公开(公告)号：US12043648B2

公开(公告)日：2024-07-23

申请号：US17934054

申请日：2022-09-21

申请人： Roche Sequencing Solutions, Inc.

发明人： Michael Dorwart ,  Daniel Korenblum

IPC分类号： C07K14/31 ,  C12Q1/6869

CPC分类号： C07K14/31 ,  C12Q1/6869 ,  C12Q1/6869 ,  C12Q2565/631

摘要： Described herein are variants of alpha-hemolysin having at least one mutation selected from T12R, T12K, N17R, N17K or combinations of T12 and N17 mutations. The variants in some embodiments may further comprise H144A. The α-hemolysin variants have a decreased time to thread.

公开(公告)号：US11965183B2

公开(公告)日：2024-04-23

申请号：US17500831

申请日：2021-10-13

申请人： Oxford Nanopore Technologies PLC

发明人： Andrew John Heron ,  Rebecca Victoria Bowen ,  Mark Bruce ,  Lakmal Jayasinghe ,  Joseph Hargreaves Lloyd ,  Szabolcs Soeroes ,  Elizabeth Jayne Wallace ,  Christopher Peter Youd

IPC分类号： C12N9/14 ,  C12Q1/68 ,  C12Q1/6869

CPC分类号： C12N9/14 ,  C12Q1/68 ,  C12Q1/6869 ,  C12Y306/04012 ,  C12Q1/6869 ,  C12Q2521/513 ,  C12Q2565/631

摘要： The invention relates to modified Dda helicases which can be used to control the movement of polynucleotides and are particularly useful for sequencing polynucleotides.

公开(公告)号：US11921103B2

公开(公告)日：2024-03-05

申请号：US16449272

申请日：2019-06-21

申请人： Oxford Nanopore Technologies PLC

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

IPC分类号： G01N33/487 ,  B82Y15/00 ,  C12Q1/6869 ,  G01N27/447 ,  G01N33/483 ,  G06F17/18 ,  G06N7/01 ,  G16B30/00 ,  G16B30/10

CPC分类号： G01N33/48721 ,  C12Q1/6869 ,  G01N27/44791 ,  G01N33/483 ,  G06F17/18 ,  G06N7/01 ,  G16B30/00 ,  G16B30/10 ,  B82Y15/00 ,  C12Q1/6869 ,  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.

公开(公告)号：US11920184B2

公开(公告)日：2024-03-05

申请号：US17071778

申请日：2020-10-15

申请人： Roche Sequencing Solutions, Inc.

发明人： Mark Stamatios Kokoris ,  Robert N. McRuer

IPC分类号： C12Q1/6806 ,  C12Q1/6869 ,  G01N33/543

CPC分类号： C12Q1/6806 ,  C12Q1/6869 ,  G01N33/54373 ,  C12Q1/6869 ,  C12Q2563/131 ,  C12Q2565/531 ,  C12Q2565/631

摘要： Methods and related products are disclosed that improve the probability of interaction between a target molecule and a nanopore by capturing the target molecule on a surface comprising the nanopore. The captured target molecule, the nanopore, or both, are able to move relative to each other along the surface. When the leader of the target molecule is in proximity with the nanopore, interaction of the target portion of the target molecule with the nanopore occurs, thereby permitting sensing of the target portion. Confining the target molecule and nanopore in this manner leads to significantly enhanced interaction with the nanopore.

公开(公告)号：US11913941B2

公开(公告)日：2024-02-27

申请号：US16652381

申请日：2018-10-02

申请人： The Regents of the University of California ,  Brigham Young University

发明人： Holger Schmidt ,  Aaron Roe Hawkins ,  David W. Deamer

IPC分类号： G01N33/53 ,  B01L3/00 ,  C12Q1/70 ,  G01N33/487 ,  C12Q1/6825 ,  G01N35/00 ,  G01N33/543

CPC分类号： G01N33/5302 ,  B01L3/50273 ,  C12Q1/6825 ,  C12Q1/70 ,  G01N33/48721 ,  G01N33/54333 ,  G01N35/00 ,  B01L2200/0668 ,  G01N2035/00247 ,  C12Q1/6825 ,  C12Q2565/631 ,  C12Q2565/629 ,  C12Q2565/519 ,  C12Q1/70 ,  C12Q2565/631 ,  C12Q2565/629 ,  C12Q2565/519

摘要： A disclosed system uses modulations of ionic current across a nanopore in a membrane to detect target molecules passing through the nanopore. This principle has been applied mainly to nucleic acid sequencing, but can also be used to detect other molecular targets such as proteins and small molecules. In addition, the system delivers target molecules to a nanopore to provide label-free single molecule analysis using a chip-based system. Target molecules are concentrated on microscale carrier beads, and the beads are delivered and optically trapped in an area within the capture radius of the nanopore. The target molecules are released from the beads and detected using nanopore current modulation. In addition, the disclosed system combines sample preparation (e.g. purification, extraction, and pre-concentration) with nanopore-based readout on a microfluidic chip. Finally, target molecules can be specifically bound to carrier beads and particles are positioned within the capture volume of a nanopore using a chip-based microfluidic platform proven to handle specific detection of molecular targets from milliliters of raw sample.

公开(公告)号：US11892444B2

公开(公告)日：2024-02-06

申请号：US17076508

申请日：2020-10-21

申请人： Roche Sequencing Solutions, Inc.

发明人： Morgan Mager ,  John Mannion

IPC分类号： C12Q1/6869 ,  G01N33/487 ,  C12Q1/6874 ,  G01N27/447 ,  G16B20/00 ,  G01N27/327 ,  G16B30/00 ,  B82Y5/00 ,  B82Y15/00 ,  G01N27/416

CPC分类号： G01N33/48721 ,  C12Q1/6869 ,  C12Q1/6874 ,  G01N27/3278 ,  G01N27/44791 ,  G16B20/00 ,  G16B30/00 ,  B82Y5/00 ,  B82Y15/00 ,  C12Q2563/116 ,  C12Q2565/631 ,  G01N27/4163 ,  C12Q1/6869 ,  C12Q2537/165 ,  C12Q2565/631

摘要： Improved multi-cell nanopore-based sequencing chips and methods can employ formation, characterization, calibration, and/or normalization techniques. For example, various methods may include one or more steps of performing physical checks of cell circuitry, forming and characterizing a lipid layer on the cells, performing a zero point calibration of the cells, forming and characterizing nanopores on the lipid layers of each cell, performing a sequencing operation to accumulate sequencing signals from the cells, normalizing those sequencing signals, and determining bases based on the normalized sequencing signals.

公开(公告)号：US11860152B2

公开(公告)日：2024-01-02

申请号：US16923193

申请日：2020-07-08

申请人： Taiwan Semiconductor Manufacturing Company Limited

发明人： Kun-Lung Chen ,  Tung-Tsun Chen ,  Cheng-Hsiang Hsieh ,  Yu-Jie Huang ,  Jui-Cheng Huang

IPC分类号： G01N33/487 ,  C12Q1/6874 ,  G01N27/414 ,  C12Q1/6869

CPC分类号： G01N33/48721 ,  C12Q1/6874 ,  G01N27/4145 ,  G01N27/4146 ,  G01N27/4148 ,  C12Q1/6869 ,  C12Q1/6869 ,  C12Q2565/607 ,  C12Q2565/629 ,  C12Q2565/631

摘要： A semiconductor device includes a circuit layer and a nanopore layer. The nanopore layer is formed on the circuit layer and is formed with a pore therethrough. The circuit layer includes a circuit unit configured to drive a biomolecule through the pore and to detect a current associated with a resistance of the nanopore layer, whereby a characteristic of the biomolecule can be determined using the currents detected by the circuit unit.

公开(公告)号：US11788132B2

公开(公告)日：2023-10-17

申请号：US17683890

申请日：2022-03-01

申请人： Roche Sequencing Solutions, Inc.

发明人： John Mannion ,  Morgan Mager

IPC分类号： C12Q1/6869 ,  G16B30/00 ,  G01N27/447 ,  G16B40/00 ,  G16B45/00 ,  G16B40/20 ,  G01N33/487

CPC分类号： C12Q1/6869 ,  G01N27/44791 ,  G01N33/48721 ,  G16B40/00 ,  G16B40/20 ,  G16B45/00 ,  C12Q1/6869 ,  C12Q2535/122 ,  C12Q2537/165 ,  C12Q2565/631

摘要： Techniques for measuring sequences of nucleic acids are provided. Time-based measurements (e.g., forming a histogram) particular to a given sequencing cell can be used to generate a tailored model. The model can include probability functions, each corresponding to different states (e.g., different states of a nanopore). Such probability functions can be fit to a histogram of measurements obtained for that cell. The probability functions can be updated over a sequencing run of the nucleic acid so that drifts in physical properties of the sequencing cell can be compensated. A hidden Markov model can use such probability functions as emission probabilities for determining the most likely nucleotide states over time. For sequencing cells involving a polymerase, a 2-state classification between bound and unbound states of the polymerase can be performed. The bound regions can be further analyzed by a second classifier to distinguish between states corresponding to different bound nucleotides.

公开(公告)号：US11754549B2

公开(公告)日：2023-09-12

申请号：US17839085

申请日：2022-06-13

申请人： Roche Sequencing Solutions, Inc.

发明人： Steven Henck

IPC分类号： G01N33/487 ,  C12Q1/6869 ,  G01N27/447

CPC分类号： G01N33/48721 ,  C12Q1/6869 ,  G01N27/44791 ,  C12Q1/6869 ,  C12Q2565/631

摘要： Devices for sequencing linear biomolecules (e.g., DNA, RNA, polypeptides, proteins, and the like) using quantum tunneling effects, and methods of making and using such devices, are provided. A nanofabricated device can include a small gap formed by depositing a thin film between two electrodes, and subsequently removing the film using an etching process. The width of the resulting gap can correspond with the size of a linear biomolecule such that when a part of the biomolecule (e.g., a nucleobase or amino acid) is present in the gap, a change in tunneling current, voltage, or impedance can be measured and the part of the biomolecule identified. The gap dimensions can be precisely controlled at the atomic-scale by, for example, atomic layer deposition (ALD) of the sacrificial film. The device can be made using existing integrated circuit fabrication equipment and facilities, and multiple devices can be formed on a single chip.

公开(公告)号：US11725236B2

公开(公告)日：2023-08-15

申请号：US17242098

申请日：2021-04-27

申请人： Roche Sequencing Solutions, Inc.

发明人： Randall W. Davis ,  Edward Shian Liu ,  Eric Takeshi Harada ,  Anne Aguirre ,  Andrew Trans ,  James Pollard ,  Cynthia Cech

IPC分类号： C12Q1/6869 ,  G01N33/487 ,  C12M1/34 ,  G01N27/327 ,  G01N27/447

CPC分类号： C12Q1/6869 ,  C12M1/34 ,  G01N27/3277 ,  G01N27/3278 ,  G01N27/44791 ,  G01N33/48721 ,  C12Q1/6869 ,  C12Q2565/607 ,  C12Q2565/631

摘要： This disclosure provides a biochip comprising a plurality of wells. The biochip includes a membrane that is disposed in or adjacent to an individual well of the plurality of wells. The membrane comprises a nanopore, and the individual well comprises an electrode that detects a signal upon ionic flow through the pore in response to a species passing through or adjacent to the nanopore. The electrode can be a non-sacrificial electrode. A lipid bilayer can be formed over the plurality of wells using a bubble.