The Cancer Genome Anatomy Projects Genetic Annotation Initiative

群体遗传学实验室研究项目的一个共同主线是使用综合基因组学方法来解决癌症的起源和分子特征。在他们的工作中，LPG研究人员经常进行中等到高通量测序，基因分型和基因表达实验。这些实验产生的大量信息需要专门的数据分析和数据管理支持。为了确保来自不同实验的数据是互补的，LPG必须有一套通用的协议、分析工具和注释数据集。液化石油气生物信息学核心解决了这些具体需求，并通过应用开发、项目管理和促进实验室之间的沟通进一步支持液化石油气。核心成员开发的软件供LPG和更广泛的癌症研究界使用。为了简化从数据库中检索实验室数据，核心员工参与创建和维护LPG数据集的web界面。其中包括：LPG发现的snp注释（http://lpgws.nci.nih.gov/cgi-bin/imagemaps.html）；预测snp的功能后果（http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi）；注释Affymetrix GeneChip探针（http://pgws.nci.nih.gov/cgi-bin/AffyViewer.cgi）；以及lpimage组织微阵列免疫组织化学数据集（http://LPGimage.nci.nih.gov）。Core制作了定量PCR引物数据库（http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer.cgi）的搜索引擎。LPG生物信息学核心负责维护和完善LPG实验室信息管理系统。Core的成员已经与Science Applications International Corporation （SAIC）合作修改了开源caLIMS 1.2应用程序，以简化其编译和安装，提高其稳定性并使其独立于平台（http://gforge.nci.nih.gov/projects/lpglims）。LPG生物信息学核心与NCI生物信息学中心、SAIC、NCI弗雷德里克分子技术实验室、亚利桑那研究实验室和明尼苏达州公共卫生实验室合作，开发caLIMS II的核心组件，这是下一代符合caBIG标准的实验室信息管理系统（http://gforge.nci.nih.gov/projects/calims2）。液化石油气生物信息学核心有两个作用。第一是通过数据分析和管理，以及促进实验室内部的沟通，支持液化石油气的活动。第二是为更广泛的癌症研究团体提供资源。核心为液化石油气的研究人员提供技术支持。核心小组的成员为亨特实验室开发了一个库存管理应用程序。他们与Zhang团队合作，为Affymetrix人类和小鼠基因表达阵列制作了基于基因的芯片定义文件。核心小组还为Buetow实验室肝癌和乳腺癌项目提供技术、分析和管理支持。核心成员参加了国家癌症研究所的遗传注释倡议（GAI），该倡议扩大了用于癌症研究的基于基因的遗传分析试剂的收集。GAI通过分析公开可用的表达序列标签色谱图，已经鉴定出超过40,000个候选人类单核苷酸多态性（snp）。已经鉴定出超过16,000个候选小鼠snp。GAI已经通过质谱法验证了8000多个人类snp。生物信息学核心与LPG成员合作开发和维护各种基于网络的癌症研究工具。集成的遗传和物理SNP图谱，一个基于java的工具，用于在EST装配上下文中查看候选SNP，试剂信息（包括PCR引物和延伸引物）和SNP搜索引擎可在http://lpgws.nci.nih.gov/GAI/上获得。一个浏览器可以显示mRNA序列、开放阅读框、蛋白质基序和三维蛋白质结构域结构的多态性，可访问http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi/。Affymetrix人类和小鼠基因芯片表达数组集的注释可在http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi上获得。Core的成员还与Jen实验室合作，增强lpimage应用程序的功能（http://LPGimage.nci.nih.gov）。Core开发并维护了一个基于网络的工具，用于访问由NCI-Frederick基因表达实验室创建的定量PCR引物数据库。通过这个搜索引擎http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer，研究人员可以检索到用于测量人类和小鼠基因表达的pcr试剂的信息。生物信息学核心与SAIC合作定制和扩展开放源代码实验室信息管理系统caLIMS 1.2。修订后的应用程序lpgLIMS 1.3可从http://gforge.nci.nih.gov/projects/lpglims下载。核心成员维护lpgLIMS的Buetow实验室实例，并培训实验室人员使用它。Core是开发caLIMS II（完全符合caBIG标准的实验室信息管理系统）联盟的主要成员

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