The Cancer Genome Anatomy Projects Genetic Annotation Initiative

LPG生物信息学核心的主要作用是为LPG内的研究人员提供技术支持。Core提供数据管理支持，并对Buetow实验室肝癌GWAS项目中生成的基因分型、拷贝数和基因表达数据进行分析。该核心为影响对他莫昔芬反应的遗传因素的研究（与Barbara Dunn博士合作）和NCI60细胞系中基因表达如何改变以响应药物治疗的研究（与Anne Monks博士合作）提供了分析支持。此外，核心的成员已经研究了小鼠成纤维细胞中的基因表达如何响应TAF7的敲除而改变（与Dinah Singer博士一起）。生物信息学核心还支持李实验室的研究工作。核心工作人员分析了来自Lee实验室生成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。他们检查了食管癌中的拷贝数改变和杂合性丢失（与Philip Taylor博士合作）。对于Lee Labs与Lalage韦克菲尔德博士的合作，核心分析了涉及MCF 10 A系列乳腺癌细胞系研究的拷贝数变异、基因表达、甲基化和ChIP数据。 该中心与生物医学信息学和信息技术中心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鉴定的SNP是否有害来为TCGA项目做出贡献。这些数据出现在Cancer Genome WorkBench中。目前的核心工作集中在开发一个融合基因产品的TCGA项目中确定的观众。 Bioinformatics Core正在与caBIG Annotation Imaging Markup项目的Carl Jaffe和John Freymann博士合作，研究胶质母细胞瘤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，LPG生物信息学核心领导了一个正在开发caLIMS 2的联盟，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组织库应用程序和caArray微阵列库集成。

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.