The Cancer Genome Anatomy Projects Genetic Annotation In

LPG生物信息学核心小组扮演两个角色。第一个是通过数据分析和管理以及促进实验室内部的沟通来支持实验室的活动。第二是提供资源供更广泛的癌症研究界使用。核心小组为研究小组内的研究人员提供技术支持。核心成员与Struewing和Lee实验室合作设计了一种癌症基因重测序微阵列，该微阵列将用于识别与癌症相关的79个基因座中的新突变。他们与Zhang团队合作，为Affyandroid人类和小鼠基因表达阵列生产基于基因的芯片定义文件。核心小组还为Buetow实验室的肝癌和乳腺癌项目提供技术、分析和管理支持。核心小组成员参加了国家癌症研究所的遗传注释倡议（GAI），该倡议扩大了癌症研究中基于基因的遗传分析试剂的收集。GAI已经通过分析公开可用的表达序列标签色谱图确定了超过40，000个候选人类单核苷酸多态性（SNP）。已经鉴定了超过16，000个候选小鼠SNP。GAI已经通过质谱法验证了8,000多个人类SNP。生物信息学核心小组与LPG成员合作，开发和维护各种基于网络的癌症研究工具。整合的遗传和物理SNP图谱、用于在EST组装的背景下查看候选SNP的基于Java的工具、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/获得。在mRNA序列、开放阅读框架、蛋白质基序和三维蛋白质结构域结构的背景下显示多态性的浏览器可在http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi/上访问。用于Affymble人和小鼠基因芯片表达阵列集的注释可在http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi.The上获得核心组开发并维护用于访问由NCI-Frederick的基因表达实验室创建的定量PCR引物数据库的基于网络的工具。通过这个搜索引擎http：//lpgws.nci.nih.gov/cgi-bin/PrimerViewer，研究人员可以检索有关用于测量人类和小鼠基因表达的PCR试剂的信息。该数据库包括2055个人类和290个小鼠引物集。生物信息学核心小组正在与科学应用国际公司合作，定制和扩展开源实验室信息管理系统caLIMS。lpgLIMS将包括用于AffyxD基因表达和映射微阵列的适配器，并且将具有改进的安装简易性。

The LPG Bioinformatics Core Group 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 Group provides technical support to researchers within the LPG. Members of the Core worked with the Struewing and Lee labs to design a cancer gene resequencing microarray, which will be used to identify novel mutations in 79 loci associated with cancer. 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 Group 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 Group 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 Core Group 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 database includes 2055 human and 290 mouse primer sets.The Bioinformatics Core Group is working with Science Applications International Corporation to customize and extend the open source laboratory information management system caLIMS. lpgLIMS will include adaptors for Affymetrix gene expression and mapping microarrays and will feature improved ease of installation.