Usually—depending on the interview of the patient and after a clinical exam which includes a neurological exam, and an ophthalmological exam—a CT scan and or MRI scan will be performed. A special dye may be injected into a vein before these scans to provide contrast and make tumors easier to identify. The neoplasm will be clearly visible.

If a tumor is found, it will be necessary for a neurosurgeon to perform a biopsy of it. This simply involves the removal of a small amount of tumorous tissue, which is then sent to a (neuro)pathologist for examination and staging. The biopsy may take place before surgical removal of the tumor or the sample may be taken during surgery.

Craniopharyngiomas are usually successfully managed with a combination of adjuvant chemotherapy and neurosurgery. Recent research describes the rare occurrence of malignant transformations of these normally benign tumors. Malignant craniopharyngiomas can occur at any age, are slightly more common in females, and are usually of the adamantinomatous type.

The malignant transformations can take years to occur (although 1 in 5 of the diagnosed cases were de novo transformations), hence the need for lengthier follow up in patients diagnosed with the more common benign forms.

There was no link found between malignancy and initial chemo-radiotherapy treatment, and the overall survival rate was very poor with median survival being 6 months post diagnosis of malignancy.

There are a few scans and tests that the physician can conduct in order to diagnose a person with craniopharyngioma. Your doctor may order a high-resolution magnetic resonance imaging (MRI) scan. This test is valuable because it allows the neuroradiologist to view the tumor from different angles.

In some cases, a powerful 3T (Tesla) MRI scanner can help define the location of critical brain structures affected by the tumor.The histologic pattern consists of nesting of squamous epithelium bordered by radially arranged cells. It is frequently accompanied by calcium deposition and may have a microscopic papillary architecture.A computed tomography (CT) scan is also a good diagnostic tool as it detects calcification in the tumor.

Two distinct types are recognized:

- Adamantinomatous craniopharyngiomas, which resemble ameloblastomas (the most common type of odontogenic tumor), are characterized by activating CTNNB1 mutations; and,

- Papillary craniopharyngiomas are characterized by BRAFv600E mutations.

In the adamantinomatous type, calcifications are visible on neuroimaging and are helpful in diagnosis.

The papillary type rarely calcifies. A vast majority of craniopharyngiomas in children are adamantiomatous whereas both subtypes are common in adults. Mixed type tumors also occur.

On macroscopic examination, craniopharyngiomas are cystic or partially cystic with solid areas. On light microscopy, the cysts are seen to be lined by stratified squamous epithelium. Keratin pearls may also be seen. The cysts are usually filled with a yellow, viscous fluid which is rich in cholesterol crystals. Of a long list of possible symptoms, the most common presentations include: headaches, growth failure, and bitemporal hemianopsia.

Microscopically, an astrocytoma is a mass that looks well-circumscribed and has a large cyst. The neoplasm may also be solid.

Under the microscope, the tumor is seen to be composed of bipolar cells with long "hairlike" GFAP-positive processes, giving the designation "pilocytic" (that is, made up of cells that look like fibers when viewed under a microscope). Some pilocytic astrocytomas may be more fibrillary and dense in composition. There is often presence of Rosenthal fibers, eosinophilic granular bodies and microcysts. Myxoid foci and oligodendroglioma-like cells may also be present, though non-specific. Long-standing lesions may show hemosiderin-laden macrophages and calcifications.

The standard work-up for AT/RT includes:

- Magnetic resonance imaging (MRI) of the brain and spine

- Lumbar puncture to look for M1 disease

- Computed tomography (CT) of chest and abdomen to check for a tumor

- Bone marrow aspiration to check for bone tumors. Sometimes the physician will perform a stem cell transplant

- Bone marrow biopsy

- Bone scan

The initial diagnosis of a tumor is made with a radiographic study (MRI or CT-). If CT was performed first, an MRI is usually performed as the images are often more detailed and may reveal previously undetected metastatic tumors in other locations of the brain. In addition, an MRI of the spine is usually performed. The AT/RT tumor often spreads to the spine. AT/RT is difficult to diagnose only from radiographic study; usually, a pathologist must perform a cytological or genetic analysis.

Examination of the cerebrospinal fluid is important (CSF), as one-third of patients will have intracranial dissemination with involvement of the CSF. Large tumor cells, eccentricity of the nuclei, and prominent nucleoli are consistent findings. Usually only a minority of AT/RT biopsies have rhabdoid cells, making diagnosis more difficult. Increasingly it is recommended that a genetic analysis be performed on the brain tumor, especially to find if a deletion in the INI1/hSNF5 gene is involved (appears to account for over 80% of the cases). The correct diagnosis of the tumor is critical to any protocol. Studies have shown that 8% to over 50% of AT/RT tumors are diagnosed incorrectly.

The purpose of radiologic imaging is to locate the lesion, evaluate for signs of invasion and detect metastasis. Features of GIST vary depending on tumor size and organ of origin. The diameter can range from a few millimeters to more than 30 cm. Larger tumors usually cause symptoms in contrast to those found incidentally which tend to be smaller and have better prognosis. Large tumors tend to exhibit malignant behavior but small GISTs may also demonstrate clinically aggressive behavior.

Plain radiographs are not very helpful in the evaluation of GISTs. If an abnormality is seen, it will be an indirect sign due to the tumor mass effect on adjacent organs. On abdominal x-ray, stomach GISTs may appear as a radiopaque mass altering the shape of the gastric air shadow. Intestinal GISTs may displace loops of bowel and larger tumors may obstruct the bowel and films will show an obstructive pattern. If cavitations are present, plain radiographs will show collections of air within the tumor. Calcification is an unusual feature of GIST but if present can be visible on plain films.

Barium fluoroscopic examinations and CT are commonly used to evaluate the patient with abdominal complaints. Barium swallow images show abnormalities in 80% of GIST cases. However, some GISTs may be located entirely outside the lumen of the bowel and will not be appreciated with a barium swallow. Even in cases when the barium swallow is abnormal, an MRI or CT scan must follow since it is impossible to evaluate abdominal cavities and other abdominal organs with a barium swallow alone. In a CT scan, abnormalities may be seen in 87% of patients and it should be made with both oral and intravenous contrast. Among imaging studies, MRI has the best tissue contrast, which aids in the identification of masses within the GI tract (intramural masses). Intravenous contrast material is needed to evaluate lesion vascularity.

Preferred imaging modalities in the evaluation of GISTs are CT and MRI, and, in selected situations, endoscopic ultrasound. CT advantages include its ability to demonstrate evidence of nearby organ invasion, ascites, and metastases. The ability of MRI to produce images in multiple planes is helpful in determining the bowel as the organ of origin (which is difficult when the tumor is very large), facilitating diagnosis.

CT scanning is often undertaken (see the "radiology" section).

The definitive diagnosis is made with a biopsy, which can be obtained endoscopically, percutaneously with CT or ultrasound guidance or at the time of surgery. A biopsy sample will be investigated under the microscope by a pathologist physician. The pathologist examines the histopathology to identify the characteristics of GISTs (spindle cells in 70-80%, epitheloid aspect in 20-30%). Smaller tumors can usually be confined to the muscularis propria layer of the intestinal wall. Large ones grow, mainly outward, from the bowel wall until the point where they outstrip their blood supply and necrose (die) on the inside, forming a cavity that may eventually come to communicate with the bowel lumen.

When GIST is suspected—as opposed to other causes for similar tumors—the pathologist can use immunohistochemistry (specific antibodies that stain the molecule CD117 [also known as "c-kit"] —see below). 95% of all GISTs are CD117-positive (other possible markers include CD34, DOG-1, desmin, and vimentin). Other cells that show CD117 positivity are mast cells.

If the CD117 stain is negative and suspicion remains that the tumor is a GIST, the newer antibody DOG-1 (Discovered On GIST-1) can be used. Also sequencing of Kit and PDGFRA can be used to prove the diagnosis.

Cytogenetics is the study of a tumor’s genetic make-up. Fluorescent "in situ" hybridization may be able to help locate a mutation or abnormality that may be allowing tumor growth. This technique has been shown to be useful in identifying some tumors and distinguishing two histologically similar tumors from each other (such as AT/RTs and PNETs). In particular, medulloblastmas/PNETs may possibly be differentiated cytogenetically from AT/RTs, as chromosomal deletions of 17p are relatively common with medulloblastoma and abnormalities of 22q11.2 are not seen. However, chromosomal 22 deletions are very comomon in AT/RTs.

In importance of the "hSNF5/INI1" gene located on chromosomal band 22q11.2 is highlighted, as the mutation’s presence is sufficient to change the diagnosis from a medulloblastoma or PNET to the more aggressive AT/RT classification. However, this mutation is not present in 100% of cases. Therefore, if the mutation is not present in an otherwise classic AT/RT immunohistochemical and morphologic pattern then the diagnosis remains an AT/RT.

Treatment of choroid plexus carcinoma depends on the location and severity of the tumor. Possible interventions include inserting shunts, surgical resection, radiotherapy, and chemotherapy. Inserting a shunt could help to drain the CSF and relieve pressure on the brain. The best outcomes occur when total resection of the tumor is combined with adjuvant chemotherapy and radiotherapy. In the event of subtotal resection or widespread leptomeningeal disease, craniospinal irradiation is often used.

Choroid plexus tumors have an annual incidence of about 0.3 per 1 million cases.

It is seen mainly in children under the age of 5, representing 5% of all pediatric tumors and 20% of tumors in children less than 1 year old. There has been no link between sex and occurrence.

Although choroid plexus carcinomas are significantly more aggressive and have half the survival rate as choroid plexus papillomas, they are outnumbered in incidence by 5:1 in all age groups. Clinical studies have shown that patients who receive a total resection of a tumor have a 86% survival rate, while patients who only receive a partial resection have a 26% 5-year survival rate. Many incomplete resections result in recurrence within 2 years of primary surgery.

Choroid plexus papillomas are benign tumors that are usually cured by surgery; malignant progression has been rarely reported.

The 5-year disease-free survival for age >5 years is 50-60%. Another report found a similar 5-year survival at about 65% with 51% progression-free survival. The 10-year disease-free survival is 40-50%. Younger ages showed lower 5 and 10-year survival rates. A 2006 study that observed 133 patients found 31 (23.3%) had a recurrence of the disease within a five-year period.

Use of telomerase inhibitors such as Imetelstat seem to have very low toxicity compared to other chemotherapy. The only known side effect of most telomerase inhibitors is dose-induced neutropenia. Neuropsychological deficits can result from resection, chemotherapy, and radiation, as well as endocrinopathies. Additionally, an increase in gastrointestinal complications has been observed in survivors of pediatric cancers.

Imaging studies such as X-rays, computed tomography scans, or MRI may be required to diagnose clear-cell sarcoma together with a physical exam. Normally a biopsy is also necessary. Furthermore, a chest CT, a bone scan and positron emission tomography (PET) may be part of the tests in order to evaluate areas where metastases occur.

Internationally tumors of the choroid plexus are rare, accounting for 0.4-0.6% of all intracranial neoplasms. It most commonly affects young children under the age of 5 with a mean patient age of 5.2 years.

Recurrence is common, although the recurrence rates for block resection followed by bone graft are lower than those of enucleation and curettage. Follicular variants appear to recur more than plexiform variants. Unicystic tumors recur less frequently than "non-unicystic" tumors. Persistent follow-up examination is essential for managing ameloblastoma. Follow up should occur at regular intervals for at least 10 years. Follow up is important, because 50% of all recurrences occur within 5 years postoperatively. Recurrence within a bone graft (following resection of the original tumor) does occur, but is less common. Seeding to the bone graft is suspected as a cause of recurrence. The recurrences in these cases seem to stem from the soft tissues, especially the adjacent periosteum. Recurrence has been reported to occur as many as 36 years after treatment.

To reduce the likelihood of recurrence within grafted bone, meticulous surgery with attention to the adjacent soft tissues is required.

Pituitary incidentalomas are pituitary tumors that are characterized as an incidental finding. They are often discovered by computed tomography (CT) or magnetic resonance imaging (MRI), performed in the evaluation of unrelated medical conditions such as suspected head trauma, in cancer staging or in the evaluation of nonspecific symptoms such as dizziness and headache. It is not uncommon for them to be discovered at autopsy. In a meta-analysis, adenomas were found in an average of 16.7% in postmortem studies, with most being microadenomas (<10mm); macrodenomas accounted for only 0.16% to 0.2% of the decedents. While non-secreting, noninvasive pituitary microadenomas are generally considered to be literally as well as clinically benign, there are to date scant studies of low quality to support this assertion.

It has been recommended in the current Clinical Practice Guidelines (2011) by the Endocrine Society - a professional, international medical organization in the field of endocrinology and metabolism - that all patients with pituitary incidentalomas undergo a complete medical history and physical examination, laboratory evaluations to screen for hormone hypersecretion and for hypopituitarism. If the lesion is in close proximity to the optic nerves or optic chiasm, a visual field examination should be performed. For those with incidentalomas which do not require surgical removal, follow up clinical assessments and neuroimaging should be performed as well follow-up visual field examinations for incidentalomas that abut or compress the optic nerve and chiasm and follow-up endocrine testing for macroincidentalomas.

While chemotherapy, radiation therapy, curettage and liquid nitrogen have been effective in some cases of ameloblastoma, surgical resection or enucleation remains the most definitive treatment for this condition. In a detailed study of 345 patients, chemotherapy and radiation therapy seemed to be contraindicated for the treatment of ameloblastomas. Thus, surgery is the most common treatment of this tumor. Because of the invasive nature of the growth, excision of normal tissue near the tumor margin is often required. Some have likened the disease to basal cell carcinoma (a skin cancer) in its tendency to spread to adjacent bony and sometimes soft tissues without metastasizing. While rarely not a cancer that actually invades adjacent tissues, ameloblastoma is suspected to spread to adjacent areas of the jaw bone via marrow space. Thus, wide surgical margins that are clear of disease are required for a good prognosis. This is very much like surgical treatment of cancer. Often, treatment requires excision of entire portions of the jaw.

Radiation is ineffective in many cases of ameloblastoma. There have also been reports of sarcoma being induced as the result of using radiation to treat ameloblastoma. Chemotherapy is also often ineffective. However, there is some controversy regarding this and some indication that some ameloblastomas might be more responsive to radiation that previously thought.

Unlike tumors of the posterior Pituitary, Pituitary adenomas are classified as endocrine tumors (not brain tumors). Pituitary adenomas are classified based upon anatomical, histological and functional criteria.

- Anatomically pituitary tumors are classified by their size based on radiological findings; either microadenomas (less than <10 mm) or macroadenomas (equal or greater than ≥10 mm).

- Histological classification utilizes an immunohistological characterization of the tumors in terms of their hormone production. Historically they were classed as either basophilic, acidophilic, or chromophobic on the basis of whether or not they took up the tinctorial stains hematoxylin and eosin. This classification has fallen into disuse, in favor of a classification based on what type of hormone is secreted by the tumor. Approximately 20-25% of adenomas do not secrete any readily identifiable active hormones ('non-functioning tumors') yet they are still sometimes referred to as 'chromophobic'.

- Functional classification is based upon the tumors endocrine activity as determined by serum hormone levels and pituitary tissue cellular hormone secretion detected via immunohistochemical staining. The "Percentage of hormone production cases" values are the fractions of adenomas producing each related hormone of each tumor type as compared to all cases of pituitary tumors, and does not directly correlate to the percentages of each tumor type because of smaller or greater incidences of absence of secretion of the expected hormone. Thus, nonsecretive adenomas may be either "null cell adenomas" or a more specific adenoma that, however, remains nonsecretive.

2004 research showed that CCSK patients exhibit an improved relapse-free survival from a longer course of therapy when using vincristine, doxorubicin, and dactinomycin, but their long-term survival is unchanged compared with patients receiving 6 months of therapy.

Treatment depends upon the site and the extent of the disease. Clear cell sarcoma is usually treated with surgery in the first place in order to remove the tumor. The surgical procedure is then followed by radiation and sometimes chemotherapy. Few cases of clear cell sarcoma respond to chemotherapy. Several types of targeted therapy that may be of benefit to clear cell sarcoma patients are currently under investigation.

GCNIS is not palpable, and not visible on macroscopic examination of testicular tissue. Microscopic examination of affected testicular tissue most commonly shows germ cells with enlarged hyperchromatic nuclei with prominent nucleoli and clear cytoplasm. These cells are typically arranged along the basement membrane of the tubule, and mitotic figures are frequently seen. The sertoli cells are pushed toward the lumen by the neoplastic germ cells, and spermatogenesis is almost always absent in the affected tubules. Pagetoid spread of GCNIS into the rete testis is common. Immunostaining with placental alkaline phosphatase (PLAP) highlights GCNIS cell membranes in 95 percent of cases. OCT3/4 is a sensitive and specific nuclear stain of GCNIS.

Its presence is associated with either pilocytic astrocytoma (more common) or Alexander's disease (a rare leukodystrophy). They are also seen in the context of fucosidosis.

Pilocytic astrocytoma is the most common primitive tumor in pediatric patients.

A Rosenthal fiber is a thick, elongated, worm-like or "corkscrew" eosinophilic (pink) bundle that is found on H&E staining of the brain in the presence of long-standing gliosis, occasional tumors, and some metabolic disorders.

Research in 2005 showed that CCSK can arise within a renal mesenchymal cell that shows a wide variety of neural markers. Typical presentation is between 1 and 4 years of age, and a 2:1 male-to-female ratio is observed.