ADVANCED QUANTITATIVE IMAGING FOR DNA PHYSICAL MAPPING

用于 DNA 物理绘图的先进定量成像

• 批准号: 3333444
• 负责人: LEWIS J THOMAS
• 金额: $ 24.22万
• 依托单位: WASHINGTON UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1989
• 资助国家: 美国
• 起止时间: 1989-07-01 至 1993-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/3333444
• 关键词: DNA; autoradiography; biotechnology; fluorescent dye /probe; gel electrophoresis; genetic mapping; genetic markers; image enhancement; image processing; linkage mapping; online computer; restriction fragment length polymorphism; restriction mapping; yeasts

The broad goal of this multi-disciplinary project is to advance genetics research in large-scale DNA mapping by developing a computer-based system for: 1) expediting the physical mapping of large regions of DNA on the scale of individual yeast chromosomes; and 2) improving large-scale human linkage mapping. To be developed and fields is an advanced image- acquisition and processing system for extracting information from fractionated mixtures of nucleic-acid molecules separated by slab-gel electrophoresis. Specific aims are to: 1) develop a system for direct (non-photographic) imaging of gels stained with fluorescent DNA-binding dyes; 2) extend the system to accommodate autoradio-grams used in RFLP mapping; 3) develop quantitative-imaging algorithms for automated, high-resolution detection and intensity estimation of gel bands for fragment-size determination from band mobilities and for data-integrity evaluation; 4) apply methods for geometric-distortion compensation of gel images to allow direct analytic comparisons of images obtained by different methods and from different laboratories; 5) develop an interactive software system for rapid and efficient expert interpretation and analysis of digitized gel images in a state-of-the-art workstation environment; and 6) evaluate the system's effectiveness in meeting the needs of the genetic research. Methods include using an advanced CCD imaging device to avoid photographic limitations; applying locally developed image-estimation algorithms to improve quantitative analysis of DNA digested by restriction enzymes; using "warping" algorithms to compensate for electrophoretic aberrancies; performing receiver-operating-characteristic (REC) and evaluation-database studies to assess detection-algorithm performance; providing image-processing utilities for enhancing gel-image features; and aiding interactive interpretation of gel images by constructing a user interface based on accepted windowing and networking standards to ensure software portability and ease of future exportation. This three-way collaboration involves the Department of Genetics, the Department of Computer Science (CS), and the Biomedical Computer Laboratory, all at Washington University. The independently funded CS components is developing a DNA analysis system for maintaining and analyzing large amounts of both DNA-fragment-size data and gel-image data to be generated using the system here proposed.

这个多学科项目的广泛目标是提高遗传学 通过开发基于计算机的系统的大规模DNA映射研究 对于：1）加快大型DNA的物理映射 单个酵母染色体的比例； 2）改善大型人 链接映射。 要开发和字段是一个高级图像 - 从中获取信息的采集和处理系统 核酸分子的分离混合物被平板凝胶分离 电泳。 具体目的是：1）开发直接的系统（非光摄影） 用荧光DNA结合染料染色的凝胶成像； 2）扩展 适用于RFLP映射中使用的自动载体的系统； 3）发展 自动化高分辨率检测的定量成像算法 凝胶带的强度估计用于碎片大小测定 从频段移动和数据整合评估； 4）应用方法 用于凝胶图像的几何延伸补偿，以允许直接 通过不同方法获得的图像的分析比较 不同的实验室； 5）开发一个交互式软件系统 快速有效的专家解释和分析数字化凝胶 在最先进的工作站环境中的图像； 6）评估 系统在满足遗传研究需求方面的有效性。 方法包括使用高级CCD成像设备避免 摄影限制；应用本地开发的图像估计 改善对DNA消化的定量分析的算法 限制酶；使用“翘曲”算法补偿 电泳劣质；执行接收器操作特征 （REC）和评估数据库研究，以评估检测算象 表现;提供图像处理实用程序来增强凝胶图像 特征;通过帮助对凝胶图像的互动解释 基于接受的窗口和网络构建用户界面 确保软件可移植性和易于未来出口的标准。 这种三路的合作涉及遗传学系 计算机科学系（CS）和生物医学计算机 实验室，都在华盛顿大学。 独立资助的CS 组件正在开发一种DNA分析系统，用于维护和 分析大量DNA碎片大小的数据和凝胶图像数据 使用此处提出的系统生成。