Optimization of Nanopore Genomic DNA Sequencing

该建议涉及酶，孔和单分子计算方法的优化 基因组DNA片段的测序。它是基于一个经过验证的纳米孔设备实现了我们的 在UCSC。该装置由一个传感器组成，该传感器接触并检查内部的每个核苷酸。 一条被捕获的DNA链作为一个前进的酶马达推进该链。虽然总体目标是 纳米孔测序是在非常长的链上从头读取，在这里我们还将关注纳米孔的重测序。 来自基础研究中重要生物体的DNA（小鼠，E. coli & Arabidopsis）和医疗保健 （人类）。我们专注于从头测序和重测序有两个原因：1）纳米孔测序 生物DNA还没有被公开记录。因此，参考的纳米孔重测序 标准是社区接受所必需的，而且，重要的是，要揭示 影响从头测序准确性技术; 2）该应用中的纳米孔重测序 术语“表观遗传修饰”是指直接阅读基因组DNA，因此将包括表观遗传修饰。这将是 这是对研究界的一个直接而重要的贡献。

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.