DNA Analysis of Tumor Tissue Samples From Patients With Diffuse Brain Stem Glioma

Since very little is known about the biology of diffuse brainstem glioma, the goal of this
protocol is to undertake a systematic analysis of DNA abnormalities, and of RNA and protein
expression in prospectively collected fresh-frozen and fixed tumor samples and correspondent
normal tissue from patients affected with this tumor.

OBJECTIVES:

- Perform genome-wide analysis of DNA gains and losses and RNA expression in tumor
samples and normal tissue from patients with diffuse brain stem glioma.

- Identify regions of genomic gain or loss using either array comparative genomic
hybridization or single nucleotide polymorphism arrays.

- Investigate genome-wide expression patterns of RNA derived from tumor samples and
normal tissue from these patients via Affymetrix gene expression profiling.

- Validate the results of the genome-wide analysis by conducting further evaluation of
candidate genes or by investigating the expression of relevant gene products at the RNA
and protein levels.

- Perform analysis of mutations in candidate tumor-suppressor genes and oncogenes
(including whole genome sequencing studies) using direct sequence analysis of tumor DNA
and confirm the tumor-specific nature of these mutations by analyzing the correspondent
constitutional DNA.

- Confirm genomic gains or losses identified by means of fluorescence in situ
hybridization (FISH) performed on tissue microarray using non-neoplastic brain tissue
from each patient as control when available.

- Explore protein expression patterns identified by immunohistochemistry or western blot
and compare them to normal brain stem tissue.

- To obtain a follow-up (questionnaire and/or telephone interview) after autopsy with
parent(s), legal guardian(s), or family members of research participants in the United
States to assess aspects associated with this procedure, including potential benefits
and drawbacks

Inclusion Criteria

- Patients of any age with clinical and radiologic diagnosis of diffuse brainstem
glioma

- Patients with other high-grade gliomas originating in the brainstem

- Patients with focal gliomas (WHO grade I/II) of the brainstem

- Enrollment in the current version of the St. Jude Tissue Bank protocol for patients
whose tissue samples were obtained at diagnosis and who received treatment at St.
Jude Children's Research Hospital (SJCRH), or correspondent tissue banking consent
for patients treated in other institutions if tissue was obtained prior to death (as
applicable, depending on the standard of each institution)

Exclusion Criteria

- Patients with any type of infiltrative low-grade (WHO grade II) or high-grade glioma
(WHO grade III and IV) originating outside the brainstem

- Patients harboring primary brainstem tumors with other histologic diagnoses (e.g.,
PNET)