The Cancer Genome Anatomy Projects Genetic Annotation Initiative

液化石油气生物信息学核心的主要作用是为液化石油气内的研究人员提供技术支持。该中心提供数据管理支持，并对Buetow实验室肝癌Gwas项目产生的基因分型、拷贝数和基因表达数据进行分析。该中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NCI60细胞系在药物治疗后基因表达如何改变的研究(与Anne Monks博士合作)提供分析支持。此外，CORE的成员研究了小鼠成纤维细胞中的基因表达是如何随着TAF7基因敲除而改变的(与Dinah Singer博士)。生物信息学核心也支持Lee实验室的研究努力。核心工作人员分析了Lee实验室产生的乳腺癌肿瘤和细胞系的高通量基因分型、甲基化和基因表达数据。他们研究了食道癌的拷贝数改变和杂合性丢失(与菲利普·泰勒博士合作)。在Lee实验室与Lalage Wakefield博士的合作中，Core分析了涉及MCF10A系列乳腺癌细胞系的研究的拷贝数变异、基因表达、甲基化和芯片数据。核心与生物医学信息学中心和信息技术生物信息学小组密切合作。生物信息学核心通过预测在肿瘤中发现的SNPs是否有害，为TCGA项目做出了贡献。这些数据出现在癌症基因组工作台上。目前的核心工作集中在为TCGA项目中确定的融合基因产品开发一个查看器。生物信息学核心正在与caBIG注释成像标记项目的Carl Jaffe和John Freymann博士合作，调查在胶质母细胞瘤的MRI图像中观察到的特征是否与分子特征或临床结果相关。最后，液化石油气生物信息学核心牵头的财团正在开发caLIMS2，即caBIG实验室信息管理系统应用程序。CaLIMS2开发的一个关键目标是与caTIssue组织银行应用程序和caArray微阵列储存库集成。

A major role of the LPG Bioinformatics Core is to provide technical support to researchers within the LPG. The Core provided data management support and performed analyses of genotyping, copy number and gene expression data generated in the Buetow lab liver cancer GWAS project. The Core provided 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 NCI60 cell lines in response to drug treatment (a collaboration with Dr. Anne Monks). In addition, members of the Core have examined how gene expression in mouse fibroblasts is altered in response to the knockout of TAF7 (with Dr. Dinah Singer).The Bioinformatics Core also supports the research efforts of the Lee Laboratory. Core staff have analyzed high-throughput genotyping, methylation and gene expression data from breast cancer tumors and cell lines that have been generated by the Lee Lab. They examined copy number alterations and loss-of-heterozygosity in esophageal cancer (in 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 Core works closely with the Center for Biomedical Informatics and Information Technology bioinformatics group. The Bioinformatics Core contributed to the TCGA project by predicting whether SNPs identified in tumors are deleterious. This data appears in the Cancer Genome WorkBench. Current Core efforts focus on developing a viewer for fusion gene products identified in the TCGA project. The Bioinformatics Core is working with Drs. Carl Jaffe and John Freymann of the caBIG Annotation Imaging Markup project to investigate whether features observed in MRI images of glioblastoma correlate with molecular characteristics or clinical outcome. Finally, the LPG Bioinformatics Core leads a consortium that is developing caLIMS2, the caBIG laboratory information management system application. A key goal of caLIMS2 development is integration with the caTissue tissue banking application and the caArray microarray repository.