Novel Low Cost, High Throughput DNA Sequencing Platform

描述（由申请人提供）：我们的目标是商业化的新技术，快速测序DNA。该技术可以应用于（通过适当的预处理步骤）全基因组测序，以及其他测定，包括转录组学、转录因子活性、miRNA表达、DNA甲基化和SNP分析。目前的STTR第一阶段提案要求提供一年的支持，以完成初步的原则研究证明。目前的DNA测序技术太慢（即12-15兆碱基/小时）和昂贵（即7 - 70美元/兆碱基），不能广泛应用于全基因组测序或其他上述应用。目前的建议是开发和提供新的技术，生物医学研究界，可以更充分地实现通过一个新的合资企业，完美表达DNA测序的承诺，将开发和提供一个产品，DNA计数，这将提供一个更便宜和更好的替代现有的测序技术。特别是，DNACount将取代定性和嘈杂的微阵列，ChIP和miRNA高通量检测与基因序列的数字读出。在某些情况下，替代qPCR测定甚至可能具有成本效益。DNACount通过高通量方式分离、扩增和测序每个分子来测量每个基因的实际浓度。我们的方法与其他方法不同之处在于提供更高质量（即长度）和数量的读数。我们使用合成测序，使用内源性dNTP来产生长读段（即> 250 bp），同时使用流动池和玻璃固定技术来最大化平行读段的数量（即约4000万）。DNACount使用现成的光学器件和微流体技术，以最大限度地降低测序的资本（<100，000美元）和运营（<1000美元/次）成本。我们的目标是以低成本提供一种台式解决方案，使DNA测序变得像PCR一样普遍。这将为基础和临床研究人员开辟新的途径。 公共卫生相关性：我们的目标是将一种快速测序DNA的新技术商业化。该技术可以应用于（通过适当的预处理步骤）全基因组测序，以及其他测定，包括转录组学、转录因子活性、miRNA表达、DNA甲基化和SNP分析。目前的STTR第一阶段提案要求提供一年的支持，以完成初步的原则研究证明。目前的DNA测序技术太慢（即12-15兆碱基/小时）和昂贵（即7 - 70美元/兆碱基），不能广泛应用于全基因组测序或其他上述应用。目前的建议是开发和提供新的技术，生物医学研究界，可以更充分地实现通过一个新的合资企业，完美表达DNA测序的承诺，将开发和提供一个产品，DNA计数，这将提供一个更便宜和更好的替代现有的测序技术。特别是，DNACount将取代定性和嘈杂的微阵列，ChIP和miRNA高通量检测与基因序列的数字读出。在某些情况下，替代qPCR测定甚至可能具有成本效益。DNACount通过高通量方式分离、扩增和测序每个分子来测量每个基因的实际浓度。我们的方法与其他方法不同之处在于提供更高质量（即长度）和数量的读数。我们使用合成测序，使用内源性dNTP来产生长读段（即> 250 bp），同时使用流动池和玻璃固定技术来最大化平行读段的数量（即约4000万）。DNACount使用现成的光学器件和微流体技术，以最大限度地降低测序的资本（<100，000美元）和运营（<1000美元/次）成本。我们的目标是以低成本提供一种台式解决方案，使DNA测序变得像PCR一样普遍。这将为基础和临床研究人员开辟新的途径。

DESCRIPTION (provided by applicant): We aim to commercialize a new technology to rapidly sequence DNA. This technology can be applied (with proper preprocessing steps) to whole genome sequencing, and other assays including transcriptomics, transcription factor activity, miRNA expression, DNA methylation, and SNP analysis. The present STTR Phase I proposal requests one year of support to complete initial proof of principle studies. Current DNA sequencing technologies are too slow (i.e. 12-15 Megabases/hour) and expensive (i.e. $7- $70/Megabases) to be widely applied to whole genome sequencing or other aforementioned applications. The present proposal is to develop and provide new technology to the biomedical research community that can more fully realize the promise of DNA sequencing through a new venture, PerfectExpression, that will develop and offer a product, DNACount, that will provide a cheaper and better alternative to existing sequencing technologies. In particular, DNACount will replace qualitative and noisy microarray, ChIP, and miRNA high throughput assays with digital readouts of gene sequences. In certain circumstances, it may even be cost effective to replace qPCR assays. DNACount measures the actual concentration of each gene by isolating, amplifying, and sequencing each individual molecule in a high throughput manner. Our approach differs from other approaches by providing higher quality (i.e. length) and quantity reads. We use sequencing by synthesis using endogenous dNTP's to produce long reads (i.e. > 250 bp) while using flow cells and glass immobilization technologies to maximize the number of parallel reads (i.e. ~40 million). DNACount uses off-the-shelf optics and microfluidics to minimize capital (< $100,000) and operational (<$1000/run) costs of sequencing. Our goal is to provide a bench-top solution at a low cost such that DNA sequencing becomes as pervasive as PCR. This will open new avenues to basic and clinical researchers. PUBLIC HEALTH RELEVANCE: We aim to commercialize a new technology to rapidly sequence DNA. This technology can be applied (with proper preprocessing steps) to whole genome sequencing, and other assays including transcriptomics, transcription factor activity, miRNA expression, DNA methylation, and SNP analysis. The present STTR Phase I proposal requests one year of support to complete initial proof of principle studies. Current DNA sequencing technologies are too slow (i.e. 12-15 Megabases/hour) and expensive (i.e. $7- $70/Megabases) to be widely applied to whole genome sequencing or other aforementioned applications. The present proposal is to develop and provide new technology to the biomedical research community that can more fully realize the promise of DNA sequencing through a new venture, PerfectExpression, that will develop and offer a product, DNACount, that will provide a cheaper and better alternative to existing sequencing technologies. In particular, DNACount will replace qualitative and noisy microarray, ChIP, and miRNA high throughput assays with digital readouts of gene sequences. In certain circumstances, it may even be cost effective to replace qPCR assays. DNACount measures the actual concentration of each gene by isolating, amplifying, and sequencing each individual molecule in a high throughput manner. Our approach differs from other approaches by providing higher quality (i.e. length) and quantity reads. We use sequencing by synthesis using endogenous dNTP's to produce long reads (i.e. > 250 bp) while using flow cells and glass immobilization technologies to maximize the number of parallel reads (i.e. ~40 million). DNACount uses off-the-shelf optics and microfluidics to minimize capital (< $100,000) and operational (<$1000/run) costs of sequencing. Our goal is to provide a bench-top solution at a low cost such that DNA sequencing becomes as pervasive as PCR. This will open new avenues to basic and clinical researchers.