Single Molecule Sequencing by Nanopore induced Photon Emission (SM-SNIPE)

描述（由申请人提供）：我们的小组已经为开发一种独特的基于纳米孔的方法奠定了基础，该方法用于通过纳米孔诱导的光子发射（SNIPE）进行DNA测序，该方法利用光学检测而不是更普遍的电学检测。 我们的方法是上级其他纳米孔的方法，因为读出不涉及酶，并行化是直接的，和读出是非破坏性的。 在这项资助中，我们提出了三个不同的目标（平行发展），当它们结合在一起时，将使DNA测序在速度（>2 10^6碱基/秒）和极低的成本方面达到前所未有的规模。 我们的首要目标是大幅提高SNIPE的吞吐量、速度和准确性。 为了实现这一目标，我们将集中精力通过纳米孔阵列（高达100 x100）实现系统的并行化、将读数从2种颜色转换为4种颜色，并增加读数的S/B。 我们的第二个目标是开发和优化我们专有的DNA转化方法，环状DNA转化（CDC）。 我们计划通过使用商用台式系统实现CDC的自动化和优化来实现这一目标。 CDC优化后，我们计划开发一种能够转换整个人类基因组的微流体设备。 我们的第三个目标是开发数据分析算法，用于碱基识别、共识构建、序列组装和防错。 在完成这三个目标的过程中，我们将开发一个全新的、具有成本效益的DNA测序平台，能够实现长读长、高速和高准确性。 预计这将对基础和应用生物医学研究以及个性化医疗保健产生广泛影响。 公共卫生相关性：超低成本测序对生物医学研究、比较基因组学和癌症生物学的非凡广泛影响正在推动多种DNA测序方法的发展。 我们的小组一直在开发一种纳米孔DNA测序方法，该方法利用来自数百个纳米孔的光学检测，因为分子被拉过孔。 这项提议将使我们能够开发这种方法来解决1,000美元的基因组挑战。

DESCRIPTION (provided by applicant): Our group has laid the groundwork in developing a unique, nanopore based method for DNA sequencing by nanopore induced photon emission (SNIPE), which utilizes optical detection rather than the more ubiquitous electrical detection. Our approach is superior to other nanopore approaches as the readout does not involve enzymes, parallelization is straightforward, and the readout is non-destructive. In this grant we propose three distinct aims (developed in parallel), which when brought together, will enable DNA sequencing at an unprecedented scale in terms of speed (>2 10^6 bases/s,) and extremely low cost. Our first aim is to dramatically increase the throughput, speed and accuracy of SNIPE. In order to achieve this, we will concentrate our efforts on parallelization of the system through arrays of nanopores (up to 100x100), transformation of the readout from 2 to 4 colors, and increasing the S/B of the readout. Our second Aim is to develop and optimize our proprietary DNA conversion approach, Circular DNA conversion (CDC). We plan on achieving this first though automation and optimization of CDC using a commercially available benchtop system. Post CDC optimization, we plan on developing a microfluidic device capable of converting an entire human genome. Our third Aim is the development of data analysis algorithms needed for base calling, consensus building, sequence assembly, and error proofing. In completing these three aims we will have achieved in developing a radically new, cost-effective DNA sequencing platform, capable of long read lengths, high speed, and high accuracy. This is expected to have a wide-ranging impact on both basic and applied biomedical research and personalized healthcare. PUBLIC HEALTH RELEVANCE: The extraordinary broad impact of ultra-low cost sequencing on biomedical research, comparative genomics and cancer biology, is driving the development of a plurality of DNA sequencing methods. Our group has been developing a nanopore DNA sequencing method that utilizes optical detection from hundreds of nanopores, as the molecules are pulled electrophoretically driven through the pores. This proposal will allow us to develop this method to address the $1,000 genome challenge.