Optimization of Nanopore Genomic DNA Sequencing

纳米孔基因组 DNA 测序的优化

• 批准号: 8901265
• 负责人: MARK A AKESON
• 金额: $ 72.9万
• 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/8901265
• 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; Health; 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; sensor; single molecule

DESCRIPTION (provided by applicant): 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.

描述（由申请人提供）：该提案涉及基因组 DNA 片段单分子测序的酶、孔和计算方法的优化。它基于我们在 UCSC 团队实施的经过验证的纳米孔设备。该装置由一个传感器组成，当持续酶马达推进DNA链时，该传感器接触并检查捕获的DNA链内的每个核苷酸。尽管纳米孔测序的总体目标是对很长的链进行从头读取，但这里我们还将重点关注对基础研究（小鼠、大肠杆菌和拟南芥）和医疗保健（人类）中重要的生物体进行 DNA 重测序。我们关注从头测序和重测序有两个原因：1）生物 DNA 的纳米孔测序尚未公开记录。因此，需要对参考标准进行纳米孔重测序以获得社区认可，更重要的是，揭示影响从头测序准确性的技术弱点； 2)本应用中的纳米孔重测序意味着直接读取基因组DNA，因此将包括表观遗传修饰。这将是对研究界的直接、重要的贡献。