DNA Multiplex Hybridization Kinetics and SNP Assays

DNA 多重杂交动力学和 SNP 检测

• 批准号: 7415302
• 负责人: Albert S BENIGHT
• 金额: $ 109.48万
• 依托单位: PORTLAND BIOSCIENCE
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-05-01 至 2008-08-09
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7415302
• 关键词: Address; Adult; Base Pair Mismatch; Biological Assay; Blindness; Characteristics; Clinical; DNA; Detection; Development; Diagnostic; Discrimination; Environment; Foundations; Genes; Genomics; Genotype; Kinetics; Length; Macular degeneration; Measurement; Methodology; Numbers; Phase; Positioning Attribute; Preparation; Principal Investigator; Process; Protocols documentation; Quantitative Evaluations; Reaction; Relative (related person); Reverse Transcriptase Polymerase Chain Reaction; Sampling; Single Nucleotide Polymorphism; Small Business Funding Mechanisms; Small Business Innovation Research Grant; Solid; Solutions; Standards of Weights and Measures; Temperature; Testing; Theoretical model; Thermodynamics; Time; Urination; age related; analytical method; base; design; design and construction; improved; novel; novel diagnostics; research and development

DESCRIPTION (provided by applicant): This is a SBIR Fast-Track application to address two currently unmet needs. These are for a quantitative theoretical understanding of DNA multiplex hybridization reactions; and a general design methodology for developing rapid, reliable, multiplex genotyping assays. First, in a broader sense there is presently a void in theoretical understanding of DNA multiplex hybridization. For example, current analytical understanding of the thermodynamics and kinetics of the multiplex microarray hybridization process is minimal. Plans in Phase I include development and implementation of our theoretical multiplex analytical methods, and experimentally demonstrate feasibility of using temperature dependent kinetics to discriminate a perfect match duplex from one containing a single base pair mismatch, i.e. SNP, on a microarray. If feasibility can be established, the first part of Phase II is focused on quantitative evaluation of essential experimental parameters, and further parameterization of the theoretical model. This will establish a solid and more rigorous analytical basis for understanding DNA multiplex hybridization reactions. This theoretical foundation will immediately enable more insightful design, more accurate analysis, and greatly expanded and enhanced predictive capabilities for novel and improved design of microarray based assays. This analytical foundation will also support development and applications of novel diagnostic microarray formats that incorporate and utilize time and temperature as key assay parameters. In the second part of Phase II, to demonstrate capability and immediate utility of our analytical process, we will design, build, test and validate a rapid genotyping panel test for 11 single nucleotide polymorphisms in eight genes that have been associated with Adult Macular Degeneration, a leading cause of age related vision loss. The developed process can be generally applied to the design of multiplex genotyping assays for the detection of virtually any SNP panel for any standard microarray platform. Principal Investigator: Benight, Albert S. Project Narrative The goal of this SBIR Fast-Track project is to develop new and powerful analytical tools that will be parameterized and implemented to provide capabilities of quantitative modeling of the temperature dependence of DNA multiplex hybridization kinetics on a microarrray. The developed tools will be readily applicable to address prescient needs in custom diagnostic assay design. A demonstration of the developed technology will be a rapid and cheap genotyping assay for detection of Single Nucleotide Polymorphisms (SNPs) that may be associated with Adult Macular Degeneration, a genetic disease responsible for nearly 50% of age related vision loss in developed countries.

描述（由申请人提供）：这是一个SBIR快速通道申请，以解决两个目前未满足的需求。这些是DNA多重杂交反应的定量理论理解，以及开发快速，可靠，多重基因分型检测的一般设计方法。首先，从更广泛的意义上说，目前在理论上理解DNA多重杂交的空白。例如，目前对多重微阵列杂交过程的热力学和动力学的分析理解是最少的。第一阶段的计划包括开发和实施我们的理论多重分析方法，并通过实验证明使用温度依赖性动力学在微阵列上区分完全匹配的双链体与包含单碱基对错配（即SNP）的双链体的可行性。如果可行性可以建立，第二阶段的第一部分是重点定量评估的基本实验参数，并进一步参数化的理论模型。这将建立一个坚实的和更严格的分析基础，了解DNA多重杂交反应。这一理论基础将立即使更有见地的设计，更准确的分析，并大大扩大和增强预测能力的新的和改进的设计，基于微阵列的测定。这一分析基础也将支持新的诊断微阵列格式的开发和应用，这些格式将时间和温度作为关键检测参数。在第二阶段的第二部分，为了证明我们的分析过程的能力和即时效用，我们将设计、构建、测试和验证与成人黄斑变性相关的8个基因中的11个单核苷酸多态性的快速基因分型面板测试，这是年龄相关视力丧失的主要原因。所开发的方法通常可以应用于设计多重基因分型测定，用于检测任何标准微阵列平台的几乎任何SNP组。主要研究者：Benight，Albert S. SBIR快速通道项目的目标是开发新的、功能强大的分析工具，这些工具将被参数化和实现，以提供对微阵列上DNA多重杂交动力学的温度依赖性进行定量建模的能力。开发的工具将很容易适用于解决定制诊断检测设计中的预见性需求。开发的技术的示范将是用于检测可能与成人黄斑变性相关的单核苷酸多态性（SNP）的快速和廉价的基因分型测定，成人黄斑变性是一种遗传性疾病，在发达国家造成近50%的年龄相关视力丧失。