Novel Low Cost, High Throughput DNA Sequencing Platform

新型低成本、高通量 DNA 测序平台

• 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
• 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

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。该技术可以应用于全基因组测序（适当的预处理步骤），以及其他分析，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第一阶段建议要求一年的支持，以完成初步的原理证明研究。目前的DNA测序技术速度太慢（即12-15兆碱基/小时），价格昂贵（即7- 70美元/兆碱基），无法广泛应用于全基因组测序或其他上述应用。目前的提议是为生物医学研究界开发和提供新技术，通过一个新的企业PerfectExpression来更充分地实现DNA测序的承诺，该企业将开发和提供一种产品dnaccount，这将为现有的测序技术提供更便宜、更好的替代方案。特别是，dnaccount将用基因序列的数字读数取代定性和嘈杂的微阵列、ChIP和miRNA高通量分析。在某些情况下，取代qPCR检测甚至可能具有成本效益。dnaccount通过高通量方式分离、扩增和测序每个单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的不同之处在于提供更高质量（即长度）和数量的读取。我们使用内源性dNTP合成测序来产生长reads（即> 250bp），同时使用流式细胞和玻璃固定技术来最大化平行reads的数量（即~ 4000万）。dnaccount使用现成的光学和微流体，以尽量减少资本（<$ 100,000）和操作（<$1000/运行）的测序成本。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。