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GenomicsNational Cancer Institute Cancer Genome Characterization Initiative (CGCI)

The Office of Cancer Genomics at the National Cancer Institute is sponsoring a series of studies as part of the Cancer Genome Characterization Initiative (CGCI) to assess novel e...
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  • Medulloblastoma (MB) - Medulloblastoma is the most common malignant brain tumor found in children. In order to identify the genetic alterations in MB, copy number alterations were sought using high-density microarrays and sequenced all known protein-coding genes and miRNA genes using Sanger sequencing in a set of 22 pediatric MB samples and one matched normal blood sample. All tumor samples were obtained at the time of original surgery (pre-treatment) except for one sample, which was obtained at the time of MB recurrence.

    Protein-encoding transcripts to be targeted for sequencing were derived from transcripts present in the Ensembl (file date 8/27/2008), RefSeq (file date 1/18/2009), and CCDS (file date 2/02/2009) databases and downloaded from the UCSC Genome Bioinformatics site. The protein encoding transcripts were supplemented with microRNA transcripts downloaded from the Sanger miRBase Sequence Database (Release 13.0) in order to yield a combined set of transcripts representing 24,893 genes (24,178 protein encoding and 715 microRNA). The regions of interest (ROIs) targeted for sequencing comprised the entire transcribed portion of the microRNA exons and the protein encoding portion plus 4 bases of flanking sequence for the protein encoding exons. Illumina Infinium II Whole Genome Genotyping Assay employing the BeadChip platform was used to analyze the same set of tumor samples at 1,199,187 (1M-Duo) SNP loci in order to detect copy number alterations in the same set of tumors.

    • The projects currently involved in CGCI will provide various data to include whole genomic, transcriptomic and mutational analyses of the tumor types being studied. This page will be amended as additional projects and characterization platforms are added to the CGCI portfolio.

    phs000235.v3.p1 | EGA
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