GENOME WIDE ANALYSIS OF DNA COPY NUMBER BY ARRAY

通过阵列对 DNA 拷贝数进行全基因组分析

• 批准号: 2906699
• 负责人: DANIEL PINKEL
• 金额: $ 63.87万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-03-25 至 2002-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2906699
• 关键词: clinical research; fluorescent dye /probe; genome; human genetic material tag; loss of heterozygosity; neoplasm /cancer diagnosis; neoplasm /cancer genetics; nucleic acid hybridization; nucleic acid quantitation /detection; technology /technique development

DESCRIPTION: (Applicant's Description) Comparative genomic hybridization (CGH) has demonstrated its ability to provide a unique insight into the genetic abnormalities involved in the development of cancer. By co-hybridizing total genomic DNA from a specimen and from normal cells to metaphase chromosomes, it provides a genome-wide map of the DNA sequence copy number variation with cytogenetic scale resolution, - 20 Mb. Application of CGH to a wide variety of tumor types has found that most of them contain copy number changes that recurrently affect many regions of the genome, indicating the locations of known and many yet to be discovered oncogenes and tumor suppressor genes. We have recently demonstrated the feasibility of a new form of CGH that detects copy number variations comparative hybridization to a DNA microarray containing clones from any set of well mapped loci. Resolution with array CGH is more than 100 fold better than with standard CGH and the copy number variations are mapped relative to the genetic and physical maps being produced by the human genome project. We are proposing to develop a robust, flexible implementation of array CGH the human genome. This will require 1) selecting appropriate target clones with a goal of providing 1 Mb resolution (-3000 clones) throughout the genome. 2) improving methods for making arrays, and for acquiring and analyzing fluorescence signals. 3) improving methods for hybridization and for genomic DNA amplification to minimize the amount of specimen needed for analysis and to assure accurate results. 4) developing informatics for managing the project and displaying and analyzing the data. The project is designed so that it begins to provide useful measurement capability in its first year, and continues to improve throughout the 5 year project period. The performance of array CGH will be tested within the project as is necessary for technical development, and it will be evaluated in practice in collaboration with the national breast cancer SPORE projects. In summary, this project will develop the technology to permit human genome-wide, high throughput analysis of DNA copy number. The availability of this technique will facilitate positional cloning of cancer genes, and very large scale studies of the correlation of genetic abnormalities with biological and clinical behavior of tumors. The combination of array CGH data with data from other sources, for example microarray measurements of mRNA expression. will provide an even more powerful window on the genetic events involved in cancer development and progression.

描述：（申请人的描述）比较基因组 杂交（CGH）已经证明了其提供独特的能力 洞悉涉及发展的遗传异常 癌症。通过从试样共同杂交总基因组DNA 正常细胞与中期染色体，它提供了全基因组图的 DNA序列拷贝数随细胞遗传学量表变化 分辨率，-20 MB。将CGH应用于多种肿瘤类型 发现其中大多数包含复制号更改 影响基因组的许多区域，表明已知和 许多尚未发现的癌基因和肿瘤抑制基因。我们有 最近证明了一种新形式的CGH的可行性 拷贝数变化与DNA微阵列的比较杂交 包含来自任何绘制良好基因座的克隆。解决方案 Array CGH比标准CGH好100倍以上 拷贝数变化相对于遗传和物理映射 人类基因组项目生产的地图。 我们建议开发出强大，灵活的数组实现 CGH人类基因组。这将需要1）选择适当的目标 克隆的目标是提供1 MB分辨率（-3000克隆） 在整个基因组中。 2）改进制作数组的方法 获取和分析荧光信号。 3）改进方法 杂交和基因组DNA扩增以最大程度地减少量 分析所需的标本并确保准确的结果。 4） 开发用于管理项目和显示的信息学 分析数据。该项目的设计使其开始提供 第一年有用的测量能力，并继续 在整个5年期间的改进。阵列的性能 CGH将在项目中对技术进行测试 开发，将在实践中与 国家乳腺癌孢子项目。 总而言之，该项目将开发该技术以允许人类 全基因组，DNA拷贝数的高吞吐量分析。这 此技术的可用性将有助于位置克隆 癌症基因，以及遗传相关性的非常大规模的研究 肿瘤的生物学和临床行为异常。这 例如 mRNA表达的微阵列测量。将提供更多 关于癌症发展涉及的遗传事件的强大窗口和 进展。