The Cancer Genome Anatomy Projects Genetic Annotation Initiative

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A major role of the LPG Bioinformatics Core is to provide technical support to researchers within the LPG. The Core provided data management support and performed analyses of genotyping, copy number and gene expression data generated in the Buetow lab liver cancer GWAS project. The Core provided analytical support for a study of genetic factors affecting response to tamoxifen (a collaboration with Dr. Barbara Dunn) and a study of how gene expression is altered in the NCI60 cell lines in response to drug treatment (a collaboration with Dr. Anne Monks). In addition, members of the Core have examined how gene expression in mouse fibroblasts is altered in response to the knockout of TAF7 (with Dr. Dinah Singer). The Bioinformatics Core also supports the research efforts of the Lee Laboratory. Core staff have analyzed high-throughput genotyping, methylation and gene expression data from breast cancer tumors and cell lines that have been generated by the Lee Lab. They examined copy number alterations and loss-of-heterozygosity in esophageal cancer (in collaboration with Dr. Philip Taylor). For the Lee Labs collaboration with Dr. Lalage Wakefield, the Core analyzed copy number variation, gene expression, methylation and ChIP data from studies involving the MCF10A series of breast cancer cell lines. The Core works closely with the Center for Biomedical Informatics and Information Technology bioinformatics group. The Bioinformatics Core contributed to the TCGA project by predicting whether SNPs identified in tumors are deleterious. This data appears in the Cancer Genome WorkBench. Current Core efforts focus on developing a viewer for fusion gene products identified in the TCGA project. The Bioinformatics Core is working with Drs. Carl Jaffe and John Freymann of the caBIG Annotation Imaging Markup project to investigate whether features observed in MRI images of glioblastoma correlate with molecular characteristics or clinical outcome. Finally, the LPG Bioinformatics Core leads a consortium that is developing caLIMS2, the caBIG laboratory information management system application. A key goal of caLIMS2 development is integration with the caTissue tissue banking application and the caArray microarray repository.