Representational analysis of DNA copy number/methylation

DNA 拷贝数/甲基化的代表性分析

• 批准号: 6691586
• 负责人: KEVIN L GUNDERSON
• 金额: $ 9.97万
• 依托单位: ILLUMINA, INC.
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-09-30 至 2004-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6691586
• 关键词: DNA methylation; DNA replication; experimental designs; functional /structural genomics; genetic models; genome; high throughput technology; human genetic material tag; microarray technology; model design /development; polymerase chain reaction; representational difference analysis; restriction endonucleases; subtraction hybridization; technology /technique development

DESCRIPTION (provided by applicant): Changes in methylation state and DNA copy number within the genome play a key role in cancer development and progression. Localization and quantification of these changes is important to the discovery of new tumor suppressor genes and oncogenes, and offers great potential in classifying cancer for clinical disease management. As such, the overall objective of this project is to develop a high-throughput array-based commercial technology to globally scan the genome for changes in DNA copy number (goal to detect two-fold differences) and methylation state. This will be accomplished via a reduced complexity representation approach using comparative genomic hybridization (CGH) and restriction landmark genome scanning (RLGS) technology on a BeadArrayTM platform. There are several immediate benefits offered by this representation approach. First of all, amplification of the representations will enhance signal to noise on the array. Secondly, improvements in generating representations will provide a more reproducible and robust process, allowing accurate detection of DNA copy number and methylation changes especially from archival samples exhibiting DNA degradation. Finally by converting RLGS from a 2-D gel-based approach (approximately 1000-2000 loci) to a BeadArrayTM-based analysis (approximately 1000-50,000 loci), a much higher locus resolution and sample throughput will be realized. This should enable the large-scale analysis of hundreds to thousands of tumor samples and lead to improved understanding of tumorogenesis. Phase II will apply this technology to the analysis of tumor samples and cell lines.

描述（由申请人提供）：基因组中甲基化状态和DNA拷贝数的变化在癌症发展和进展中起关键作用。这些变化的定位和量化对于发现新的肿瘤抑制基因和肿瘤基因很重要，并且为临床疾病管理分类提供了巨大的潜力。因此，该项目的总体目标是开发基于高通量阵列的商业技术，以全球扫描基因组的DNA拷贝数（目标差异两倍）和甲基化状态。这将通过比较基因组杂交（CGH）和限制性地标基因组扫描（RLGS）技术在BeadarrayTM平台上通过降低的复杂性表示方法来实现。这种代表方法提供了一些直接的好处。首先，表示形式的放大将增强阵列上噪声的信号。其次，生成表示形式的改进将提供更可再现和健壮的过程，从而可以准确检测DNA拷贝数和甲基化变化，尤其是从表现出DNA降解的档案样品中。最后，通过将RLG从基于2-D凝胶的方法（约1000-2000个位点）转换为基于BeadarrayTM的分析（大约1000-50,000个位点），将实现更高的基因座分辨率和样品吞吐量。这应该可以对数百至数千种肿瘤样本进行大规模分析，并提高人们对肿瘤发生的理解。第二阶段将把这项技术应用于肿瘤样品和细胞系的分析。