The Cancer Genome Anatomy Projects Genetic Annotation Initiative

癌症基因组解剖计划遗传注释计划

• 批准号: 7966627
• 负责人: Kenneth Buetow
• 金额: $ 29.36万
• 依托单位: DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7966627
• 关键词: Address; Affect; Amino Acid Motifs; Bioinformatics; Biological Sciences; Breast Cancer Cell; Cancer Genome Anatomy Project; Cancer cell line; Cell Line; Characteristics; Collaborations; Communication; Communities; Copy Number Polymorphism; Data; Data Analyses; Data Set; Databases; Development; Ensure; Expressed Sequence Tags; Extramural Activities; Gene Expression; Genetic; Genetic Annotation Initiative; Genetic Polymorphism; Genomics; Genotype; Goals; Human; Human Resources; International; Java; Laboratories; Laboratory Personnel; Link; Loss of Heterozygosity; Malignant Neoplasms; Malignant neoplasm of esophagus; Malignant neoplasm of liver; Management Information Systems; Messenger RNA; Methods; Methylation; Molecular; Mus; Online Systems; Open Reading Frames; Pharmaceutical Preparations; Play; Primer Extension; Protocols documentation; Reagent; Research; Research Personnel; Resources; Retrieval; Role; Science; Series; Single Nucleotide Polymorphism Map; Structure; Tamoxifen; Tertiary Protein Structure; Training; Work; anticancer research; base; cancer Biomedical Informatics Grid; cancer genome; data management; fusion gene; genome wide association study; improved; member; next generation; novel; open source; platform-independent; population genetics laboratory; programs; research study; response; software development; tool; web interface

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.

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。对于Buetow实验室肝癌GWAS项目，Core提供了数据管理支持，并对基因分型、拷贝数和基因表达数据进行了分析。生物信息学核心为影响他莫昔芬反应的遗传因素研究（与Barbara Dunn博士合作）和NCI 60细胞系对药物治疗反应的基因表达改变研究（与Anne Monks博士合作）提供数据管理和分析支持。通过预测项目中发现的snp是否有害，Core支持Buetow实验室在TCGA项目上的工作。这些数据出现在癌症基因组工作台中。目前的工作重点是开发融合基因的观察器。生物信息学核心成员也为李氏实验室提供数据分析支持。他们分析了食管癌的拷贝数改变和杂合性缺失（与Philip Taylor博士合作）。在Lee实验室与Lalage Wakefield博士的合作中，Core分析了涉及乳腺癌细胞系MCF10A系列研究的拷贝数变异、基因表达、甲基化和ChIP数据。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。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。LPG生物信息学核心是开发caLIMS2的联盟的主要成员，caLIMS2是一个开源的、符合caBIG标准的实验室信息管理系统（https://wiki.nci.nih.gov/display/caLIMS2/; http://gforge.nci.nih.gov/projects/calims2）。caLIMS2开发的一个关键目标是与现有的caBIG应用程序caTissue和caArray集成；核心正在与caBIG生命科学治理团队密切合作。

项目成果

Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China.

• DOI: 10.1158/0008-5472.can-08-4622
• 发表时间: 2009-07-15
• 期刊: Cancer research
• 影响因子: 11.2
• 作者: Hu N;Wang C;Ng D;Clifford R;Yang HH;Tang ZZ;Wang QH;Han XY;Giffen C;Goldstein AM;Taylor PR;Lee MP
• 通讯作者: Lee MP