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.

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.

Medulloblastomas affect just under two people per million per year, and affect children 10 times more than adults. Medulloblastoma is the second-most frequent brain tumor in children after pilocytic astrocytoma and the most common malignant brain tumor in children, comprising 14.5% of newly diagnosed cases. In adults, medulloblastoma is rare, comprising fewer than 2% of CNS malignancies.

The rate of new cases of childhood medulloblastoma is higher in males (62%) than females (38%), a feature which is not seen in adults. Medulloblastoma and other PNET`s are more prevalent in younger children than older children. About 40% of medulloblastoma patients are diagnosed before the age of five, 31% are between the ages of 5 and 9, 18.3% are between the ages of 10 and 14, and 12.7% are between the ages of 15 and 19.

The cumulative relative survival rate for all age groups and histology follow-up was 60%, 52%, and 47% at 5 years, 10 years, and 20 years, respectively. Patients diagnosed with a medulloblastoma or PNET are 50 times more likely to die than a matched member of the general population.

The most recent population-based (SEER) 5-year relative survival rates are 69% overall, but 72% in children (1–9 years) and 67% in adults (20+ years). The 20-year survival rate is 51% in children. Children and adults have different survival profiles, with adults faring worse than children only after the fourth year after diagnosis (after controlling for increased background mortality). Before the fourth year, survival probabilities are nearly identical. Longterm sequelae of standard treatment include hypothalamic-pituitary and thyroid dysfunction and intellectual impairment. The hormonal and intellectual deficits created by these therapies causes significant impairment of the survivors.

Esthesioneuroblastoma is a slow developing but malignant tumor with high reoccurrence rates because of its anatomical position. The tumor composition, location and metastatic characteristics as well as the treatment plan determine prognosis. Common clinical classification systems for esthesioneuroblastoma include the Kadish classification and the Dulguerov classfictation. Histopathological characteristics on top of Kadish classification can further determine cancer prognosis. In severe, Kadish class C tumors, Haym's grades of pathology are important for prognosis. Patients with low grade Kadish class C tumors have a 10-year survival rate of 86 percent compared to patients with high grade class C tumors who have a survival rate of 28 percent. Surgically treated patients with high grade tumors are more likely to experience leptomeningeal metastases or involvement of the cerebral spinal fluid unlike patients with low grade tumors who usually only see local recurrence. Survival rates for treated esthesioneuroblastoma are best for surgery with radiotherapy (65%), then for radiotherapy and chemotherapy (51%), just surgery (48%), surgery, radiotherapy and chemotherapy (47) and finally just radiotherapy (37%). From the literature, radiotherapy and surgery seem to boast the best outcome for patients. However, it is important to understand that to some degree, prognosis is related to tumor severity. More progressed, higher grade tumors would result in chemotherapy or radiotherapy as the only treatment. It is no surprise that the prognosis would be worse in these cases.

If the eye examination is abnormal, further testing may include imaging studies, such as computerized tomography (CT), magnetic resonance imaging (MRI), and ultrasound. CT and MRI can help define the structure abnormalities and reveal any calcium depositions. Ultrasound can help define the height and thickness of the tumor. Bone marrow examination or lumbar puncture may also be done to determine any metastases to bones or the brain.

Esthesioneuroblastoma can resemble small blue cell tumors like squamous cell carcinoma, sinonasal undifferentiated carcinoma, extranodal NK/T cell lymphoma, nasal type, rhabdomyosarcoma, Ewing/PNET, mucosal malignant melanoma and neuroendocrine carcinomas (NEC) that occur in the intranasal tract. Compared to other tumors in the region, esthesioneuroblastoma has the best prognosis, with an overall 5 year survival rate of 60-80%. Fewer than 700 cases have been documented in the United States alone. Esthesioneuroblastoma is characterized by neurofibrillary stroma and neurosecretary granules that are not seen concurrently by any other pathologies in the region. Histological tests such as keratin, CK5/6, S-100 protein or NSE can be run to further differentiate esthesioneuroblastoma from other tumors.

Identifying the "RB1" gene mutation that led to a child's retinoblastoma can be important in the clinical care of the affected individual and in the care of (future) siblings and offspring.It may run in the family.

1. Bilaterally affected individuals and 13-15% of unilaterally affected individuals, are expected to show an RB1 mutation in blood. By identifying the "RB1" mutation in the affected individual, (future) siblings, children, and other relatives can be tested for the mutation; if they do not carry the mutation, child relatives are not at risk of retinoblastoma so need not undergo the trauma and expense of examinations under anaesthetic. For the 85% of unilaterally affected patients found not to carry either of their eye tumor RB1 mutations in blood, neither molecular testing nor clinical surveillance of siblings is required.

2. If the "RB1" mutation of an affected individual is identified, amniotic cells in an at-risk pregnancy can be tested for the family mutation; any fetus that carries the mutation can be delivered early, allowing early treatment of any eye tumors, leading to better visual outcomes.

3. For cases of unilateral retinoblastoma where no eye tumor is available for testing, if no "RB1" mutation is detected in blood after high sensitivity molecular testing (i.e. >93% RB1 mutation detection sensitivity), the risk of a germline "RB1" mutation is reduced to less than 1%, a level at which only clinic examination (and not examinations under anaesthetic) is recommended for the affected individual and their future offspring (National Retinoblastoma Strategy, Canadian Guidelines for Care).

Because of the rarity of these tumors, there is still a lot of unknown information. There are many case studies that have been reported on patients who have been diagnosed with this specific type of tumor. Most of the above information comes from the findings resulting from case studies.

Since Papillary Tumors of the Pineal Region were first described in 2003, there have been seventy cases published in the English literature. Since there is such a small number of cases that have been reported, the treatment guidelines have not been established. A larger number of cases that contain a longer clinical follow-up are needed to optimize the management of patients with this rare disease.

Even though there is a general consensus on the morphology and the immunohistochemical characteristics that is required for the diagnosis, the histological grading criteria have yet to be fully defined and its biological behavior appears to be variable. This specific type of tumor appears to have a high potential for local recurrence with a high tumor bed recurrence rate during the five years after the initial surgery. This suggests the need for a tumor bed boost radiotherapy after surgical resection.

As stated above, the specific treatment guidelines have not yet been established, however, gross total resection of the tumor has been the only clinical factor associated overall and progression-free survival. The value of radiotherapy as well as chemotherapy on disease progression will need to be investigated in future trials. With this information, it will provide important insight into long-term management and may further our understanding of the histologic features of this tumor.

The diagnosis of salivary gland tumors utilize both tissue sampling and radiographic studies. Tissue sampling procedures include fine needle aspiration (FNA) and core needle biopsy (bigger needle comparing to FNA). Both of these procedures can be done in an outpatient setting. Diagnostic imaging techniques for salivary gland tumors include ultrasound, computer tomography (CT) and magnetic resonance imaging (MRI).

Fine needle aspiration biopsy (FNA), operated in experienced hands, can determine whether the tumor is malignant in nature with sensitivity around 90%. FNA can also distinguish primary salivary tumor from metastatic disease.

Core needle biopsy can also be done in outpatient setting. It is more invasive but is more accurate compared to FNA with diagnostic accuracy greater than 97%. Furthermore, core needle biopsy allows more accurate histological typing of the tumor.

In terms of imaging studies, ultrasound can determine and characterize superficial parotid tumors. Certain types of salivary gland tumors have certain sonographic characteristics on ultrasound. Ultrasound is also frequently used to guide FNA or core needle biopsy.

CT allows direct, bilateral visualization of the salivary gland tumor and provides information about overall dimension and tissue invasion. CT is excellent for demonstrating bony invasion. MRI provides superior soft tissue delineation such as perineural invasion when compared to CT only.

It is classified into two types, based on location in the body: peripheral PNET and CNS PNET.

Intracranial germinoma occurs in 0.7 per million children. As with other germ cell tumors (GCTs) occurring outside the gonads, the most common location of intracranial germinoma is on or near the midline, often in the pineal or suprasellar areas; in 5-10% of patients with germinoma in either area, the tumor is in both areas. Like other (GCTs), germinomas can occur in other parts of the brain. Within the brain, this tumor is most common in the hypothalamic or hypophyseal regions. In the thalamus and basal ganglia, germinoma is the most common GCT.

The diagnosis of an intracranial germinoma usually is based on biopsy, as the features on neuroimaging appear similar to other tumors.

Cytology of the CSF often is studied to detect metastasis into the spine. This is important for staging and radiotherapy planning.

Intracranial germinomas have a reported 90% survival to five years after diagnosis. Near total resection does not seem to influence the cure rate, so gross total resection is not necessary and can increase the risk of complications from surgery. The best results have been reported from craniospinal radiation with local tumor boost of greater than 4,000 cGy.

Pineoblastoma (also pinealoblastoma) is a malignant tumor of the pineal gland. A pineoblastoma is a supratentorial midline primitive neuroectodermal tumor.

Pineoblastoma may occur in patients with hereditary uni- or bilateral retinoblastoma. When retinoblastoma patients present with pineoblastoma this is characterized as "trilateral retinoblastoma". Up to 5% of patients with hereditary retinoblastoma are at risk of developing trilateral retinoblastoma. Prognosis of patients with trilateral retinoblastoma is dismal, only a few patients have survived more than 5 years after diagnosis; all survivors were diagnosed with small tumors in a subclinical stage. Recent advances in (high-dose) chemotherapy treatment regimens and early detection have improved survival of patients with trilateral retinoblastoma to up to 50%.

Germinomas, like several other types of germ cell tumor, are sensitive to both chemotherapy and radiotherapy. For this reason, treatment with these methods can offer excellent chances of longterm survival, even cure.

Although chemotherapy can shrink germinomas, it is not generally recommended alone unless there are contraindications to radiation. In a study in the early 1990s, carboplatinum, etoposide and bleomycin were given to 45 germinoma patients, and about half the patients relapsed. Most of these relapsed patients were then recovered with radiation or additional chemotherapy.

MEM comprises a heterogeneous group of neoplasms believed to originate from the neural crest. First hints to this type of tumor were probably from Shuangshoti and Nestky (1971) and from Holimon and Rosenblum (1971) (2-3). Additional contributions were provided thereafter by Naka et al. (1975), Karcioglu et al. (1977), Cozzutto et al. (1982) and Kawamoto et al. (1987).

Kosem et al. collected 44 cases of MEM in a 2004 review and examined management data finding out that resection with pre- or post-surgery chemotherapy yielded the best results with one death only in 13. In the five cases reported by Mouton et al. an aggressive chemotherapy and adequate surgical excision granted a disease-free interval for 7 to 50 months. The attainability of radical surgical

ablation seems the most important prognostic factor (10).

Papillary tumors of pineal region are extremely rare, constituting 0.4-1% of all central nervous system tumors. These tumors most commonly occur in adults with the mean age being 31.5. There have been cases reported for people between the ages 5 to 66 years. There is a slight predominance of females who have these tumors.

The peripheral PNET (pPNET) is now thought to be virtually identical to Ewing sarcoma:

"Current evidence indicates that both Ewing's sarcoma and PNET have a similar neural phenotype and, because they share an identical chromosome translocation, they should be viewed as the same tumor, differing only in their degree of neural differentiation. Tumors that demonstrate neural differentiation by light microscopy, immunohistochemistry, or electron microscopy have been traditionally labeled PNETs, and those that are undifferentiated by these analyses have been diagnosed as Ewing's sarcoma."

The main features of this tumor is to comprise either ectodermal derivatives (neuroblasts and ganglion cells) or mesenchymal components mostly represented by plump, elongated cells in interlacing bundles often showing rhabdomyoblastic differentiation, including strap-like and racket-shaped cells (2-6). A myofibril-like structure and cross striations can be identified. Liposarcoma-like and chondroid foci can be an additional finding. Fibrosarcoma-like and fibrous histiocytoma-like areas can be observed as well as neurofibromatous and neuroblastic components with rosette formation. Ganglion cells can appear immature and atypical, they can be bi- or multinucleated and showing evidence of Nissl substance (2-6).

Rhabdomyoblasts and poorly differentiated small cells display positivity for desmin and myosin while neural areas are variably sensitive to S-100. Ganglion cells are strongly positive for NSE. It is important to point out that the ectodermal component may be sometimes scanty and can be overlooked whereas in specimens after chemotherapy the ganglioneuroma component is increased and even overwhelming.

Differential diagnosis should consider rhabdomyosarcoma, Triton tumor, teratoma, Wilms tumor and benign, mature ectomesenchymoma (ectomesenchymal hamartoma).

The Ewing family of tumors is a group of cancers that includes Ewing tumor of bone (ETB or Ewing sarcoma of bone), extraosseous Ewing tumors (EOE tumors), primitive neuroectodermal tumors (PNET or peripheral neuroepithelioma), and Askin tumors (PNET of the chest wall). These tumors all come from the same type of stem cell. Also called EFTs.

Trilateral retinoblastoma (TRb) is a malignant midline primitive neuroectodermal tumor occurring in patients with inherited uni- or bilateral retinoblastoma. In most cases trilateral retinoblastoma presents itself as pineoblastoma (pineal TRb). In about a fourth of the cases the tumor develops in another intracranial region, most commonly supra- or parasellar (non-pineal TRb), but there are reported cases with non-pineal TRb in the 3rd ventricle. In most cases pineal TRb is diagnosed before the age of 5, but after the diagnosis of retinoblastoma. Non-pineal TRb, however, is often diagnosed simultaneous with retinoblastoma. Prognosis of patients with trilateral retinoblastoma is dismal, only a few patients have survived more than 5 years after diagnosis; all survivors were diagnosed with small tumors in a subclinical stage. Recent advances in (high-dose) chemotherapy treatment regimens and early detection have improved survival of patients with trilateral retinoblastoma.

Most of these tumors are treated with surgical removal. It is non recurrent.

The 1997 International Germ Cell Consensus Classification is a tool for estimating the risk of relapse after treatment of malignant germ cell tumor.

A small study of ovarian tumors in girls reports a correlation between cystic and benign tumors and, conversely, solid and malignant tumors. Because the cystic extent of a tumor can be estimated by ultrasound, MRI, or CT scan before surgery, this permits selection of the most appropriate surgical plan to minimize risk of spillage of a malignant tumor.

Access to appropriate treatment has a large effect on outcome. A 1993 study of outcomes in Scotland found that for 454 men with non-seminomatous (non-germinomatous) germ cell tumors diagnosed between 1975 and 1989, 5-year survival increased over time and with earlier diagnosis. Adjusting for these and other factors, survival was 60% higher for men treated in a cancer unit that treated the majority of these men, even though the unit treated more men with the worst prognosis.

Choriocarcinoma of the testicles has the worst prognosis of all germ cell cancers

Medical imaging plays a central role in the diagnosis of brain tumors. Early imaging methods – invasive and sometimes dangerous – such as pneumoencephalography and cerebral angiography have been abandoned in favor of non-invasive, high-resolution techniques, especially magnetic resonance imaging (MRI) and computed tomography (CT) scans. Neoplasms will often show as differently colored masses (also referred to as processes) in CT or MRI results.

- Benign brain tumors often show up as hypodense (darker than brain tissue) mass lesions on CT scans. On MRI, they appear either hypodense or isointense (same intensity as brain tissue) on T1-weighted scans, or hyperintense (brighter than brain tissue) on T2-weighted MRI, although the appearance is variable.

- Contrast agent uptake, sometimes in characteristic patterns, can be demonstrated on either CT or MRI scans in most malignant primary and metastatic brain tumors.

- Pressure areas where the brain tissue has been compressed by a tumor also appear hyperintense on T2-weighted scans and might indicate the presence a diffuse neoplasm due to an unclear outline. Swelling around the tumor known as "peritumoral edema" can also show a similar result.

This is because these tumors disrupt the normal functioning of the BBB and lead to an increase in its permeability. However, it is not possible to diagnose high- versus low-grade gliomas based on enhancement pattern alone.

The definitive diagnosis of brain tumor can only be confirmed by histological examination of tumor tissue samples obtained either by means of brain biopsy or open surgery. The histological examination is essential for determining the appropriate treatment and the correct prognosis. This examination, performed by a pathologist, typically has three stages: interoperative examination of fresh tissue, preliminary microscopic examination of prepared tissues, and follow-up examination of prepared tissues after immunohistochemical staining or genetic analysis.

Most myelolipomas are unexpected findings on CT scans and MRI scans of the abdomen. They may sometimes be seen on a plain X-ray films.

Fine needle aspiration may be performed to obtain cells for microscopic diagnosis.

Women with benign germ cell tumors such as mature teratomas (dermoid cysts) are cured by ovarian cystectomy or oophorectomy. In general, all patients with malignant germ cell tumors will have the same staging surgery that is done for epithelial ovarian cancer. If the patient is in her reproductive years, an alternative is unilateral salpingoophorectomy, while the uterus, the ovary, and the fallopian tube on the opposite side can be left behind. This isn't an option when the cancer is in both ovaries. If the patient has finished having children, the surgery involves complete staging including salpingoophorectomy on both sides as well as hysterectomy.

Most patients with germ cell cancer will need to be treated with combination chemotherapy for at least 3 cycles. The chemotherapy regimen most commonly used in germ cell tumors is called PEB (or BEP), and consists of bleomycin, etoposide, a platinum-based antineoplastic (cisplatin).