Patents by Inventor Gavin Harper
Gavin Harper 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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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: 20220127669Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: ApplicationFiled: October 8, 2021Publication date: April 28, 2022Applicant: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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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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Patent number: 11261487Abstract: The claimed invention relates to a method of processing a polynucleotide, by obtaining a sense polynucleotide strand comprising a homopolymeric region that is longer that the reading section of a nanopore; synthesizing an antisense polynucleotide strand under conditions in which a nucleotide analog is incorporated at random in a reverse complement of the homopolymer region, such that the length of the homopolymer region in the antisense polynucleotide strand is shorter than the reading section of the nanopore; and moving the antisense polynucleotide strand through the nanopore such that a proportion of the antisense polynucleotide strand interacts with the nanopore.Type: GrantFiled: February 5, 2020Date of Patent: March 1, 2022Assignee: Oxford Nanopore Technologies PLCInventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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Patent number: 11168363Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: GrantFiled: May 31, 2019Date of Patent: November 9, 2021Assignee: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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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: 10851409Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: GrantFiled: June 10, 2016Date of Patent: December 1, 2020Assignee: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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Publication number: 20200239950Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: ApplicationFiled: February 5, 2020Publication date: July 30, 2020Applicant: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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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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Patent number: 10597713Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: GrantFiled: April 3, 2018Date of Patent: March 24, 2020Assignee: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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Publication number: 20200024655Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: ApplicationFiled: May 31, 2019Publication date: January 23, 2020Applicant: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White
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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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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: 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: 20180291441Abstract: The invention relates to a new method of sequencing a double stranded target polynucleotide. The two strands of the double stranded target polynucleotide are linked by a bridging moiety. The two strands of the target polynucleotide are separated using a polynucleotide binding protein and the target polynucleotide is sequenced using a transmembrane pore.Type: ApplicationFiled: April 3, 2018Publication date: October 11, 2018Applicant: Oxford Nanopore Technologies Ltd.Inventors: Clive Gavin Brown, James Anthony Clarke, Graham Hall, Gavin Harper, Andrew John Heron, James White