Genome Characterization Center (GCC)

描述（由申请人提供）：我们建议为国家癌症研究所的癌症基因组图谱（TCGA）运营基因组表征中心。我们的目标是与TCGA研究网络的合作者一起，在5年内描述10，000种人类癌症的基因组和转录组。 鉴于基因组分析的持续革命，我们的中心将从目前的微阵列技术过渡到下一代测序技术，用于癌症基因组表征。我们将通过对下一代技术与TCGA试点项目中使用的最先进阵列技术进行基准测试来实现这一目标。 我们的中心是唯一合格的这一努力，因为我们在下一代测序以及当前一代微阵列生产和技术开发的专业知识，我们的知识和证明在癌症基因组学的成就，以及我们的承诺和经验与多机构合作，包括TCGA的试点项目。具体而言，我们打算实现TCGA的以下目标：目标1。使用微阵列技术：在第1年期间表征来自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）在第一年期间，通过对300个癌症/正常样本对的DNA和100个癌症样本的RNA进行表征，对三个替代平台进行直接比较和验证。(ii)在第1年年底，根据结果并与NCI工作人员一起选择最具成本效益的测序平台。 (iii)在第2-5年实施该测序平台，以表征来自2000个癌症样本和适当对照的DNA和RNA。(iv)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.