Cancer Genomics Center

描述(由申请者提供)：我们正在寻求支持在波士顿建立一个癌症基因组表征中心。这项拟议工作的目标是在三年内分析3000个肿瘤样本，并确定一组可以由癌症基因组图谱(TCGA)项目的成员重新测序的基因。众所周知，肿瘤基因组中被扩增、杂合性缺失或缺失的区域含有对肿瘤的发生和发展起重要作用的基因。我们建议通过进行阵列比较基因组杂交(ACGH)来识别癌症基因组中的这些区域。基于对许多不同平台的详细比较，我们选择使用高密度的安捷伦寡核苷酸阵列进行研究。在拟议拨款的第一年，我们已经有能力处理1000个样品。我们计划在授权期的剩余时间内继续改进程序并降低获取这些数据的成本。扩增或缺失区域包含许多基因。在这些区间内识别关键基因的最佳方法是通过对肿瘤RNA进行基因表达谱分析。有几种表达谱分析平台，其中一种信息量最大的方法是使用一种称为基因表达序列分析(SAGE)的平台。尽管SAGE功能强大，但它涉及到“标记”库的构建和对这些库的排序。用传统方法对每个文库进行排序的成本高得令人望而却步。我们已经开发并验证了一种名为“Polony”测序的方法，该方法能够以传统的电泳法或焦磷酸测序法所需的一小部分成本提供高度准确的测序信息。我们已经成功地使用这种方法从少量的Polya RNA中获得了表达谱，并建议在拟议的拨款期限内使用该方法从3000个肿瘤样本中生成数据。在前六个月，我们将实施这一方法，并将能够实现以每年1,000个肿瘤的速度生成数据的目标。我们还建议使用我们开发或实现的强大的信息学工具来整合aCGH和表达谱数据，并提取最感兴趣的基因列表进行重新测序。我们已经建立了屡获殊荣的IT基础设施，将用于LIMS、数据存储、数据检索、数据分析和与caBIG的接口。我们提出的方法还能够为肿瘤和患者分层产生更多有用的数据。

DESCRIPTION (provided by applicant): We are seeking support to establish a Cancer Genome Characterization Center in Boston. The goal of the proposed effort is to analyze 3000 tumor samples over a three-year period of time and identify a set of genes that can be resequenced by the members of The Cancer Genome Atlas (TCGA) project. It is well established that regions of the cancer genome that are amplified or show loss of heterozygosity or deletion harbor genes that are important for tumor initiation and progression. We propose to identify such regions in the cancer genome by conducting array comparative genomic hybridization (aCGH). Based upon detailed comparisons of many different platforms we have chosen to use the high-density Agilent oligonucleotide arrays for our studies. We already have the ability to have a throughput of processing a thousand samples during the first year of the proposed grant. We plan to continually improve the processes and reduce the cost of obtaining these data during the remaining portion of the grant period. The regions of amplification or deletion harbor many genes. An optimal way to identify the critical gene within these intervals is through gene expression profiling of RNA from tumors. There are several platforms for expression profiling and one of the most informative methods is through the use of a platform called Serial Analysis of Gene Expression (SAGE). Although SAGE is powerful it involves construction of "Tag" libraries and sequencing these libraries. The cost of sequencing each of the libraries with conventional methodologies is prohibitive. We have developed and validated a method called "Polony" sequencing that is capable of providing highly accurate sequencing information at a small fraction of cost required for conventional electrophoresis or pyrosequencing based methods. We have already successfully used this method to obtain expression profiles from small amount of polyA RNA and we propose to utilize this method to generate data from 3000 tumor samples in the proposed grant period. During the first six months we will implement this method and will be able to achieve the goal of generating data at the rate of 1,000 tumors/year. We also propose to use powerful informatics tools that we have developed or implemented to integrate the aCGH and expression profiling data and extract a list of most interesting genes for resequencing. We have established an award winning IT infrastructure that will be deployed for LIMS, data storage, data retrieval, data analysis and interface with caBIG. Our proposed approach also has the ability to generate additional useful data for tumor and patient stratification.