Genome Characterization Center (GCC)

描述(由申请人提供)：我们建议运营国家癌症研究所癌症基因组图谱的基因组表征中心(TCGA)。我们的目标是与TCGA研究网络的合作者一起，在5年内表征10,000个人类癌症的基因组和转录本。鉴于基因组分析领域正在进行的革命，我们的中心将从当前一代的微阵列技术过渡到用于癌症基因组表征的下一代测序技术。我们将通过将下一代技术与TCGA试点项目中使用的最先进的阵列技术进行基准比较来实现这一点。由于我们在下一代测序以及当代微阵列生产和技术开发方面的专业知识，我们在癌症基因组学方面的知识和已证明的成就，以及我们对包括TCGA试点项目在内的多机构合作的承诺和经验，我们的中心是唯一有资格开展这项工作的机构。具体地说，我们打算为TCGA实现以下目标：目标1.使用微阵列技术：在第一年内表征2000个癌症样本和适当对照的DNA和RNA。目标2.使用下一代测序：(I)在第一年通过表征300个癌症/正常样本对的DNA和100个癌症样本的RNA，对三个可选平台进行直接比较和验证。(Ii)根据结果，并与NCI的工作人员一起，在第一年结束时选择最具成本效益的排序平台。(3)实施这一测序平台，在第2-5年对2000个癌症样本和适当的对照样本进行DNA和RNA特征分析。(4)继续降低成本，提高基因组分析的分辨率。

DESCRIPTION (provided by applicant): We propose to operate a Genome Characterization Center for The Cancer Genome Atlas (TCGA) of the National Cancer Institute. Our goal is to characterize the genomes and transcriptomes of 10,000 human cancers over 5 years, together with the collaborators of TCGA Research Network. Given the ongoing revolution in genome analysis, our Center will transition from current-generation microarray technologies to next-generation sequencing technologies for cancer genome characterization. We will accomplish this by benchmarking the next-generation technologies against state-of-the-art array technologies used in the pilot project of TCGA. Our Center is uniquely qualified for this effort, because of our expertise in next-generation sequencing as well as current-generation microarray production and technology development, our knowledge and demonstrated accomplishments in cancer genomics, and our commitment to and experience with multi-institutional collaborations including the pilot project of TCGA. Specifically, we intend to accomplish the following aims for TCGA: Aim 1. Using microarray technologies: Characterize DNA and RNA from 2000 cancer samples and appropriate controls during year 1. Aim 2. Using next-generation sequencing: (i) Perform direct comparison and validation of the three alternative platforms during year 1, by characterizing DNA from 300 cancer/normal sample pairs and RNA from 100 cancer samples. (ii) Select the most cost-effective sequencing platform at the end of year 1, based on the results and in conjunction with NCI staff. (iii) Implement this sequencing platform to characterize DNA and RNA from 2000 cancer samples and appropriate controls in Years 2-5. (iv) Continue to decrease cost and increase resolution of genomic analysis.