The Cancer Genome Anatomy Projects Genetic Annotation Initiative

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The LPG Bioinformatics Core performs two roles. The first is to support the activities of the LPG through data analysis and management, as well as by facilitating communication within the Laboratory. The second is to provide resources for use by the wider cancer research community. The Core provides technical support to researchers within the LPG. For the Buetow lab liver cancer GWAS project, the Core provided data management support and performed analyses of genotyping, copy number and gene expression data. The Bioinformatics Core provided data management and 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 NCI 60 cell lines in response to drug treatment (a collaboration with Dr. Anne Monks). The Core supported the Buetow Labs work on the TCGA project by predicting whether SNPs identified in the project are deleterious. This data appears in the Cancer Genome WorkBench. Current efforts focus on developing a viewer for fusion genes. Bioinformatics Core members also provided data analysis support to the Lee Lab. They analyzed copy number alterations and loss-of-heterozygosity in esophageal cancer (a 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 Bioinformatics Core works with members of the LPG to develop and maintain a variety of web-based tools for cancer research. Integrated genetic and physical SNP maps, a Java-based tool for viewing candidate SNPs in the context of EST assemblies, reagent information (including PCR primers and extension primers) and a SNP search engine are available at http://lpgws.nci.nih.gov/GAI/. A browser that displays polymorphisms in the context of mRNA sequences, open reading frames, protein motifs and three-dimensional protein domain structures is accessible at http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi/. Annotation for Affymetrix human and mouse GeneChip expression array sets are available at http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi. The Bioinformatics Core worked with SAIC to customize and extend the open source laboratory information management system caLIMS 1.2. The revised application, lpgLIMS 1.3, is available for download at http://gforge.nci.nih.gov/projects/lpglims. Members of the Core maintain the Buetow lab instance of lpgLIMS and train laboratory personnel in its use. The LPG Bioinformatics Core is a leading member of a consortium that is developing caLIMS2, an open-source, caBIG compliant laboratory information management system (https://wiki.nci.nih.gov/display/caLIMS2/; http://gforge.nci.nih.gov/projects/calims2). A key goal of caLIMS2 development is integration with the existing caBIG applications caTissue and caArray; the Core is working closely with the caBIG Life Sciences Governance Team in this effort.