High Pressure Sample Preparation Instrumentation for DNA Sequencing

用于 DNA 测序的高压样品制备仪器

• 批准号: 8833419
• 负责人: Alexander V Lazarev
• 金额: $ 51.56万
• 依托单位: PRESSURE BIOSCIENCE, INC.
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2016-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8833419
• 关键词: Adoption; Automation; Bacteria; Biological Preservation; Biomedical Research; Caliber; Cells; Chemicals; Collection; Computer software; Cytolysis; DNA; DNA Damage; DNA Fragmentation; DNA Repair; DNA Sequence; Development; Devices; Drops; Elements; Ensure; Equilibrium; Equipment; Feedback; Generations; Genomic DNA; Geometry; Goals; Health; Healthcare; Hydrostatic Pressure; Injection of therapeutic agent; Laboratories; Lead; Ligation; Liquid substance; Mechanics; Methods; Monitor; Performance; Phase; Polishes; Preparation; Process; Protocols documentation; Pump; Readiness; Recovery; Running; Sampling; Secure; Sequence Analysis; Site; Staging; System; Techniques; Technology; Temperature; Testing; Time; Tissues; Validation; Vendor; Viscosity; Yeasts; active control; base; cell type; cost; design; ds-DNA; genome sequencing; improved; instrument; instrumentation; miniaturize; next generation sequencing; personalized diagnostics; pressure; programs; prototype; research and development; software development; tool

DESCRIPTION (provided by applicant): Developments in next generation sequencing (NGS) continue to increase throughput and reduce the costs for whole-genome sequencing. Unfortunately, DNA preparation methods lag behind in both throughput and DNA quality, slowing the pace of adoption of new sequencing techniques. This Phase II proposal focuses on the development of an automated, commercial prototype DNA shearing device that matches the requirements of many popular and emerging NGS platforms. In Phase II we will develop a miniature self-cleaning active shearing nozzle and integrate it with a constant pressure pump to allow for a flow-through shearing design and easy sample introduction and collection. In addition we will build on our progress from Phase I to optimize the range of parameters (pressure, flow rate, orifice diameter and design) necessary for optimal DNA shearing to generate fragments in predictable, narrow size ranges. We will manufacture two prototype instruments for placement at our R&D laboratory and at a collaborator site, and will characterize the performance of the automated system prototypes. We have identified vendors for critical system components and secured academic collaborators to validate the performance of the new platform. We expect to achieve manufacturing readiness by the conclusion of this Phase II period. In Specific Aim #1 we will develop a miniature automatic self-cleaning active shearing nozzle, followed by Specific Aim #2 where we will integrate the shearing nozzle with a constant pressure pump and the means of sample introduction and collection. In this Aim we will also develop computer software to facilitate automatic control of the active nozzle and sample management. In Specific Aim #3 we will identify the range of parameters (pressure, flow, temperature, and viscosity) necessary for optimal performance of proposed integrated system. In Specific Aim #4 we will characterize the performance of the automated system prototypes for DNA shearing applications and develop corresponding applications. Finally in Specific Aim #5 we will evaluate the suitability of the system for cell lysis and homogenization and optimize the hardware components for that purpose. We have identified vendors for most critical components and secured academic collaborators to validate performance of the new platform, therefore we expect to achieve the manufacturing readiness by the conclusion of this Phase II period

描述（由申请人提供）：下一代测序（NGS）的发展继续增加吞吐量并降低全基因组测序的成本。不幸的是，DNA制备方法在吞吐量和DNA质量方面都落后，从而减慢了新测序技术的采用速度。该第二阶段提案的重点是开发自动化的商业原型DNA剪切设备，该设备符合许多流行和新兴的NGS平台的要求。在第二阶段，我们将开发微型自我清洁的活动剪切喷嘴，并将其与恒压泵整合在一起，以允许流通剪切设计以及易于介绍和收集。此外，我们将基于从I阶段的进度来建立，以优化最佳DNA剪切所需的参数范围（压力，流速，孔口直径和设计），以在可预测的窄尺寸范围内产生片段。我们将制造两种原型仪器，用于在研发实验室和合作者站点上放置，并将表征自动系统原型的性能。 We have identified vendors for critical system components and secured academic collaborators to validate the performance of the new platform.我们希望通过这一第二阶段时期的结论来实现制造准备。在特定的目标＃1中，我们将开发一个微型自动自我清洁的主动剪切喷嘴，然后是特定的目标＃2，我们将将剪切喷嘴与恒定压力泵和样品引入和收集的方式集成在一起。在此目标中，我们还将开发计算机软件，以促进自动控制主动喷嘴和样品管理。在特定的目标＃3中，我们将确定所需的集成系统最佳性能所需的参数范围（压力，流动，温度和粘度）。在特定的目标＃4中，我们将表征用于DNA剪切应用的自动化系统原型的性能并开发相应的应用。最后，在特定的目标＃5中，我们将评估系统对细胞裂解和均质化的适用性，并为此目的优化硬件组件。我们已经确定了大多数关键组成部分的供应商，并确保了学术合作者来验证新平台的性能，因此我们希望通过这一II阶段时期的结论来实现制造业准备