Hybrid Nanochannel Arrays for Single Molecule Linear Genome Analysis

用于单分子线性基因组分析的混合纳米通道阵列

• 批准号: 8046433
• 负责人: Michael David Austin
• 金额: $ 28.76万
• 依托单位: BIONANOMATRIX, INC.
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-09-26 至 2011-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8046433
• 关键词: Architecture; Biochemical; Biochemical Process; Blood capillaries; Buffers; Cells; Collection; Color; Complex; Copy Number Polymorphism; DNA; DNA Fragmentation; DNA Sequence; DNA analysis; Data; Development; Device Designs; Devices; Diagnostic; Disease; Environment; Equipment; Failure; Genetic; Genetic Variation; Genome; Genomic Instability; Genomics; Genotype; Haplotypes; Health; Hereditary Disease; Hour; Human Genetics; Human Genome; Hybrids; Image; Industry; Investigation; Joystick; Label; Lead; Length; Liquid substance; Manuals; Maps; Medical; Medical Genetics; Medicine; Methods; Microfluidics; Microscope; Microscopy; Molecular; Nanoarray Analytical Device; Other Genetics; Performance; Phase; Plastics; Preparation; Production; Protocols documentation; Pump; Repetitive Sequence; Research; Research Personnel; Resolution; Sampling; Semiconductors; Sensitivity and Specificity; Silicon; Staging; Standardization; Structure; System; Technology; Variant; abstracting; base; biochip; cancer genetics; capillary; color detection; cost effective; ds-DNA; epigenomics; fluorescence microscope; insight; nanochannel; nanodevice; nanofabrication; nanofluidic; pressure; scale up; single molecule; system architecture; tool; user-friendly

DESCRIPTION (provided by applicant): Hybrid Nanochannel Arrays for Single Molecule Linear Genome Analysis Abstract The objective of this proposal is to develop a fully integrated nanofluidic device for single molecule analysis of long, linearized, native state genomic DNA. The project will result in a simple, disposable chip that will allow direct, fluorescent single molecule analysis of structural, CNV, haplotype and epigenomic variations at the single molecule level. The resulting commercial system will permit researchers and clinicians to directly visualize genomic variations from a few kilobases to megabases in length, from as little as a single cell to common bulk preparation methods, on common microscope imaging systems. Advances in technologies to analyze complex genomes have allowed for significant collection and analysis of a wide range of genetic data including gross structural variation, repetitive elements, genotypes, haplotypes and more generically, the DNA sequence. But current technologies suffer from relatively low sensitivity and specificity due to data generated from averaged heterogeneous bulk sample preparations or difficulties in standardizing and scaling up the analytical platform and biochemical protocols. The proposed hybrid micro/nanofluidic device will allow isolation, manipulation and direct imaging of single molecule features without significantly changing upstream biochemical process of the samples. Leveraging high quality mass micro/nanofabrication technology developed by the semiconductor industry, these devices could be made truly affordable to end users while allowing consistent and comparable results on a standardized format. Based upon phase I results, we will optimize a nearly universal, high resolution single molecule level DNA analysis device. The specific aims of phase II are to 1) develop fluorescent standards and sample buffer for evaluating device performance, 2)develop a simple, disposable chip cartridge that can be easily loaded by standard pipetting, 3) develop a modular joystick control system for manipulating the flow of DNA within the device while mounted on standard microscopy systems. Completion of this project will result in an integrated biochip device capable of providing statistically significant, single-molecule-level analysis of megabase DNA with sub-kilobase resolution. This technology could greatly enhance our ability to understand many different types of genetic variations and of genomic instabilities related to cancer and other genetic diseases with consistent and reproducible performance that will enable broad incorporation of single molecule analysis into diagnostic and medical genetics applications. PUBLIC HEALTH RELEVANCE: The development of an open architecture, single molecule, linear DNA analysis system will provide researchers and clinicians alike a new tool for genomic investigation, providing new insights into the complexity of human genetic disease and genome structure. The availability of an inexpensive, disposable nanodevice compatible with common microscopy systems will enable broad access to single molecule research of human genome variation, such as structural mapping, haplotyping and even copy number variation, as well as the characterization of overall genomic state. This will help expand the use of genomic analysis as a tool for understanding complex disorders and will help enable the realization of practical, cost effective personalized medicine.

描述（由申请人提供）：单分子线性基因组分析的混合纳米渠道阵列摘要该提案的目的是开发一种完全集成的纳米流体设备，用于对长，线性，天然状态基因组DNA进行单分子分析。该项目将导致简单，一次性的芯片，该芯片将允许对单分子水平的结构，CNV，单倍型和表观基因组变异进行直接的荧光单分子分析。所得的商业系统将使研究人员和临床医生能够直接可视化从几千座到巨型群的基因组变异，从单个细胞到普通显微镜成像系统，从单个细胞到常见的大量制备方法。分析复杂基因组的技术的进步允许对广泛的遗传数据进行大量收集和分析，包括总体结构变化，重复元素，基因型，单倍型以及更一般的DNA序列。但是，由于平均异构体积样本制剂产生的数据或在标准化和扩展分析平台和生化方案时，当前技术的灵敏度和特异性相对较低。所提出的杂化微/纳米流体设备将允许对单分子特征进行分离，操纵和直接成像，而不会显着改变样品的上游生化过程。利用半导体行业开发的高质量微型/纳米制作技术，这些设备可以使最终用户真正负担得起，同时允许在标准化格式上保持一致且可比的结果。基于I期结果，我们将优化几乎通用的高分辨率单分子水平DNA分析设备。 II期的具体目的是1）开发荧光标准和样品缓冲液以评估设备性能，2）开发一个简单的一次性芯片弹药筒，可以通过标准移液轻松加载，3）开发一个模块化的操纵杆控制系统，以操纵DNA在设备中的操作，同时安装在标准的显微镜系统上。该项目的完成将导致一个综合的生物芯片设备，能够通过统计，单分子级分析具有亚kilobase分辨率。这项技术可以极大地增强我们了解许多不同类型的遗传变异以及与癌症和其他遗传疾病有关的基因组不稳定性，具有一致且可重复的性能，这将使单分子分析能够将单分子分析广泛融合到诊断和医学遗传学应用中。公共卫生相关性：开放架构，单分子，线性DNA分析系统的开发将为研究人员和临床医生提供基因组研究的新工具，从而为人类遗传疾病和基因组结构的复杂性提供了新的见解。与常见显微镜系统兼容的廉价，一次性纳米模型的可用性将使人们能够广泛访问人类基因组变异的单分子研究，例如结构映射，单倍分型甚至拷贝数变化，以及整体基因组状态的表征。这将有助于扩大基因组分析作为理解复杂疾病的工具的使用，并有助于实现实用，具有成本效益的个性化医学。