Hybridization-Assisted Nanopore Sequencing

描述（由申请人提供）：开发能够实现极廉价、高速测序的技术的基本原理已经得到充分确立。其中最主要的是个性化医疗的实现。目前正在开发的几种技术有望显着降低人类基因组测序的成本。然而，目前还不清楚这些技术中的任何一种是否能够彻底地做到这一点，从而使全基因组测序成为一种常规的临床工具。此外，在这个成本参数上最有前途的那些技术看起来好像它们将面临关于性能特征（例如读取长度）的困难。基于纳米孔的测序是一种有望廉价、快速并提供长读取长度的技术。然而，迄今为止，纳米孔测序面临着许多技术挑战。杂交辅助纳米孔测序（HANS）方法克服了这些障碍。HANS利用探针文库来检测靶DNA中的杂交测序（SBH）。然而，HANS与SBH的不同之处在于，还提取了位置信息，从而完全规避了SBH的限制，并使基因组长度测序可行。HANS平台将能够以低于1000美元的价格对人类基因组进行测序。此外，它承诺这样做迅速和准确。我们的具体目标如下：1）合成和测试寡核苷酸标签以增强纳米孔检测寡核苷酸在靶DNA上的存在和确定寡核苷酸在靶DNA上的位置的能力。2)确定序列重建的最佳算法方法，并估计测序平台性能特征的值。

DESCRIPTION (provided by applicant): The rationales for the development of technology that will enable extremely cheap, high speed sequencing are well established. Chief among these is the enablement of personalized medicine. There are currently in development several technologies that promise to markedly decrease the cost of sequencing a human genome. It is unclear, however, that any of these will be able to do so drastically enough to allow whole genome sequencing to become a routine clinical tool. Additionally, those technologies which are most promising on this cost parameter look as if they will face difficulties with respect to performance characteristics such as read length. One technology that promises to be cheap and fast and to provide long read lengths is nanopore-based sequencing. To date, however, nanopore sequencing has faced a number of technical challenges. The method of Hybridization-Assisted Nanopore Sequencing (HANS) overcomes these hurdles. HANS utilizes libraries of probes to detect subsequences in the target DNA as in sequencing by hybridization (SBH). HANS differs from SBH, however, in that positional information is also extracted thus completely circumventing, the limitations of SBH and making genome length sequencing feasible. The HANS platform will be capable of sequencing a human genome for substantially less than $1000. Additionally, it promises to do so quickly and accurately. Our specific aims are as follows: 1) Synthesize and test oligonucleotide tags for their ability to enhance the nanopore's capacity to detect the presence and determine the positions of the oligonucleotides on the target DNA. 2) Determine the optimal algorithmic approach for sequence reconstruction and estimate values for the performance characteristics of the sequencing platform.