Studying Biomarkers in Samples From Younger Patients With Malignant Germ Cell Tumor Progression

Genomic Signatures of Malignant Germ Cell Tumor Progression: A Retrospective Study of Banked Specimens

RATIONALE: Studying samples of blood and tissue from patients with cancer in the laboratory may help doctors learn more about changes that occur in DNA and identify biomarkers related to cancer. It may also help doctors find better ways to treat cancer.

PURPOSE: This research trial studies samples from younger patients with malignant germ cell tumor progression.

OBJECTIVES:

• Explore inter-tumoral heterogeneity in DNA methylation by tumor histology.
• Determine the genomic methylation pattern in the tumors.
• Correlate methylation pattern with tumor histology and clinical characteristics.
• Carry out exome capture and massively parallel sequencing on selected germ cell tumors (GCTs) and matched normal tissue.
• Perform exome capture and Solexa sequencing on a selected set of GCTs.
• Validate candidate mutations in an independent set of tumors.
• Determine the expression profile of mRNAs, lincRNAs and microRNAs in the tumors using RNA Seq.

OUTLINE: Archived blood and tumor tissue samples are analyzed for genomic methylation pattern, exome capture and sequencing, and candidate mutations by methylation-specific PCR techniques, single nucleotide polymorphism (SNP) arrays, and Solexa sequencing methods. Results are validated by using pyrosequencing assays and primer-extension assays. Methylation pattern is also associated with each patient's tumor histology and clinical data.

DISEASE CHARACTERISTICS:

• Tumor and blood specimens from patients registered on the Children Oncology Group (COG) Germ Cell Tumor Protocols, and from other study sites for non-COG patients, including Children's Medical Center, Dallas and the Dana-Farber Cancer Institute, Boston
• Patients' clinical data

PATIENT CHARACTERISTICS:

• Not specified

PRIOR CONCURRENT THERAPY:

• Not specified