Microfluidic DNA Sequencing

微流控 DNA 测序

• 批准号: 8725992
• 负责人: TAL RAZ
• 金额: $ 149.99万
• 依托单位: GNUBIO, INC.
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-09-14 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8725992
• 关键词: Algorithms; Bar Codes; Biological Assay; Color; DNA; DNA Library; DNA Resequencing; DNA Sequence; Data Analyses; Detection; Devices; Drops; Dyes; Funding; Genetic; Genome; Genomic DNA; Health Care Costs; Healthcare; Hour; Human Genome; Informatics; Lead; Length; Libraries; Marketing; Medical; Medicine; Methodology; Methods; Microfluidic Microchips; Microfluidics; Outcome; Persons; Phase; Physicians; Preparation; Process; Protocols documentation; Reading; Reagent; Research Personnel; Running; Schedule; Site; Small Business Innovation Research Grant; Sorting - Cell Movement; System; Systems Analysis; Testing; Time; Variant; Work; base; cost; genome sequencing; improved; instrument; meetings; public health relevance; sensor; synthetic construct; user-friendly

DESCRIPTION (provided by applicant): This is a Phase II SBIR proposal to increase the throughput of our DNA sequencing instrument to enable whole genome sequencing with high efficiency and accuracy for a cost of under $1000 per genome. In Phase I, we developed a working sequencing assay, a microfluidic platform and camera system, and analysis methodology that enable genome alignment and variant calling. We have demonstrated sequencing using both synthetic DNA and genomic DNA amplicons with read lengths up over 600bp and accuracy higher than 99.9% per base. Using internal funds, we are upgrading the Phase I device to become a field ready beta test device for placement into several sites. This will be a single channel device that is capable of inline selection of 250 sequencing targets (average of 200BP long), sequence at 40X coverage, and variant calling in less than 2.5 hours of total run time. The Specific Aim of Phase II is to increase the throughput of this beta test single channel instrument to enable whole genome sequencing with high efficiency and accuracy for a cost of under $1000 per genome. To accomplish this Specific Aim, we will carry out seven Tasks: Task 1: Develop a full-genome sequencing assay protocol for the preparation of a genomic DNA library for sequencing. Task 2: Develop a sensor configuration that can scale to 100s of channels. Task 3: Develop a microfluidic device that can scale to 100s of channels Task 4: Develop a method to read droplet sizes of ~10um Task 5: Develop a sorting assay that sorts amplified DNA from empty drops Task 6: Extend current informatics pipeline for resequencing a whole genome Task 7: Extend current barcode clustering algorithms. At the conclusion of Phase II, we will have a breadboard sequencing system that will be able to demonstrate that sequencing a whole genome in about six hours, including data analysis, genome alignment and variant calling, is fully achievable. The system will support reagent volumes that will meet the per run costs target <$1000. Following Phase II, we expect to use internal funds to have a market ready product within one year.

描述（由申请人提供）：这是一个II期SBIR提案，以增加我们的DNA测序仪器的吞吐量，以使整个基因组测序具有高效率和准确性，每个基因组的成本低于1000美元。在第一阶段，我们开发了一个工作测序分析，一个微流体平台和相机系统，以及可以实现基因组比对和变体调用的分析方法。我们已经证明了使用合成DNA和基因组DNA扩增子的测序，读取长度超过600bp，精度高于每个碱的99.9％。使用内部资金，我们正在升级I期设备，成为现场就绪的Beta测试设备，以放置在多个站点中。这将是一个单个通道设备，能够在直列选择250个测序目标（平均为200bp长），40倍覆盖范围的序列以及在总运行时间不到2.5小时的时间内进行变体。 II期的具体目的是增加该Beta测试单通道仪器的吞吐量，以使整个基因组测序以高效率和准确性，每个基因组的成本低于1000美元。为了实现这一特定目标，我们将执行七个任务：任务1：开发完整基因组测序测定方案，以制备用于测序的基因组DNA库。任务2：开发一个传感器配置，该配置可以扩展到100个通道。 任务3：开发一个可以扩展到100个通道任务的微流体设备。4：开发一种读取液滴大小的方法〜10UM任务5：开发一个排序测定法，该分类测定从空滴任务6：扩展当前的信息管道管道：扩展当前的信息管道，以重述整个基因组任务7：扩展当前的条形码群集群集簇量化载体。 在第二阶段的结论中，我们将拥有一个面包板测序系统，该系统将能够证明在大约六个小时内进行整个基因组，包括数据分析，基因组比对和变体调用，这是完全可以实现的。该系统将支持符合每次运行成本目标<$ 1000的试剂量。在第二阶段之后，我们希望使用内部资金在一年内拥有市场就绪产品。