Low Cost Sequencing with Re-usable Magnetic Arrays and Nanoelectronic Sensors

利用可重复使用的磁性阵列和纳米电子传感器进行低成本测序

• 批准号: 8719766
• 负责人: HESAAME Esfandyarpour
• 金额: $ 104.75万
• 依托单位: GENAPSYS, INC.
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-14 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8719766
• 关键词: Arts; Automation; Biology; Cataloging; Catalogs; Charge; Clinical; Consumption; Containment; Cost Savings; DNA; DNA Sequence; DNA amplification; Data; Detection; Development; Devices; Diagnostic; Dideoxy Chain Termination DNA Sequencing; Disease Management; Electronics; Emulsions; Generations; Genes; Genome; Genomics; Goals; Health; Healthcare; Human; Individual; Label; Length; Ligation; Magnetism; Mainstreaming; Mediating; Medical; Medical Research; Medicine; Methods; Nucleotides; Optics; Output; Performance; Phase; Poisson Distribution; Polymerase; Preparation; Price; Process; Reaction; Reading; Reagent; Relative (related person); Research; Running; Sampling; Signal Transduction; Societies; Sorting - Cell Movement; Source; Structure; System; Techniques; Technology; Testing; Time; base; biological research; cost; cost effective; density; electric field; electric impedance; genome sequencing; improved; innovative technologies; insight; instrument; nano; nanoelectronics; nanomagnetic; nanosensors; novel; price lists; sensor; single molecule; usability; virtual

Sequencing methods allowing cost effective and accurate de novo and re-sequencing genomes are critical to provide needed insights for human health, disease management and diagnostics at the individual level. Costs still remain too high with inadequate quality, to make sequencing technologies affordable for the routine use of genomics in individual health care. The "Gene Electronic Nano-Integrated Ultra-Sensitive" (GENIUS) platform is based on innovative technologies to provide significant improvements in cost, accuracy, read length, throughput and ease of use relative to current state-of-art systems. The overall goal is to develop a sequencing system using nano-magnetic-electronic platforms. We are proposing a system that integrates sample preparation and enrichment steps with the sequencing module. Sample preparation will rely on a re-usable magnetic-electronic chip and a novel emulsion-free amplification method. After amplification, enrichment of template carrying monoclonal beads is achieved through 'sorting' based on DNA charge. Beads are then transferred and held on a micromagnet array integrated with a sequencing sensor chip consisting of high-density arrays of CMOS-based nano-electronic sensors for direct detection of extension reactions. In lieu of a reverse emulsion we are developing an easy to use, chip-based approach that will combine multiple sample processing steps in a single device. The purpose of the 'Virtual Nano-Reactor' chip is to generate clonal amplified template on high-density array of single beads. The efficient capture of beads, concentration and confinement of DNA and amplification products, may permit the elimination of whole genome amplification with its inherent bias. The re-usable 'Virtual Nano-reactor' chip provides uniform reaction conditions across the entire chip. The device will eliminate the variability in reaction volumes and double-Poisson distribution inherent in emulsion PCR. The re-usable "well-free" sequencing sensor chip provides high-sensitivity detection, efficient and uniform reagent delivery and washing, combined with the high efficiency bead capture and permits longer reads and higher accuracy by minimizing de-phasing and providing uniformity of reaction, and also reduce reagent consumption and cost. The re-usability of the chip significantly reduces the consumable cost. In summary, the simplified automatable workflow with low reagent consumption, label-free electronic detection using unmodified nucleotides and polymerase results in significant cost savings and improved accuracy. Our goal is to develop a platform to sequence a genome with consumable costs of ~$50, average read length of up to 1000 bases, and pre-assembly accuracy of > 99.7% with similar cost reduction and simplification for sample preparation.

具有成本效益且准确的基因组从头测序和重测序的测序方法对于 为个人健康、疾病管理和诊断提供所需的见解。成本 仍然过高且质量不足，无法使测序技术能够负担得起日常使用 个体医疗保健中的基因组学。 “基因电子纳米集成超灵敏”（GENIUS）平台 基于创新技术，在成本、准确性、读取长度、 相对于当前最先进的系统的吞吐量和易用性。 总体目标是开发使用纳米磁电子平台的测序系统。我们是 提出一种将样品制备和富集步骤与测序模块集成的系统。 样品制备将依赖于可重复使用的磁电子芯片和新型无乳液放大技术 方法。扩增后，通过“分选”实现携带单克隆珠的模板的富集 基于 DNA 电荷。然后，珠子被转移并固定在与微磁体阵列集成的微磁体阵列上。 测序传感器芯片由基于 CMOS 的纳米电子传感器的高密度阵列组成，用于直接 检测延伸反应。我们正在开发一种易于使用的基于芯片的技术来代替反相乳液 该方法将在单个设备中结合多个样品处理步骤。 “虚拟”的目的 Nano-Reactor'芯片是在高密度单珠阵列上生成克隆扩增模板。高效的 珠子的捕获、DNA 和扩增产物的浓缩和限制，可能允许 消除全基因组扩增及其固有的偏差。可重复使用的“虚拟纳米反应器”芯片 在整个芯片上提供均匀的反应条件。该装置将消除反应的变异性 乳液 PCR 中固有的体积和双泊松分布。可重复使用的“无孔”测序 传感器芯片提供高灵敏度检测，高效均匀的试剂输送和清洗，结合 具有高效率的珠子捕获，并通过最大限度地减少失相来允许更长的读取和更高的精度 并提供反应的均匀性，同时还减少试剂消耗和成本。的可重复使用性 芯片显着降低了耗材成本。总之，简化的自动化工作流程具有低 试剂消耗、使用未修饰的核苷酸和聚合酶的无标记电子检测结果 显着节省成本并提高准确性。 我们的目标是开发一个基因组测序平台，耗材成本约为 50 美元，平均读长 多达 1000 个底座，预组装精度 > 99.7%，并且类似的成本降低和简化 样品制备。