull is removed so the surgeon can reach the tumour. All or most of the tumour is removed. Small samples of the tumour are examined while the child is still in the operating room. This can help guide treatment, including if further surgery should be done at that time. The bone that was removed from the skull to make an opening is usually replaced after the tumour is taken out.

A stereotactic (closed) biopsy may be used for tumours that likely can’t be removed with surgery (for example, tumours that are in vital areas or deep within the brain). A local anesthetic is used to freeze the scalp. The skull and brain do not feel pain. Depending on the situation, the child may be awake or under general anesthesia. A special frame is attached to the child’s head to help the surgeon accurately target the tumour. The surgeon makes a small cut (incision) in the scalp and drills a small hole in the skull. An MRI or a CT scan is usually used along with the frame to help the surgeon guide a hollow needle into the tumour and remove tissue samples for a biopsy.

An image-guided biopsy may be used for some types of tumours. A hollow needle is guided with the aid of a computer through a small hole in the skull into the brain tumour.

A transsphenoidal biopsy may be used for some types of tumours. Instruments are inserted through the nose and sphenoid bone and into the brain.

Find out more about biopsies.

Tumour marker tests

Tumour markers are substances found in the blood, tissues or fluids removed from the body. An abnormal amount of a tumour marker may mean that a child has a brain or spinal cord tumour.

Tumour marker tests can also be used to check a child’s response to cancer treatment, but they can also be used to help diagnose certain types of brain and spinal cord tumours.

Alpha-fetoprotein (AFP) and human chorionic gonadotropin (HCG) are 2 tumour markers that may be higher than normal if a child has a germ cell tumour.

Find out more about tumour markers.

Cell and tissue studies

Doctors can use the following types of cell and tissue studies to help diagnose childhood brain and spinal cord tumours.

Cytogenetics is the analysis of a cell's chromosomes, including their number, size, shape and arrangement. Cytogenetic techniques show chromosomal abnormalities. The results of cytogenetic studies also help doctors plan treatment and predict how well the treatment will work.

Immunophenotyping is the study of proteins expressed by cells. It uses a very specific antigen-antibody reaction to identify specific proteins in tissues or cells. It uses antibodies marked with a fluorescent label that bind only to specific proteins. The fluorescent label and the pattern of proteins that are expressed can help doctors plan treatment and predict how well the treatment will work.

Some changes that doctors may look for include:

  • BRAF gene mutation
  • BRAF gene fusion
  • H3K27M gene mutation
  • H3G34R gene mutation
  • NTRK gene fusion
  • 1p19q deletion
  • IDH1 or IDH2 gene mutations
  • MGMT promoter methylation

Testing for 1p19q deletion, IDH1 or IDH2 gene mutations or MGMT promoter methylation is usually only done in adults, but it can sometimes be done for adolescents.

Find out more about cell and tissue studies.

Lumbar puncture

A lumbar puncture removes a small amount of cerebrospinal fluid (CSF) from the spine to be examined under a microscope. It may be done as part of staging to see if a brain tumour has spread to the CSF. CSF analysis can also show increased levels of human chorionic gonadotrophic (HCG) and alpha-fetoprotein (AFP), which can be higher with germ cell tumours.

Find out more about lumbar punctures.

Complete blood count (CBC)

A complete blood count (CBC) measures the number and quality of white blood cells, red blood cells and platelets. A CBC is done to give the doctors a baseline that they can check against during treatment.

Find out more about a complete blood count (CBC).

Blood chemistry tests

Blood chemistry tests measure certain chemicals in the blood. They show how well certain organs are working and can help find problems.

Find out more about blood chemistry tests.


During an angiography, a contrast dye is injected into the bloodstream and x-rays are taken to map out the size and shape of blood vessels. It is used to look at the blood vessels and the flow of blood in the brain, which is helpful in planning surgery. In recent years, angiography has been mostly replaced by other tests, such as a magnetic resonance angiography and a CT angiography.

Find out more about angiography.

Questions to ask your healthcare team

To make the decisions that are right for your child, ask the healthcare team questions about a diagnosis.

Expert review and references

  • Donna Johnston, MD
  • Nirav Thacker, MD
  • American Society of Clinical Oncology (ASCO) . Cancer.net: Central Nervous System Tumors (Brain and Spinal Cord) - Childhood. 2021: https://www.cancer.net/.
  • American Cancer Society. Brain and Spinal Cord Tumors in Children Early Detection, Diagnosis and Staging . 2018: https://www.cancer.org/.
  • Cancer Research UK. Tests for a Brain Tumour. 2019: https://www.cancerresearchuk.org/.
  • PDQ® Adult Treatment Editorial Board. Childhood Central Nervous System Germ Cell Tumors Treatment (PDQ®)–Health Professional Version . Bethesda, MD: National Cancer Institute; 2022: https://www.cancer.gov/.

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