A common thread linking research programs within the Laboratory of Population Genetics is the use of integrated genomics approaches to address the origin and molecular characteristics of cancer. In their work LPG investigators frequently perform moderate to high throughput sequencing, genotyping and gene expression experiments. The large quantity of information produced in these experiments requires dedicated data analysis and data management support. To ensure that data from different experiments are complementary the LPG must have a common set of protocols, analysis tools and annotation datasets. The LPG Bioinformatics Core addresses these specific needs and further supports the LPG through application development, project management and facilitating communication between laboratories. Members of the Core develop software for use by the LPG and the wider cancer research community. To simplify the retrieval of laboratory data from databases, Core staff are involved in the creation and maintenance of web interfaces to LPG datasets. Among these are: annotations for SNPs discovered by the LPG (http://lpgws.nci.nih.gov/cgi-bin/imagemaps.html); predictions of the functional consequences of SNPs (http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi); annotations for Affymetrix GeneChip probes (http://pgws.nci.nih.gov/cgi-bin/AffyViewer.cgi); and the LPGimage tissue microarray immunohistochemistry dataset (http://LPGimage.nci.nih.gov). The Core produced the search engine for the Quantitative PCR Primer Database (http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer.cgi). The LPG Bioinformatics Core maintains and refines the LPG laboratory information management system. Members of the Core have worked with Science Applications International Corporation (SAIC) to modify the open source caLIMS 1.2 application to simplify its compilation and installation, improve its stability and make it platform independent (http://gforge.nci.nih.gov/projects/lpglims). The LPG Bioinformatics Core collaborates with the NCI Center for Bioinformatics, SAIC, the NCI-Frederick Laboratory of Molecular Technology, the Arizona Research Laboratories and the Minnesota Public Health Laboratory to develop core components of caLIMS II, a next generation, caBIG compliant laboratory information management system (http://gforge.nci.nih.gov/projects/calims2). 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. Members of the Core developed an inventory management application for the Hunter laboratory. They collaborated with the Zhang group to produce gene-based chip definition files for Affymetrix human and mouse gene expression arrays. The Core Group also provides technical, analytic and management support for Buetow lab liver and breast cancer projects. Members of the Core participate in the National Cancer Institute's Genetic Annotation Initiative (GAI), which expands the collection of gene-based genetic analysis reagents for cancer research. The GAI has identified more than 40,000 candidate human single nucleotide polymorphisms (SNPs) by analyzing publicly available expressed sequence tag chromatograms. Over 16,000 candidate mouse SNPs have been identified. The GAI has validated more than 8,000 human SNPs via mass spectrometry. 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. Members of the Core have also worked with the Jen lab to enhance the functionality of the LPGimage application (http://LPGimage.nci.nih.gov). The Core developed and maintains a web-based tool for accessing the Quantitative PCR Primer Database created by the Gene Expression Laboratory at NCI-Frederick. Through this search engine, http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer, researchers can retrieve information about PCR-based reagents for measuring the expression of human and mouse genes. 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 Core is a leading member of a consortium developing caLIMS II, a fully caBIG compliant laboratory information management system

National Institute of Health (NIH)
National Cancer Institute (NCI)
Intramural Research (Z01)
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Division of Cancer Epidemiology and Genetics
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Clifford, Robert J; Edmonson, Michael N; Nguyen, Cu et al. (2004) Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics 20:1006-14
Clifford, Robert J; Edmonson, Michael N; Nguyen, Cu et al. (2004) Bioinformatics tools for single nucleotide polymorphism discovery and analysis. Ann N Y Acad Sci 1020:101-9