Novel Low Cost, High Throughput DNA Sequencing Platform

描述(由申请人提供)：我们的目标是将一种新技术商业化，以快速对DNA进行测序。这项技术可以应用于全基因组测序，以及包括转录、转录因子活性、miRNA表达、DNA甲基化和SNP分析在内的其他分析。目前的STTR第一阶段提案要求一年的支持，以完成初步的原则研究。目前的DNA测序技术太慢(即12-15兆基数/小时)和昂贵(即每兆基数7-70美元)，无法广泛应用于全基因组测序或其他前述应用。目前的提议是开发新技术并向生物医学研究界提供新技术，通过一家名为PerfetExpression的新企业来更充分地实现DNA测序的前景，该企业将开发并提供一种产品DNACount，它将为现有的测序技术提供一种更便宜、更好的替代方案。特别是，DNACount将用基因序列的数字读出取代定性和嘈杂的微阵列、芯片和miRNA高通量分析。在某些情况下，取代定量聚合酶链式反应检测甚至可能具有成本效益。DNACount通过以高通量的方式分离、扩增和测序每个单独的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，它提供了更高质量(即长度)和数量的阅读。我们使用内源性dNTP的合成测序来产生长读取(即&gt；250个碱基对)，同时使用流式细胞和玻璃固定化技术来最大化并行读取的数量(即约4,000万)。DNACount使用现成的光学和微流体将测序的资本(10万美元)和运营成本(1000美元/次)降至最低。我们的目标是提供一种低成本的台式解决方案，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。 与公共健康相关：我们的目标是将一种快速测序DNA的新技术商业化。这项技术可以应用于全基因组测序，以及包括转录、转录因子活性、miRNA表达、DNA甲基化和SNP分析在内的其他分析。目前的STTR第一阶段提案要求一年的支持，以完成初步的原则研究。目前的DNA测序技术太慢(即12-15兆基数/小时)和昂贵(即每兆基数7-70美元)，无法广泛应用于全基因组测序或其他前述应用。目前的提议是开发新技术并向生物医学研究界提供新技术，通过一家名为PerfetExpression的新企业来更充分地实现DNA测序的前景，该企业将开发并提供一种产品DNACount，它将为现有的测序技术提供一种更便宜、更好的替代方案。特别是，DNACount将用基因序列的数字读出取代定性和嘈杂的微阵列、芯片和miRNA高通量分析。在某些情况下，取代定量聚合酶链式反应检测甚至可能具有成本效益。DNACount通过以高通量的方式分离、扩增和测序每个单独的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，它提供了更高质量(即长度)和数量的阅读。我们使用内源性dNTP的合成测序来产生长读取(即&gt；250个碱基对)，同时使用流式细胞和玻璃固定化技术来最大化并行读取的数量(即约4,000万)。DNACount使用现成的光学和微流体将测序的资本(10万美元)和运营成本(1000美元/次)降至最低。我们的目标是提供一种低成本的台式解决方案，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.