Clinical trial NCT00899834: DNA Analysis of Tumor Tissue Samples From Patients With Diffuse Brain Stem Glioma
Official title: Comprehensive Molecular Analysis of Tumor Samples Derived From Patients With Diffuse Brainstem Glioma - A Pilot Study
Study type: OBSERVATIONAL
Overall status: COMPLETED
Conditions: Brain Tumors
Central Nervous System Tumors
Keywords: adult brain stem glioma
childhood brain stem glioma
Lead sponsor: St. Jude Children's Research Hospital
Sponsor class: OTHER
First posted: 2009-05-12
Enrollment: 81
Sex: ALL
Maximum age (years): 18
Standard ages: CHILD
ADULT
Accepts healthy volunteers: no
Observational model: CASE_ONLY
Time perspective: PROSPECTIVE
Sampling method: NON_PROBABILITY_SAMPLE
Study population: Fresh-frozen and fixed tumor samples and correspondent normal tissue from patients affected with this tumor (peripheral blood is applicable only to patients with focal brainstem gliomas and patients who undergo biopsy of a diffuse brainstem glioma at diagnosis)

Brief summary: This multi-institutional study will prospectively collect tumor and constitutional tissue samples from patients with diffuse brainstem glioma and other types of brainstem gliomas either during therapy or at autopsy to perform an extensive analysis of genetic and molecular abnormalities in these tumors.

Detailed description: 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

Eligibility criteria: 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)

Primary outcomes:
measure: DNA gains and losses and RNA expression in tumor samples and normal tissue
timeFrame: at autopsy
measure: Genome-wide expression patterns of RNA in tumor samples and normal tissue as assessed by Affymetrix gene expression profiling
timeFrame: at autopsy
measure: Validation of results of the genome-wide analysis
timeFrame: at autopsy
measure: Mutations in candidate tumor-suppressor genes and oncogenes as assessed by direct sequencing analysis of tumor DNA
timeFrame: at autopsy
measure: Confirmation of the tumor-specific nature of candidate tumor-suppressor gene and oncogene mutation as assessed by the correspondent constitutional DNA
timeFrame: at autopsy
measure: Confirmation of genomic gains or losses as assessed by fluorescence in situ hybridization (FISH) performed on tissue microarray (TMA) using non-neoplastic brain tissue
timeFrame: at autopsy
measure: Protein expression patterns as assessed by immunohistochemistry or western blot compared to normal brain stem tissue
timeFrame: at autopsy
Secondary outcomes:
measure: Assess aspects associated with this procedure, including potential benefits and drawbacks
timeFrame: at autopsy
Other outcomes:
Locations:
city: Palo Alto
country: United States
facility: Stanford University Medical Center
state: California
city: Memphis
country: United States
facility: St. Jude Children's Research Hospital
state: Tennessee
city: Seattle
country: United States
facility: Seattle Children's Hospital
state: Washington
Study officials:
affiliation: St. Jude Children's Research Hospital
name: Alberto Broniscer, MD
role: PRINCIPAL_INVESTIGATOR
References: