Patents by Inventor Jeffrey G. Mandell

Jeffrey G. Mandell 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).

  • Patent number: 11041196
    Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.
    Type: Grant
    Filed: June 12, 2019
    Date of Patent: June 22, 2021
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 10961576
    Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.
    Type: Grant
    Filed: December 9, 2019
    Date of Patent: March 30, 2021
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
  • Publication number: 20210032695
    Abstract: The present disclosure provides method and systems for improving nanopore-based analyses of polymers. The disclosure provides methods for selectively modifying one or more monomeric subunit(s) of a kind a pre-analyte polymer that results polymer analyte with a modified subunit. The polymer analyte produces a detectable signal in a nanopore-based system. The detectable signal, and/or its deviation from a reference signal, indicates the location of the modified subunit in the polymer analyte and, thus, permits the identification of the subunit at that location in the original pre-analyte polymer.
    Type: Application
    Filed: September 22, 2020
    Publication date: February 4, 2021
    Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20200348257
    Abstract: A kit includes an array of charge sensors attached to a solid-phase substrate , wherein individual charge sensors in the array respectively comprise a channel and a polymerase and are located at different addressable locations on the solid-phase substrate; and a liquid comprising a plurality of different nucleic acids, each of the different nucleic acids including a unique label to be detected by a charge sensor of the array.
    Type: Application
    Filed: March 20, 2020
    Publication date: November 5, 2020
    Inventors: Boyan BOYANOV, Jeffrey G. MANDELL, Jingwei BAI, Kevin L. GUNDERSON, Cheng-Yao CHEN, Michel PERBOST
  • Patent number: 10822652
    Abstract: The present disclosure provides method and systems for improving nanopore-based analysis of polymers. The disclosure provides methods for selectively modifying one or more monomeric subunit(s) of a kind in a re-analyte polymer that results in a polymer analyte with a modified subunit. The polymer analyte produces a detectable signal in a nanopore-based system. The detectable signal, and/or its deviation from a reference signal, indicates the location of the modified subunit in the polymer analyte and, thus, permits the identification of the subunit at that location in the original pre-analyte polymer.
    Type: Grant
    Filed: July 6, 2018
    Date of Patent: November 3, 2020
    Assignees: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20200318180
    Abstract: A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. A permanent tether can include a head region anchored to the polymerase, a tail region, and an elongated body disposed therebetween that occurs in the aperture of the nanopore. A first moiety can be disposed on the elongated body that binds to the elongated tag of a first nucleotide upon which the polymerase is acting. A reporter region can be disposed on the elongated body that indicates when the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide.
    Type: Application
    Filed: May 8, 2020
    Publication date: October 8, 2020
    Applicant: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Jeffrey G. Mandell
  • Patent number: 10787704
    Abstract: The present disclosure provides a method for sequencing nucleic acids. The method can include polymerase catalyzed incorporation of nucleotides into a nascent nucleic acid strand against a nucleic acid template, wherein the polymerase is attached to a charge sensor that detects nucleotide incorporation events. One or more non-natural nucleotide types that each produce a unique signatures at the charge sensor can be used to uniquely identify different nucleotides in the template nucleic acid.
    Type: Grant
    Filed: May 11, 2016
    Date of Patent: September 29, 2020
    Assignees: ILLUMINA, INC., THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Kevin L Gunderson, Jingwei Bai, Cheng-Yao Chen, Jeffrey G Mandell, Sergio Peisajovich, Philip G Collins, Gregory A Weiss, Boyan Boyanov
  • Publication number: 20200200693
    Abstract: A sensing system includes a charge sensor including two electrodes and an electrically conductive channel connecting the two electrodes. The sensing system also includes a charged molecule attached to the electrically conductive channel. The charged molecule includes a recognition site to reversibly bind a label of a labeled nucleotide; has an unbound favored conformation associated with an unbound charge configuration; and has a favored conformation associated with a charge configuration when the recognition site is bound to the label. The charge configuration is different from the unbound charge configuration. The sensing system further includes a polymerase attached to the electrically conductive channel or to the charged molecule.
    Type: Application
    Filed: December 3, 2019
    Publication date: June 25, 2020
    Inventors: Boyan Boyanov, Sergio Peisajovich, Jeffrey G. Mandell
  • Publication number: 20200199664
    Abstract: A method for amplifying a target nucleic acid including providing a system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.
    Type: Application
    Filed: January 6, 2020
    Publication date: June 25, 2020
    Inventor: Jeffrey G. Mandell
  • Publication number: 20200190577
    Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.
    Type: Application
    Filed: December 9, 2019
    Publication date: June 18, 2020
    Inventors: BOYAN BOYANOV, JEFFREY G. MANDELL, KEVIN L. GUNDERSON, JINGWEI BAI, LIANGLIANG QIANG, BRADLEY BAAS
  • Publication number: 20200165650
    Abstract: A method for enriching a target nucleic acid comprising providing an endonuclease system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid; contacting the target nucleic acid with the endonuclease system to form a complex; and separating the complex and thereby enriching for the target nucleic acid.
    Type: Application
    Filed: October 21, 2019
    Publication date: May 28, 2020
    Inventors: Gordon M. Cann, Jeffrey G. Mandell, Alex Aravanis, Steven Norberg, Dmitry K. Pokholok, Frank J. Steemers, Farnaz Absalan, Leila Bazargan
  • Patent number: 10648022
    Abstract: A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. A permanent tether can include a head region anchored to the polymerase, a tail region, and an elongated body disposed therebetween that occurs in the aperture of the nanopore. A first moiety can be disposed on the elongated body that binds to the elongated tag of a first nucleotide upon which the polymerase is acting. A reporter region can be disposed on the elongated body that indicates when the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide.
    Type: Grant
    Filed: June 2, 2016
    Date of Patent: May 12, 2020
    Assignee: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Jeffrey G. Mandell
  • Publication number: 20200132664
    Abstract: Example nanopore sequencers include a cis well, a trans well, and a nanopore fluidically connecting the cis and trans wells. In one example sequencer, a modified electrolyte (including an electrolyte and a cation complexing agent) is present in the cis well, or the trans well, or in the cis and the trans wells. In another example sequencer, a gel state polyelectrolyte is present in the cis well, or the trans well, or in the cis and the trans wells.
    Type: Application
    Filed: June 19, 2018
    Publication date: April 30, 2020
    Inventors: Boyan Boyanov, Rohan N. Akolkar, Jeffrey S. Fisher, Jeffrey G. Mandell, Liangliang Qiang, Steven M. Barnard
  • Publication number: 20200123603
    Abstract: The current document discusses electromechanical sequence detectors that transduce changes in the shape of a shape-change sensor component into an electrical signal from which one or more derived values are generated. In a disclosed implementation, the sequence-detection system comprises a mechanical-change sensor that changes shape when specifically interacting with entities within a target, a shape-to-signal-transduction component that transduces changes in the shape of the mechanical-change sensor into an electrical signal, an analysis subsystem that determines the types of entities within the target using the electrical signal, and a control subsystem that continuously monitors operational characteristics of the sequence-detection system and adjusts sequence-detection system operational parameters.
    Type: Application
    Filed: September 14, 2018
    Publication date: April 23, 2020
    Applicant: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia
  • Patent number: 10605766
    Abstract: A method of nucleic acid sequencing. The method can include the steps of (a) providing a polymerase tethered to a solid support charge sensor; (b) providing one or more nucleotides, whereby the presence of the nucleotide can be detected by the charge sensor; and (c) detecting incorporation of the nucleotide into a nascent strand complementary to a template nucleic acid.
    Type: Grant
    Filed: July 14, 2015
    Date of Patent: March 31, 2020
    Assignee: ILLUMINA, INC.
    Inventors: Boyan Boyanov, Jeffrey G. Mandell, Jingwei Bai, Kevin L. Gunderson, Cheng-Yao Chen, Michel Perbost
  • Patent number: 10577649
    Abstract: A method for amplifying a target nucleic acid including providing a system having a crRNA or a derivative thereof, and a Cas protein or a variant thereof. The crRNA or the derivative thereof contains a target-specific nucleotide region substantially complementary to a region of the target nucleic acid, and contacting the target nucleic acid with the system to form a complex.
    Type: Grant
    Filed: November 10, 2015
    Date of Patent: March 3, 2020
    Assignee: Illumina, Inc.
    Inventor: Jeffrey G. Mandell
  • Patent number: 10545115
    Abstract: A method of nucleic acid sequencing. The method can include the steps of (a) providing a polymerase tethered to a solid support charge sensor; (b) providing one or more nucleotides, whereby the presence of the nucleotide can be detected by the charge sensor; and (c) detecting incorporation of the nucleotide into a nascent strand complementary to a template nucleic acid.
    Type: Grant
    Filed: December 12, 2017
    Date of Patent: January 28, 2020
    Assignee: ILLUMINA, INC.
    Inventors: Boyan Boyanov, Jeffrey G. Mandell, Jingwei Bai, Kevin L. Gunderson, Cheng-Yao Chen, Michel Perbost
  • Publication number: 20200024657
    Abstract: Methods and compositions for characterizing a target polynucleotide, including, characterizing the sequence of the target polynucleotide, using the fractional translocation steps of the target polynucleotide's translocation through a pore.
    Type: Application
    Filed: June 12, 2019
    Publication date: January 23, 2020
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 10519499
    Abstract: The disclosure provides detection apparatus having one or more nanopores, methods for making apparatus having one or more nanopore and methods for using apparatus having one or more nanopores. Uses include, but are not limited to detection and sequencing of nucleic acids.
    Type: Grant
    Filed: July 29, 2015
    Date of Patent: December 31, 2019
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Jeffrey G Mandell, Kevin L Gunderson, Jingwei Bai, Liangliang Qiang, Bradley Baas
  • Publication number: 20190376135
    Abstract: Compositions, systems, and methods for detecting events are provided. A composition can include a nanopore including a first side, a second side, and an aperture extending through the first and second sides; and a permanent tether including head and tail regions and an elongated body disposed there between. The head region can be anchored to or adjacent to the first or second side of the nanopore. The elongated body including a reporter region can be movable within the aperture responsive to a first event occurring adjacent to the first side of the nanopore. For example, the reporter region is translationally movable toward the first side responsive to the first event, then toward the second side, then toward the first side responsive to a second event. The first event can include adding a first nucleotide to a polynucleotide. The second event can include adding a second nucleotide to the polynucleotide.
    Type: Application
    Filed: July 23, 2019
    Publication date: December 12, 2019
    Applicant: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach