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）：基因组内甲基化状态和 DNA 拷贝数的变化在癌症的发生和进展中发挥着关键作用。这些变化的定位和量化对于发现新的抑癌基因和癌基因非常重要，并且为临床疾病管理的癌症分类提供了巨大的潜力。因此，该项目的总体目标是开发一种基于高通量阵列的商业技术，以全局扫描基因组以发现 DNA 拷贝数（目标是检测两倍差异）和甲基化状态的变化。这将通过在 BeadArrayTM 平台上使用比较基因组杂交 (CGH) 和限制性标志基因组扫描 (RLGS) 技术的降低复杂性的表示方法来实现。这种表示方法有几个直接的好处。首先，表征的放大将增强阵列上的信噪比。其次，生成表征的改进将提供一个更具可重复性和稳健性的过程，从而能够准确检测 DNA 拷贝数和甲基化变化，尤其是来自表现出 DNA 降解的档案样本。最后，通过将 RLGS 从基于 2-D 凝胶的方法（大约 1000-2000 个位点）转换为基于 BeadArrayTM 的分析（大约 1000-50,000 个位点），将实现更高的位点分辨率和样品通量。这应该能够对数百到数千个肿瘤样本进行大规模分析，并提高对肿瘤发生的了解。第二阶段将将该技术应用于肿瘤样本和细胞系的分析。