Optimization of Nanopore Genomic DNA Sequencing

纳米孔基因组 DNA 测序的优化

• 批准号: 8749195
• 负责人: MARK A AKESON
• 金额: $ 76.06万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-08-01 至 2017-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8749195
• 关键词: Animal Model; Arabidopsis; Basic Science; Biological; Cell Nucleus; Cells; Communities; Computing Methodologies; CpG dinucleotide; Cytosine; DNA; DNA Damage; DNA Resequencing; DNA Sequence; Development; Devices; Enzymes; Epigenetic Process; Escherichia coli; Genomic DNA; Goals; Healthcare; Heterogeneity; Human; Individual; Length; Libraries; Malignant Neoplasms; Measurable; Medical Research; Methods; Methylation; Modification; Motor; Mus; Noise; Nucleotides; Organism; Proteins; Reading; Reference Standards; Regenerative Medicine; Reporting; Research; System; Techniques; Technology; Testing; Time; Touch sensation; base; biophysical properties; design; helicase; improved; motor control; mutant; nanopore; nanoscale; nucleobase; public health relevance; sensor; single molecule

This proposal concerns optimization of enzymes, pores, and computational methods for single molecule sequencing of genomic DNA fragments. It is based on a proven nanopore device implemented by our group at UCSC. This device is comprised of a sensor that touches and examines each nucleotide within a captured DNA strand as a processive enzyme motor advances the strand. Although the overall goal of nanopore sequencing is de novo reads on very long strands, here we will also focus on resequencing of DNA from organisms important in basic research (mouse, E. coli & Arabidopsis) and in healthcare (human). We are focusing on both de novo and resequencing for two reasons: 1) nanopore sequencing of biological DNA has not been documented publicly. Therefore, nanopore resequencing of reference standards is required for community acceptance, and, importantly, to reveal weaknesses in the technology that impact de novo sequencing accuracy; 2) nanopore resequencing in this application means reading genomic DNA directly and therefore will include epigenetic modifications. This would be an immediate, important contribution to the research community.

该建议涉及单分子的酶，孔和计算方法的优化 基因组DNA片段的测序。它基于我们实施的验证的纳米孔设备 UCSC的小组。该设备由一个传感器组成，该传感器触摸并检查了每个核苷酸 被捕获的DNA链作为造物酶电动机的链条。虽然总体目标 纳米孔测序是从头开始读取的，我们还将重点介绍 来自基础研究重要的生物的DNA（鼠标，大肠杆菌和拟南芥）和医疗保健 （人类）。我们专注于从头和重新陈述的原因有两个：1）纳米孔测序 生物DNA的尚未公开记录。因此，纳米孔的参考重新陈述 社区接受是必需的，重要的是要揭示弱点 影响从头测序精度的技术； 2）纳米孔在此应用程序中重新陈述 表示直接读取基因组DNA，因此将包括表观遗传修饰。这是 对研究界的直接，重要的贡献。