Patents by Inventor Stuart William Reid
Stuart William Reid has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
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Patent number: 11959906Abstract: 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 bring 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.Type: GrantFiled: January 11, 2019Date of Patent: April 16, 2024Assignee: Oxford Nanopore Technologies PLCInventors: Stuart William Reid, James Anthony Clarke, James White, Gavin Harper
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Patent number: 11921103Abstract: 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.Type: GrantFiled: June 21, 2019Date of Patent: March 5, 2024Assignee: Oxford Nanopore Technologies PLCInventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, James Anthony Clarke, Andrew John Heron
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Patent number: 11898984Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: GrantFiled: November 22, 2019Date of Patent: February 13, 2024Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera
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Publication number: 20230167494Abstract: A biochemical analysis system analyses polymers by taking measurements of a polymer from a sensor element comprising a nanopore during translocation of the polymer through the nanopore. When a polymer has partially translocated, the series of measurements is analysed using reference data derived from a reference sequence to provide a measure of similarity. Responsive to the measure of similarity, the sensor element may be selectively operated to eject the polymer and thereby make the nanopore available to receive a further polymer. Where the biochemical analysis system comprises an array of sensor elements and is takes measurements from sensor elements selected in a multiplexed manner, responsive to the measure of similarity, the biochemical analysis system ceases taking measurements from the currently selected sensor element and to starts taking measurements from a newly selected sensor element.Type: ApplicationFiled: June 28, 2022Publication date: June 1, 2023Applicant: Oxford Nanopore Technologies PLCInventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, Daniel John Turner, Andrew John Heron, Christopher James Wright
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Patent number: 11401549Abstract: A biochemical analysis system analyses polymers by taking measurements of a polymer from a sensor element comprising a nanopore during translocation of the polymer through the nanopore. When a polymer has partially translocated, the series of measurements is analysed using reference data derived from a reference sequence to provide a measure of similarity. Responsive to the measure of similarity, the sensor element may be selectively operated to eject the polymer and thereby make the nanopore available to receive a further polymer. Where the biochemical analysis system comprises an array of sensor elements and is takes measurements from sensor elements selected in a multiplexed manner, responsive to the measure of similarity, the biochemical analysis system ceases taking measurements from the currently selected sensor element and to starts taking measurements from a newly selected sensor element.Type: GrantFiled: May 12, 2020Date of Patent: August 2, 2022Assignee: Oxford Nanopore Technologies PLCInventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, Daniel John Turner, Andrew John Heron, Christopher James Wright
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Publication number: 20220213541Abstract: The invention resides in a method of determining a sequence of a target polymer, or part thereof, comprising polymer units comprising canonical and non-canonical polymer units. The method comprises taking a series of measurements of a signal relating to the target polymer wherein a measurement of the signal is dependent upon a plurality of polymer units, and wherein the polymer units of the target polymer modulate the signal, and wherein a non-canonical polymer unit modulates the signal differently from a corresponding canonical polymer unit. The series of measurements are analysed using a machine learning technique that attributes a measurement of a non-canonical polymer unit to being a measurement of a respective corresponding canonical polymer unit. The sequence of the target polymer, or part thereof, is determined from the analysed series of measurements. A non-canonical polymer unit identified from the analysis can be additionally or alternatively determined.Type: ApplicationFiled: September 4, 2019Publication date: July 7, 2022Applicant: Oxford Nanopore Technologies LimitedInventors: Clive Gavin Brown, Timothy Lee Massingham, Stuart William Reid
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Publication number: 20220064724Abstract: 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.Type: ApplicationFiled: July 7, 2021Publication date: March 3, 2022Applicant: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper
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Publication number: 20220059187Abstract: Provided herein, in some embodiments, are methods of determining whether a target nucleic acid comprises a particular barcode sequence.Type: ApplicationFiled: August 6, 2021Publication date: February 24, 2022Applicant: Oxford Nanopore Technologies LimitedInventors: Stuart William Reid, Eoghan Donal Harrington
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Patent number: 11085077Abstract: 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.Type: GrantFiled: October 17, 2018Date of Patent: August 10, 2021Assignee: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper
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Publication number: 20210079460Abstract: A biochemical analysis system analyses polymers by taking measurements of a polymer from a sensor element comprising a nanopore during translocation of the polymer through the nanopore. When a polymer has partially translocated, the series of measurements is analysed using reference data derived from a reference sequence to provide a measure of similarity. Responsive to the measure of similarity, the sensor element may be selectively operated to eject the polymer and thereby make the nanopore available to receive a further polymer. Where the biochemical analysis system comprises an array of sensor elements and is takes measurements from sensor elements selected in a multiplexed manner, responsive to the measure of similarity, the biochemical analysis system ceases taking measurements from the currently selected sensor element and to starts taking measurements from a newly selected sensor element.Type: ApplicationFiled: May 12, 2020Publication date: March 18, 2021Applicant: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, Daniel John Turner, Andrew John Heron, Christopher James Wright
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Patent number: 10689697Abstract: Analysis Of A Polymer A biochemical analysis system analyses polymers by taking measurements of a polymer from a sensor element comprising a nanopore during translocation of the polymer through the nanopore. When a polymer has partially translocated, the series of measurements is analysed using reference data derived from a reference sequence to provide a measure of similarity. Responsive to the measure of similarity, the sensor element may be selectively operated to eject the polymer and thereby make the nanopore available to receive a further polymer. Where the biochemical analysis system comprises an array of sensor elements and is takes measurements from sensor elements selected in a multiplexed manner, responsive to the measure of similarity, the biochemical analysis system ceases taking measurements from the currently selected sensor element and to starts taking measurements from a newly selected sensor element.Type: GrantFiled: October 16, 2015Date of Patent: June 23, 2020Assignee: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, Daniel John Turner, Andrew John Heron, Christopher James Wright
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Publication number: 20200080966Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: ApplicationFiled: November 22, 2019Publication date: March 12, 2020Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera
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Publication number: 20190310242Abstract: 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.Type: ApplicationFiled: June 21, 2019Publication date: October 10, 2019Applicant: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper, Clive Brown, James Anthony Clarke, Andrew John Heron
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Patent number: 10416117Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: GrantFiled: February 16, 2017Date of Patent: September 17, 2019Assignee: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera
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Publication number: 20190203286Abstract: 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.Type: ApplicationFiled: October 17, 2018Publication date: July 4, 2019Applicant: Oxford Nanopore Technologies LimitedInventors: Stuart William Reid, Gavin Harper
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Publication number: 20190187094Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: ApplicationFiled: March 6, 2019Publication date: June 20, 2019Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera
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Publication number: 20190154655Abstract: 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 bring 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.Type: ApplicationFiled: January 11, 2019Publication date: May 23, 2019Applicant: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, James Anthony Clarke, James White, Gavin Harper
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Patent number: 10131943Abstract: 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 analyze the target polynucleotide.Type: GrantFiled: December 19, 2013Date of Patent: November 20, 2018Assignee: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Gavin Harper
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Publication number: 20180321188Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: ApplicationFiled: February 26, 2018Publication date: November 8, 2018Applicant: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera
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Patent number: 9927398Abstract: To form a layer separating two volumes of aqueous solution, there is used an apparatus comprising elements defining a chamber, the elements including a body of non-conductive material having formed therein at least one recess opening into the chamber, the recess containing an electrode. A pre-treatment coating of a hydrophobic fluid is applied to the body across the recess. Aqueous solution, having amphiphilic molecules added thereto, is flowed across the body to cover the recess so that aqueous solution is introduced into the recess from the chamber and a layer of the amphiphilic molecules forms across the recess separating a volume of aqueous solution introduced into the recess from the remaining volume of aqueous solution.Type: GrantFiled: June 30, 2015Date of Patent: March 27, 2018Assignee: Oxford Nanopore Technologies Ltd.Inventors: Stuart William Reid, Terence Alan Reid, James Anthony Clarke, Steven Paul White, Gurdial Singh Sanghera