公开(公告)号：US20150344944A1

公开(公告)日：2015-12-03

申请号：US14653656

申请日：2013-12-19

申请人： OXFORD NANOPORE TECHNOLOGIES LIMITED

发明人： Stuart William Reid ,  Gavin Harper

IPC分类号： C12Q1/68

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q2525/161 ,  C12Q2525/197 ,  C12Q2565/631

摘要： A target polynucleotide is expanded. In respect of each nucleotide in the target polynucleotide, the target polynucleotide comprises clock nucleotides and at least one signal nucleotide in a predetermined order. The clock nucleotides have a predetermined sequence common to each nucleotide in the target polynucleotide. The at least one signal nucleotide is characteristic of the identity of the respective nucleotide in the target polynucleotide. During translocation of the expanded polynucleotide through a nanopore, electrical measurements dependent on the polynucleotide within the pore are made, to derive an analysis signal. Clock signals derived from the clock nucleotides are identified. Relative to the positions of the identified clock signals, nucleotide signals derived from the least one signal nucleotide are derived to analyse the target polynucleotide. The predetermined sequence of the clock nucleotides comprises a restriction site for a restriction enzyme and at least one further nucleotide that extends the predetermined sequence.

摘要翻译： 靶多核苷酸被扩增。 关于靶多核苷酸中的每个核苷酸，靶多核苷酸以预定顺序包括时钟核苷酸和至少一个信号核苷酸。 时钟核苷酸具有靶多核苷酸中每个核苷酸共有的预定序列。 至少一个信号核苷酸是目标多核苷酸中相应核苷酸的特征。 在扩增的多核苷酸在通过纳米孔的移位期间，进行取决于孔内的多核苷酸的电测量，以得到分析信号。 识别从时钟核苷酸得到的时钟信号。 相对于识别的时钟信号的位置，衍生自至少一个信号核苷酸的核苷酸信号被导出以分析靶多核苷酸。 时钟核苷酸的预定序列包​​含限制酶的限制性位点和延伸预定序列的至少一个其它核苷酸。

公开(公告)号：US20190203286A1

公开(公告)日：2019-07-04

申请号：US16162848

申请日：2018-10-17

申请人： Oxford Nanopore Technologies Limited

发明人： Stuart William Reid ,  Gavin Harper

IPC分类号： C12Q1/6869 ,  C12Q1/6806

CPC分类号： C12Q1/6869 ,  C12Q1/6806 ,  C12Q2525/161 ,  C12Q2525/197 ,  C12Q2565/631

摘要： A target polynucleotide is expanded. In respect of each nucleotide in the target polynucleotide, the target polynucleotide comprises clock nucleotides and at least one signal nucleotide in a predetermined order. The clock nucleotides have a predetermined sequence common to each nucleotide in the target polynucleotide. The at least one signal nucleotide is characteristic of the identity of the respective nucleotide in the target polynucleotide. During translocation of the expanded polynucleotide through a nanopore, electrical measurements dependent on the polynucleotide within the pore are made, to derive an analysis signal. Clock signals derived from the clock nucleotides are identified. Relative to the positions of the identified clock signals, nucleotide signals derived from the least one signal nucleotide are derived to analyse the target polynucleotide. The predetermined sequence of the clock nucleotides comprises a restriction site for a restriction enzyme and at least one further nucleotide that extends the predetermined sequence.

公开(公告)号：US20160162634A1

公开(公告)日：2016-06-09

申请号：US14346549

申请日：2012-09-21

申请人： OXFORD NANOPORE TECHNOLOGIES LIMITED

发明人： Stuart William Reid ,  Gavin Harper ,  Clive Gavin Brown ,  James Anthony Clarke ,  Andrew John Heron

IPC分类号： G06F19/22 ,  G01N33/483 ,  G06F17/18

CPC分类号： G01N33/48721 ,  B82Y15/00 ,  C12Q1/6869 ,  G01N27/44791 ,  G01N33/483 ,  G06F17/18 ,  G06N7/005 ,  G16B30/00 ,  C12Q2537/165 ,  C12Q2565/631

摘要： A sequence of polymer units in a polymer (3), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore (1), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units (4). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units. In a further embodiment, different voltages are applied across the nanopore during translocation in order to improve the resolution of polymer units.

摘要翻译： 聚合物（3）中的聚合物单元序列，例如 DNA，从与聚合物相关的至少一系列测量估计，例如。 作为通过纳米孔（1）的易位的函数的离子电流，其中每个测量的值取决于作为k个聚合物单元（4）的组的k-mer。 提供概率模型，特别是隐马尔可夫模型（HMM），包括一组可能的k-mers：转换权重，表示从原始k-mers到目的地k-mers的转换机会; 和每个k-mer的发射权重，其表示观察该k-mer的给定值的测量值的机会。 使用分析技术分析一系列测量结果，例如。 维特比解码，其是指模型并且基于通过由聚合物单元的序列产生的一系列测量的模型预测的可能性估计聚合物中的聚合物单元的至少一个估计序列。 在另一个实施方案中，在易位期间跨纳米孔施加不同的电压，以改善聚合物单元的分辨率。

公开(公告)号：US11085077B2

公开(公告)日：2021-08-10

申请号：US16162848

申请日：2018-10-17

申请人： Oxford Nanopore Technologies Limited

发明人： Stuart William Reid ,  Gavin Harper

IPC分类号： C12Q1/68 ,  C12Q1/6869 ,  C12Q1/6806

摘要： A target polynucleotide is expanded. In respect of each nucleotide in the target polynucleotide, the target polynucleotide comprises clock nucleotides and at least one signal nucleotide in a predetermined order. The clock nucleotides have a predetermined sequence common to each nucleotide in the target polynucleotide. The at least one signal nucleotide is characteristic of the identity of the respective nucleotide in the target polynucleotide. During translocation of the expanded polynucleotide through a nanopore, electrical measurements dependent on the polynucleotide within the pore are made, to derive an analysis signal. Clock signals derived from the clock nucleotides are identified. Relative to the positions of the identified clock signals, nucleotide signals derived from the least one signal nucleotide are derived to analyse the target polynucleotide. The predetermined sequence of the clock nucleotides comprises a restriction site for a restriction enzyme and at least one further nucleotide that extends the predetermined sequence.

公开(公告)号：US20150057948A1

公开(公告)日：2015-02-26

申请号：US14379242

申请日：2013-02-18

申请人： OXFORD NANOPORE TECHNOLOGIES LIMITED

发明人： Stuart Reid ,  James Anthony Clarke ,  James White ,  Gavin Harper

IPC分类号： G01N33/487 ,  G01N33/68 ,  G01N27/02

CPC分类号： G01N33/48792 ,  B82Y15/00 ,  C12Q1/6858 ,  C12Q1/6869 ,  G01N27/02 ,  G01N33/48721 ,  G01N33/6803 ,  G01N33/6875 ,  G16B30/00 ,  C12Q2537/165 ,  C12Q2565/631

摘要： A time-ordered series of measurements of a polymer made during translocation of the polymer through a nanopore are analysed. The measurements are dependent on the identity of k-mers in the nanopore, a k-mer being k polymer units of the polymer, where k is a positive integer. The method involves deriving, from the series of measurements, a feature vector of time-ordered features representing characteristics of the measurements; and determining similarity between the derived feature vector and at least one other feature vector.

摘要翻译： 分析了在聚合物通过纳米孔的位移期间制备的聚合物的时间有序的一系列测量。 测量取决于纳米孔中的k-mers的同一性，k-mer是聚合物的聚合物单元，其中k是正整数。 该方法包括从一系列测量中导出表示测量特征的时间有序特征的特征向量; 以及确定所导出的特征向量与至少一个其他特征向量之间的相似度。