Patents by Inventor Morgan Mager
Morgan Mager 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: 11892444Abstract: 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.Type: GrantFiled: October 21, 2020Date of Patent: February 6, 2024Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Patent number: 11788132Abstract: 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.Type: GrantFiled: March 1, 2022Date of Patent: October 17, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Patent number: 11740227Abstract: A nanopore cell includes a conductive layer and a working electrode disposed above the conductive layer and at the bottom of a well into which an electrolyte may be contained, such that at least a portion of a top base surface area of the working electrode is exposed to the electrolyte. The nanopore cell further includes a first insulating wall disposed above the working electrode and surrounding a lower section of a well, and a second insulating wall disposed above the first insulating wall and surrounding an upper section of the well, forming an overhang above the lower section of the well. The upper section of the well includes an opening that a membrane may span across, and wherein a base surface area of the opening is smaller than the at least a portion of the top base surface area of the working electrode that is exposed to the electrolyte.Type: GrantFiled: May 27, 2022Date of Patent: August 29, 2023Assignee: Roche Sequencing Solutions, Inc.Inventors: John Foster, Morgan Mager
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Publication number: 20220291193Abstract: A nanopore cell includes a conductive layer and a working electrode disposed above the conductive layer and at the bottom of a well into which an electrolyte may be contained, such that at least a portion of a top base surface area of the working electrode is exposed to the electrolyte. The nanopore cell further includes a first insulating wall disposed above the working electrode and surrounding a lower section of a well, and a second insulating wall disposed above the first insulating wall and surrounding an upper section of the well, forming an overhang above the lower section of the well. The upper section of the well includes an opening that a membrane may span across, and wherein a base surface area of the opening is smaller than the at least a portion of the top base surface area of the working electrode that is exposed to the electrolyte.Type: ApplicationFiled: May 27, 2022Publication date: September 15, 2022Inventors: John Foster, Morgan Mager
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Publication number: 20220267840Abstract: 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.Type: ApplicationFiled: March 1, 2022Publication date: August 25, 2022Inventors: John MANNION, Morgan MAGER
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Patent number: 11346836Abstract: A nanopore cell includes a conductive layer and a working electrode disposed above the conductive layer and at the bottom of a well into which an electrolyte may be contained, such that at least a portion of a top base surface area of the working electrode is exposed to the electrolyte. The nanopore cell further includes a first insulating wall disposed above the working electrode and surrounding a lower section of a well, and a second insulating wall disposed above the first insulating wall and surrounding an upper section of the well, forming an overhang above the lower section of the well. The upper section of the well includes an opening that a membrane may span across, and wherein a base surface area of the opening is smaller than the at least a portion of the top base surface area of the working electrode that is exposed to the electrolyte.Type: GrantFiled: September 16, 2020Date of Patent: May 31, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: John Foster, Morgan Mager
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Patent number: 11293062Abstract: 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.Type: GrantFiled: April 8, 2020Date of Patent: April 5, 2022Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Publication number: 20210130945Abstract: A nanopore cell is disclosed. The nanopore cell includes an electrolyte well having a bottom base, a surrounding sidewall, and a hydrophobic surface above the surrounding sidewall. The nanopore cell further includes a first layer of electrode material disposed on the bottom base of the electrolyte well. The nanopore cell further includes a second layer of electrode material disposed on the surrounding sidewall of the electrolyte well and electrically connected to the first layer of electrode material. The first layer of electrode material and the second layer of electrode material are configured to jointly provide capacitive coupling when an electrolyte is placed in the electrolyte well.Type: ApplicationFiled: January 13, 2021Publication date: May 6, 2021Inventors: John Foster, Morgan Mager
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Publication number: 20210109082Abstract: 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.Type: ApplicationFiled: October 21, 2020Publication date: April 15, 2021Inventors: Morgan MAGER, John MANNION
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Publication number: 20210072221Abstract: A nanopore cell includes a conductive layer and a working electrode disposed above the conductive layer and at the bottom of a well into which an electrolyte may be contained, such that at least a portion of a top base surface area of the working electrode is exposed to the electrolyte. The nanopore cell further includes a first insulating wall disposed above the working electrode and surrounding a lower section of a well, and a second insulating wall disposed above the first insulating wall and surrounding an upper section of the well, forming an overhang above the lower section of the well. The upper section of the well includes an opening that a membrane may span across, and wherein a base surface area of the opening is smaller than the at least a portion of the top base surface area of the working electrode that is exposed to the electrolyte.Type: ApplicationFiled: September 16, 2020Publication date: March 11, 2021Inventors: John Foster, Morgan Mager
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Patent number: 10920312Abstract: A nanopore cell is disclosed. The nanopore cell includes an electrolyte well having a bottom base, a surrounding sidewall, and a hydrophobic surface above the surrounding sidewall. The nanopore cell further includes a first layer of electrode material disposed on the bottom base of the electrolyte well. The nanopore cell further includes a second layer of electrode material disposed on the surrounding sidewall of the electrolyte well and electrically connected to the first layer of electrode material. The first layer of electrode material and the second layer of electrode material are configured to jointly provide capacitive coupling when an electrolyte is placed in the electrolyte well.Type: GrantFiled: August 31, 2015Date of Patent: February 16, 2021Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Foster
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Patent number: 10816537Abstract: 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.Type: GrantFiled: April 15, 2019Date of Patent: October 27, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Patent number: 10809243Abstract: A nanopore cell includes a conductive layer and a working electrode disposed above the conductive layer and at the bottom of a well into which an electrolyte may be contained, such that at least a portion of a top base surface area of the working electrode is exposed to the electrolyte. The nanopore cell further includes a first insulating wall disposed above the working electrode and surrounding a lower section of a well, and a second insulating wall disposed above the first insulating wall and surrounding an upper section of the well, forming an overhang above the lower section of the well. The upper section of the well includes an opening that a membrane may span across, and wherein a base surface area of the opening is smaller than the at least a portion of the top base surface area of the working electrode that is exposed to the electrolyte.Type: GrantFiled: August 31, 2015Date of Patent: October 20, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: John Foster, Morgan Mager
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Publication number: 20200232026Abstract: 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.Type: ApplicationFiled: April 8, 2020Publication date: July 23, 2020Inventors: John MANNION, Morgan MAGER
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Patent number: 10648027Abstract: 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.Type: GrantFiled: August 4, 2017Date of Patent: May 12, 2020Assignee: Roche Sequencing Solutions, Inc.Inventors: John Mannion, Morgan Mager
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Publication number: 20190242869Abstract: 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.Type: ApplicationFiled: April 15, 2019Publication date: August 8, 2019Inventors: Morgan MAGER, John MANNION
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Patent number: 10317392Abstract: 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.Type: GrantFiled: June 23, 2017Date of Patent: June 11, 2019Assignee: Roche Sequencing Solutions, Inc.Inventors: Morgan Mager, John Mannion
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Publication number: 20180037948Abstract: 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.Type: ApplicationFiled: August 4, 2017Publication date: February 8, 2018Inventors: John MANNION, Morgan MAGER
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Publication number: 20170370903Abstract: 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.Type: ApplicationFiled: June 23, 2017Publication date: December 28, 2017Inventors: Morgan MAGER, John MANNION
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Publication number: 20170058397Abstract: A nanopore cell is disclosed. The nanopore cell includes an electrolyte well having a bottom base, a surrounding sidewall, and a hydrophobic surface above the surrounding sidewall. The nanopore cell further includes a first layer of electrode material disposed on the bottom base of the electrolyte well. The nanopore cell further includes a second layer of electrode material disposed on the surrounding sidewall of the electrolyte well and electrically connected to the first layer of electrode material. The first layer of electrode material and the second layer of electrode material are configured to jointly provide capacitive coupling when an electrolyte is placed in the electrolyte well.Type: ApplicationFiled: August 31, 2015Publication date: March 2, 2017Inventors: Morgan Mager, John Foster