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.
