Novel Low Cost, High Throughput DNA Sequencing Platform

新型低成本、高通量 DNA 测序平台

基本信息

批准号：
7989338
负责人：
JAMES SCHWABER
金额：
$ 1.8万
依托单位：
PERFECT EXPRESSION, INC.
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2011-09-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7989338
关键词：
Area Base Sequence Binding Biological Assay Biomedical Research Buffers Capital Cells Clinical Communities Complement component C4 Computational algorithm Computer software Computers DNA Methylation DNA Sequence Data Detection Development Engineering Ensure Feasibility Studies Genes Genome Glass Goals Hour Human Genome Image Image Analysis Immobilization Individual Length Light Link Measures MicroRNAs Microfluidics Molecular Biology Nucleotides Optics Phase Population Reaction Reading Reagent Request for Proposals Research Personnel Resolution Running Series Signal Transduction Small Business Technology Transfer Research Solutions System Technology Temperature Testing Time Universities base commercialization cost cost effective density design digital enzyme substrate fluorescence microscope genome sequencing genome-wide high throughput screening image processing improved new technology novel phase 1 study polydimethylsiloxane pressure promoter public health relevance transcription factor transcriptomics

项目摘要

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.

描述（由申请人提供）：我们旨在将新技术商业化以快速序列DNA。可以将该技术应用于整个基因组测序，以及包括转录组学，转录因子活性，miRNA表达，DNA甲基化和SNP分析在内的其他测定法。目前的I阶段提案要求一年的支持以完成原则研究的初步证明。当前的DNA测序技术太慢（即12-15兆瓦/小时）和昂贵（即$ 7- $ 70/兆巴），无法广泛应用于整个基因组测序或其他上述应用程序。目前的建议是为生物医学研究社区开发和提供新技术，这些技术可以通过新的企业，完美的表达方式实现DNA测序的希望，该公司将开发和提供产品DNACount，该产品将提供更便宜，更好的替代方案到现有的测序技术。特别是，DNAcount将用基因序列的数字读数取代定性和嘈杂的微阵列，芯片和miRNA高吞吐量测定。在某些情况下，替换QPCR分析甚至可能是成本效益的。 DNAcount通过以高通量方式隔离，扩增和测序每个单独的分子来测量每个基因的实际浓度。我们的方法通过提供更高质量（即长度）和数量读取而与其他方法不同。我们使用内源性DNTP使用合成的测序来产生长读数（即> 250 bp），同时使用流动细胞和玻璃固定技术来最大化平行读数的数量（即约4000万）。 DNAcount使用现成的光学和微流体学来最大程度地减少测序的资本（<$ 100,000）和运营（<$ 1000/运行）的成本。我们的目标是以低成本提供台式解决方案，以使DNA测序变得像PCR一样普遍。这将为基础研究人员和临床研究人员开放新的途径。公共卫生相关性：我们旨在将新技术商业化以快速序列DNA。可以将该技术应用于整个基因组测序，以及包括转录组学，转录因子活性，miRNA表达，DNA甲基化和SNP分析在内的其他测定法。目前的I阶段提案要求一年的支持以完成原则研究的初步证明。当前的DNA测序技术太慢（即12-15兆瓦/小时）和昂贵（即$ 7- $ 70/兆巴），无法广泛应用于整个基因组测序或其他上述应用程序。目前的建议是为生物医学研究社区开发和提供新技术，这些技术可以通过新的企业，完美的表达方式实现DNA测序的希望，该公司将开发和提供产品DNACount，该产品将提供更便宜，更好的替代方案到现有的测序技术。特别是，DNAcount将用基因序列的数字读数取代定性和嘈杂的微阵列，芯片和miRNA高吞吐量测定。在某些情况下，替换QPCR分析甚至可能是成本效益的。 DNAcount通过以高通量方式隔离，扩增和测序每个单独的分子来测量每个基因的实际浓度。我们的方法通过提供更高质量（即长度）和数量读取而与其他方法不同。我们使用内源性DNTP使用合成的测序来产生长读数（即> 250 bp），同时使用流动细胞和玻璃固定技术来最大化平行读数的数量（即约4000万）。 DNAcount使用现成的光学和微流体学来最大程度地减少测序的资本（<$ 100,000）和运营（<$ 1000/运行）的成本。我们的目标是以低成本提供台面解决方案，以使DNA测序变得像PCR一样普遍。这将为基础研究人员和临床研究人员开放新的途径。