Center for Cancer Genome Characterization

描述（由申请人提供）：麻省理工学院和哈佛布罗德研究所的癌症基因组表征中心（CGCC）汇集了一组在癌症和基因组学方面具有广泛专业知识的研究人员，以及设定和实现里程碑的跟踪记录。作为癌症基因组图谱（TCGA）试点项目的一部分，我们计划实现以下目标：（1）表征大量癌症样本中的结构改变（扩增、缺失和洛杂合性缺失）和基因表达。具体来说，我们将使用微阵列进行高密度SNP基因分型和RNA表达谱分析。我们将在第1年、第2年和第3年分别分析1000个、1500个和2000个样本--在大致恒定的预算下，通过降低成本来增加样本数量。(2)通过设计新的、更有效的阵列，提高SNP基因分型和RNA表达谱分析的成本和性能。特别是，对于相同的信息内容，我们将减少至少2倍的总成本。到该项目结束时，将有可能在15，000个癌症样本的集合中表征基因组改变和基因表达（NCI关于TCGA的报告中建议的目标），三年内的总成本<600万美元/年。因此，这些技术将准备在TCGA内全面扩展。(3)交叉验证，整合和分析CGCC数据，以确定高通量测序的基因组改变区域。(4)与癌症研究社区快速共享数据。

DESCRIPTION (provided by applicant): The Cancer Genome Characterization Center (CGCC) at the Broad Institute of MIT and Harvard brings together a team of investigators with extensive expertise in cancer and genomics, as well as a track record of setting and attaining milestones. As part of The Cancer Genome Atlas (TCGA) pilot project, we propose to accomplish the following objectives: (1) Characterize structural alterations (amplification, deletion and LOH) and gene expression in a large collection of cancer samples. Specifically, we will use microarrays to perform high-density SNP genotyping and RNA expression profiling. We will analyze 1000, 1500 and 2000 samples in years 1, 2 and 3, respectively - with costs decreasing to allow an increasing number of samples on a roughly constant budget. (2) Improve the cost and performance of SNP genotyping and RNA expression profiling, by designing new, more efficient arrays. In particular, we will decrease total costs by a factor of at least 2-fold for the same information content. By the end of the project, it will be possible to characterize genome alteration and gene expression in a collection of 15,000 cancer samples (the target suggested in NCI's report on TCGA) at a total cost of <$6M/year over a three-year period. These technologies will thus be ready for full scale up within TCGA. (3) Cross-validate, integrate, and analyze CGCC data to determine regions of genome alteration for high-throughput sequencing. (4) Rapidly share data with the cancer research community.