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: 20250109434
    Abstract: A polymer is disposed through a nanopore that encodes a polynucleotide's sequence and includes monomer units that encode nucleotides and include first and second reporter moieties and first and second arresting constructs. The first reporter moiety is translocated into the nanopore's aperture, where a first value of an electrical property of the first reporter moiety is measured while the first arresting construct pauses translocation. The second reporter moiety is translocated into the aperture, where a second value of an electrical property of the second reporter moiety is measured while the second arresting construct pauses translocation. The first value and the second value for each monomer unit is used to identify the nucleotide encoded by that monomer unit; and distinguish the nucleotide encoded by that monomer unit from the nucleotides encoded by adjacent monomer units, including by those that encode the same type of nucleotide as that monomer unit.
    Type: Application
    Filed: September 27, 2024
    Publication date: April 3, 2025
    Applicant: Illumina, Inc.
    Inventors: Hugo Brandão, John Moon, Jeffrey G. Mandell, Erin Garcia, Lisa Savagian, Eunho Noh, Xiangyuan Yang, Sharyuen Soh, Sadeer Salam
  • Publication number: 20250109433
    Abstract: In one aspect, the disclosed technology relates to nanopore sequencing with a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a macromolecular block. In some embodiments, the macromolecular blocks are configured for slowing or halting the polynucleotide translocation through a nanopore. In some embodiments the macromolecular blocks have linear and branched structures.
    Type: Application
    Filed: September 17, 2024
    Publication date: April 3, 2025
    Inventors: Hassan Zakiruddin Bohra, Yin Nah Teo, Ramesh Neelakandan, Erin Garcia, Abdul Sadeer Abd Salam, Daniel Hartoyo Lukamto, Soumadwip Ghosh, Xiangyuan Yang, Jeffrey G. Mandell
  • Publication number: 20250101493
    Abstract: The disclosure provides compositions, methods, and kits that facilitate the characterization of omic variation in tissues while preserving spatial information related to the origin of target analytes in the tissue.
    Type: Application
    Filed: December 29, 2022
    Publication date: March 27, 2025
    Inventors: Andrea MANZO, Aathavan KARUNAKARAN, Jeffrey S. FISHER, Jeffrey G. MANDELL, Eric Hans VERMAAS, Fiona KAPER, Adam WHITE, Andrew J. PRICE, Andrew Zachary OSTROW, Jeffrey BRODIN, Sarah Munchel SHULTZABERGER
  • Publication number: 20250019758
    Abstract: Provided herein are methods for modification-based controlled polynucleotide translocation in nanopores for sequencing, modified nucleotides, and kits and systems for performing the disclosed methods. In some embodiments, modifications can be used to control polynucleotide translocation by modifying nucleotides on a strand of polynucleotide to carry a modification, where the modifications can arrest or slow translocation when encountering the nanopore. In some embodiments, application of a voltage can move one nucleotide and its attached modification through the nanopore at a time.
    Type: Application
    Filed: April 30, 2024
    Publication date: January 16, 2025
    Inventors: Abdul Sadeer Abd Salam, Xiangyuan Yang, Hassan Zakiruddin Bohra, Yin Nah Teo, Tsz Ying Yuen, Daniel Hartoyo Lukamto, Erin Garcia, Jeffrey G. Mandell
  • Publication number: 20240417787
    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: July 16, 2024
    Publication date: December 19, 2024
    Inventor: Jeffrey G. Mandell
  • Publication number: 20240377380
    Abstract: An example of a nanopore sensor device includes one or more cis wells; a cis electrode; a plurality of trans wells, each of the plurality of trans wells separated from the one or more cis wells by a lipid/solid-state membrane having a nanopore; a plurality of trans electrodes, each of the plurality of trans electrodes associated with one of the plurality of trans wells; a first concentration of an electrolyte within the one or more cis wells; and a second concentration of the electrolyte within the trans wells, wherein the first concentration is higher than the second concentration.
    Type: Application
    Filed: March 1, 2022
    Publication date: November 14, 2024
    Inventors: Boyan Boyanov, Jeffrey G. Mandell, Seth M. McDonald
  • Publication number: 20240376535
    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: March 28, 2024
    Publication date: November 14, 2024
    Inventors: Kevin L. Gunderson, Jeffrey G. Mandell
  • Publication number: 20240360502
    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: July 11, 2024
    Publication date: October 31, 2024
    Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.
    Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
  • Publication number: 20240280557
    Abstract: Polypeptide nanopores synthetically functionalized with positively charged species, and methods of making and using the same, are provided herein. In some examples, a polypeptide nanopore includes a first side, a second side, a channel extending through the first and second sides, and a mutated amino acid residue. The mutated amino acid residue may be synthetically functionalized with a positively charged species that inhibits translocation of cations through the channel.
    Type: Application
    Filed: March 10, 2022
    Publication date: August 22, 2024
    Applicant: Illumina, Inc.
    Inventors: Lisa Savagian, Burton Simpson, Sang Park, Boyan Boyanov, Jeffrey G. Mandell, Seth M. McDonald
  • Patent number: 12065695
    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: January 6, 2020
    Date of Patent: August 20, 2024
    Assignee: Illumina, Inc.
    Inventor: Jeffrey G. Mandell
  • Patent number: 12050194
    Abstract: In an example, a sensing system includes a pH sensor. The pH sensor includes two electrodes and a conductive channel operatively connected to the two electrodes. A complex is attached to the conductive channel of the pH sensor. The complex includes a polymerase linked to at least one pH altering moiety that is to participate in generating a pH change within proximity of the conductive channel from consumption of a secondary substrate in a fluid that is exposed to the pH sensor. The at least one pH altering moiety is selected from the group consisting of an enzyme, a metal coordination complex, a co-factor, and an activator.
    Type: Grant
    Filed: January 24, 2020
    Date of Patent: July 30, 2024
    Assignee: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, Brian D. Mather, Kaitlin M. Pugliese, Jeffrey G. Mandell, Maria Candelaria Rogert Bacigalupo, Boyan Boyanov
  • Publication number: 20240209438
    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: March 11, 2024
    Publication date: June 27, 2024
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia
  • Publication number: 20240167085
    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: December 8, 2023
    Publication date: May 23, 2024
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Patent number: 11976322
    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: Grant
    Filed: September 14, 2018
    Date of Patent: May 7, 2024
    Assignee: ILLUMINA, INC.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia
  • Patent number: 11970734
    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: May 8, 2020
    Date of Patent: April 30, 2024
    Assignee: Illumina, Inc.
    Inventors: Kevin L Gunderson, Jeffrey G. Mandell
  • Patent number: 11898983
    Abstract: Devices and methods of using the devices are disclosed which can provide scalability, improved sensitivity and reduced noise for sequencing polynucleotide. Examples of the devices include a biological or solid-state nanopore, a field effect transistor (FET) sensor with improved gate controllability over the channel, and a porous structure.
    Type: Grant
    Filed: June 18, 2021
    Date of Patent: February 13, 2024
    Assignee: Illumina, Inc.
    Inventors: Boyan Boyanov, Rico Otto, Jeffrey G. Mandell
  • Patent number: 11879155
    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 25, 2021
    Date of Patent: January 23, 2024
    Assignee: Illumina, Inc.
    Inventors: Eric Stava, Jens H. Gundlach, Jeffrey G. Mandell, Kevin L. Gunderson, Ian M. Derrington, Hosein Mohimani
  • Publication number: 20240011089
    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: June 29, 2023
    Publication date: January 11, 2024
    Inventors: BOYAN BOYANOV, JEFFREY G MANDELL, KEVIN L GUNDERSON, JINGWEI BAI, LIANGLIANG QIANG, BRADLEY BAAS
  • Publication number: 20240003896
    Abstract: The current document discusses a detection system comprising a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type, a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal, and an analysis subsystem that determines the types of entities within the target using the signal.
    Type: Application
    Filed: September 14, 2018
    Publication date: January 4, 2024
    Applicant: lllumina, Inc.
    Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia, Jens H. Gundlach
  • Publication number: 20230357307
    Abstract: In one aspect, the disclosed technology relates to nanopore sequencing with a polynucleotide comprising a plurality of nucleotides, wherein each nucleotide comprises a linker construct between two positions of the nucleotide, wherein the linker construct optionally comprises a reporter moiety corresponding to the identity of the nucleotide, and wherein the linker construct is a part of the cleavable cyclic loop nucleotide comprising a cleavable site. In some embodiments, the nucleotides further comprise arresting constructs for slowing or halting the polynucleotide translocation through a nanopore.
    Type: Application
    Filed: May 3, 2023
    Publication date: November 9, 2023
    Inventors: Abdul Sadeer Abd Salam, Xiangyuan Yang, Hassan Zakiruddin Bohra, Yin Nah Teo, Min Yen Lee, Ramesh Neelakandan, Jeffrey G. Mandell, Erin Garcia, Sharyuen Soh, Daniel Hartoyo Lukamto