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).

  • 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
  • Patent number: 10457969
    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: Grant
    Filed: July 20, 2015
    Date of Patent: October 29, 2019
    Assignee: Illumina, Inc.
    Inventors: Gordon M. Cann, Jeffrey G. Mandell, Alex Aravanis, Steven Norberg, Dmitry K. Pokholok, Frank J. Steemers, Farnaz Absalan, Leila Bazargan
  • Patent number: 10364462
    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: May 26, 2017
    Date of Patent: July 30, 2019
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 10364463
    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 therebetween. 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: Grant
    Filed: June 16, 2017
    Date of Patent: July 30, 2019
    Assignee: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
  • Publication number: 20190136303
    Abstract: A method for enriching or amplifying a target nucleic acid including providing a system having a guide nucleic acid, and a Cas or Argonaute protein or a variant thereof. The guide nucleic acid 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: May 10, 2017
    Publication date: May 9, 2019
    Inventors: Jeffrey G. Mandell, Molly He
  • Publication number: 20190106740
    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: Application
    Filed: July 6, 2018
    Publication date: April 11, 2019
    Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20180237850
    Abstract: Sequencing-by-synthesis (SBS) method is provided that includes providing a detection apparatus that includes an array of magnetically-responsive sensors. Each of the magnetically-responsive sensors is located proximate to a respective designated space to detect a magnetic property therefrom. The detection apparatus also includes a plurality of nucleic acid template strands located within corresponding designated spaces. The method also includes conducting a plurality of SBS events to grow a complementary strand by incorporating nucleotides along each template strand. At least some of the nucleotides are attached to corresponding magnetic particles having respective magnetic properties. Each of the plurality of SBS events includes detecting changes in electrical resistance at the magnetically-responsive sensors caused by the respective magnetic properties of the magnetic particles.
    Type: Application
    Filed: August 12, 2016
    Publication date: August 23, 2018
    Inventors: Jeffrey G. Mandell, Lisa Kwok
  • Patent number: 10017814
    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 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: Grant
    Filed: September 2, 2014
    Date of Patent: July 10, 2018
    Assignees: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20180155774
    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: June 2, 2016
    Publication date: June 7, 2018
    Inventors: Kevin L. GUNDERSON, Jeffrey G. MANDELL
  • Publication number: 20180155773
    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: Application
    Filed: May 11, 2016
    Publication date: June 7, 2018
    Inventors: Kevin L Gunderson, Jingwei Bai, Cheng-Yao Chen, Jeffrey G Mandell, Sergio Peisajovich, Philip G Collins, Gregory A Weiss, Boyan Boyanov
  • Publication number: 20180112265
    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: Application
    Filed: December 12, 2017
    Publication date: April 26, 2018
    Inventors: Boyan BOYANOV, Jeffrey G. MANDELL, Jingwei BAI, Kevin L. GUNDERSON, Cheng-Yao CHEN, Michel PERBOST
  • Publication number: 20170369942
    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 therebetween. 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.
    Type: Application
    Filed: June 16, 2017
    Publication date: December 28, 2017
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
  • Publication number: 20170342474
    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: November 10, 2015
    Publication date: November 30, 2017
    Inventor: Jeffrey G. Mandell
  • Publication number: 20170268055
    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: May 26, 2017
    Publication date: September 21, 2017
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Publication number: 20170260582
    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: July 29, 2015
    Publication date: September 14, 2017
    Inventors: BOYAN BOYANOV, JEFFREY G MANDELL, KEVIN L GUNDERSON, JINGWEI BAI, LIANGLIANG QIANG, BRADLEY BAAS
  • Patent number: 9708655
    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 therebetween. 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: Grant
    Filed: June 2, 2015
    Date of Patent: July 18, 2017
    Assignee: Illumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Jens H. Gundlach
  • Patent number: 9689033
    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: November 26, 2014
    Date of Patent: June 27, 2017
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 9689031
    Abstract: The invention is in general directed to the rapid exponential amplification of short DNA or RNA sequences at a constant temperature.
    Type: Grant
    Filed: July 14, 2007
    Date of Patent: June 27, 2017
    Assignee: Ionian Technologies, Inc.
    Inventors: Brian K. Maples, Rebecca C. Holmberg, Andrew P. Miller, Jarrod W. Provins, Richard B Roth, Jeffrey G. Mandell
  • Publication number: 20160222444
    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 2, 2014
    Publication date: August 4, 2016
    Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20160017416
    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: Application
    Filed: July 14, 2015
    Publication date: January 21, 2016
    Applicant: ILLUMINA, INC
    Inventors: Boyan BOYANOV, Jeffrey G. MANDELL, Jingwei BAI, Kevin L. GUNDERSON, Cheng-Yao CHEN, Michel Perbost