Patents Assigned to University of Washington through its Center for Commercialization
  • Patent number: 12258629
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: July 3, 2019
    Date of Patent: March 25, 2025
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 12241123
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: August 2, 2021
    Date of Patent: March 4, 2025
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 12216124
    Abstract: The present invention provides, among other aspects, stabilized chromophoric nanoparticles. In certain embodiments, the chromophoric nanoparticles provided herein are rationally functionalized with a pre-determined number of functional groups. In certain embodiments, the stable chromophoric nanoparticles provided herein are modified with a low density of functional groups. In yet other embodiments, the chromophoric nanoparticles provided herein are conjugated to one or more molecules. Also provided herein are methods for making rationally functionalized chromophoric nanoparticles.
    Type: Grant
    Filed: November 23, 2022
    Date of Patent: February 4, 2025
    Assignee: University of Washington through its Center for Commercialization
    Inventors: Daniel T. Chiu, Changfeng Wu, Xuanjun Zhang, Jiangbo Yu, Fangmao Ye
  • Publication number: 20250035636
    Abstract: The present invention provides, among other aspects, stabilized chromophoric nanoparticles. In certain embodiments, the chromophoric nanoparticles provided herein are rationally functionalized with a pre-determined number of functional groups. In certain embodiments, the stable chromophoric nanoparticles provided herein are modified with a low density of functional groups. In yet other embodiments, the chromophoric nanoparticles provided herein are conjugated to one or more molecules. Also provided herein are methods for making rationally functionalized chromophoric nanoparticles.
    Type: Application
    Filed: October 10, 2024
    Publication date: January 30, 2025
    Applicant: University of Washington through its Center for Commercialization
    Inventors: Daniel T. Chiu, Changfeng Wu, Xuanjun Zhang, Jiangbo Yu, Fangmao Ye
  • Patent number: 12167864
    Abstract: A method for attempting to fragment or comminute an object in a body using ultrasound includes producing a burst wave lithotripsy (BWL) waveform by a therapy transducer. The BWL waveform is configured to fragment or comminute the object. The BWL waveform includes a first burst of continuous ultrasound cycles and a second burst of continuous ultrasound cycles. A burst frequency corresponds to a frequency of repeating the bursts of the BWL waveform. The method also includes determining a cycle frequency f of the continuous ultrasound cycles within the first burst and the second burst based on a target fragment size D, where the cycle frequency is: f(MHz)=0.47/D(mm).
    Type: Grant
    Filed: January 6, 2023
    Date of Patent: December 17, 2024
    Assignee: University of Washington through its Center for Commercialization
    Inventors: Adam D. Maxwell, Bryan W. Cunitz, Wayne Kreider, Oleg A. Sapozhnikov, Ryan S. Hsi, Michael R. Bailey
  • 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: 20240294980
    Abstract: The present disclosure provides methods and reagents for improving nanopore-based analyses of polymers. Specifically, the disclosure provides a method of analyzing a polymer that includes a polymer analyte that contains an end domain that has at least one charged moiety. The disclosure also provides a method of increasing the interaction rate between a polymer analyte and a nanopore, wherein the polymer analyte contains an end domain that has at least one charged moiety. The disclosure also provide compositions for use with the described methods, including adapter compositions that contain charged moieties, such as phosphate or sulfate groups, and that are configured to being linked to an polymer analyte domain.
    Type: Application
    Filed: October 12, 2023
    Publication date: September 5, 2024
    Applicant: University of Washington through its Center for Commercialization
    Inventors: Jens H. Gundlach, Andrew Laszlo
  • Publication number: 20240287507
    Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.
    Type: Application
    Filed: April 29, 2024
    Publication date: August 29, 2024
    Applicant: University of Washington through its Center for Commercialization
    Inventors: Jay Ashok Shendure, Jerrod Joseph Schwartz, Andrew Colin Adey, Cho li Lee, Joseph Brian Hiatt, Jacob Otto Kitzman, Akash Kumar
  • Publication number: 20240263214
    Abstract: Methods, devices, and systems for performing digital assays are provided. In certain aspects, the methods, devices, and systems can be used for the amplification and detection of nucleic acids. In certain aspects, the methods, devices, and systems can be used for the recognition, detection, and sizing of droplets in a volume. Also provided are compositions and kits suitable for use with the methods and devices of the present disclosure.
    Type: Application
    Filed: February 20, 2024
    Publication date: August 8, 2024
    Applicant: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Daniel T. CHIU, Jason E. KREUTZ, Gloria S. YEN, Bryant S. FUJIMOTO
  • Publication number: 20240254288
    Abstract: Polymers, monomers, chromophoric polymer dots and related methods are provided. Highly fluorescent chromophoric polymer dots with narrow-band emissions are provided. Methods for synthesizing the chromophoric polymers, preparation methods for forming the chromophoric polymer dots, and biological applications using the unique properties of narrow-band emissions are also provided.
    Type: Application
    Filed: May 15, 2023
    Publication date: August 1, 2024
    Applicant: University of Washington through its Center for Commercialization
    Inventors: Daniel T. Chiu, Changfeng Wu, Yu Rong, Yong Zhang, Yi-Che Wu, Yang-Hsiang Chan, Xuanjun Zhang, Jiangbo Yu, Wei Sun
  • Patent number: 12042531
    Abstract: The compositions described herein include an epitope of a peptide that may elicit an immune response in a subject following administration. The compositions may comprise nucleic acids. The compositions may comprise peptides. The methods described herein include administering a composition comprising an epitope of a peptide to a subject in need thereof.
    Type: Grant
    Filed: October 20, 2021
    Date of Patent: July 23, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Mary L. Disis, Denise Cecil, Meredith Slota
  • Patent number: 12024747
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: July 3, 2019
    Date of Patent: July 2, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 12006545
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: August 2, 2021
    Date of Patent: June 11, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11999951
    Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes. The methods described herein pursue cost-effective, massively parallel capture of contiguity information at different scales.
    Type: Grant
    Filed: April 8, 2022
    Date of Patent: June 4, 2024
    Assignee: University of Washington through its Center for Commercialization
    Inventors: Jay Ashok Shendure, Jerrod Joseph Schwartz, Andrew Colin Adey, Cho li Lee, Joseph Brian Hiatt, Jacob Otto Kitzman, Akash Kumar
  • Patent number: 11993815
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: August 2, 2021
    Date of Patent: May 28, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Publication number: 20240158846
    Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.
    Type: Application
    Filed: October 12, 2023
    Publication date: May 16, 2024
    Applicant: University of Washington through its Center for Commercialization
    Inventors: Jens Gundlach, Ian M. Derrington, Andrew Laszlo, Elizabeth Manrao
  • Patent number: 11982678
    Abstract: Provided herein, among other aspects, are methods and apparatuses for ranking aliquots from a suspension containing bioparticles. In certain embodiments, the bioparticles may be cells, organelles, proteins, DNAs, debris of biological origin, microbeads coated with biological compounds, or viral particles. As such, the methods and apparatuses provided herein may be used to quantify rare cells such as circulating cancer cells, fetal cells and other rare cells present in bodily fluids for disease diagnosis, prognosis, or treatment.
    Type: Grant
    Filed: October 26, 2018
    Date of Patent: May 14, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Daniel T. Chiu, Perry G. Schiro, Jason S. Kuo
  • Patent number: 11970740
    Abstract: Next Generation DNA sequencing promises to revolutionize clinical medicine and basic research. However, while this technology has the capacity to generate hundreds of billions of nucleotides of DNA sequence in a single experiment, the error rate of approximately 1% results in hundreds of millions of sequencing mistakes. These scattered errors can be tolerated in some applications but become extremely problematic when “deep sequencing” genetically heterogeneous mixtures, such as tumors or mixed microbial populations. To overcome limitations in sequencing accuracy, a method Duplex Consensus Sequencing (DCS) is provided. This approach greatly reduces errors by independently tagging and sequencing each of the two strands of a DNA duplex. As the two strands are complementary, true mutations are found at the same position in both strands. In contrast, PCR or sequencing errors will result in errors in only one strand.
    Type: Grant
    Filed: August 2, 2021
    Date of Patent: April 30, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 11959133
    Abstract: The present disclosure generally relates to the methods and compositions to efficiently analyze polymer characteristics using nanopore-based assays. Specifically disclosed is a method for generating reference signals for polymer analysis in a nanopore system, wherein the nanopore system has a multi-subunit output signal resolution. The method comprises translocating a reference sequence through a nanopore to generate a plurality of reference output signals, wherein each possible multi-subunit sequence that can determine an output signal appears only once in the reference sequence. The output signals are compiled into a reference map for nanopore analysis of an analyte polymer. Also provided are methods and compositions for calibrating the nanopore system for optimized polymer analysis.
    Type: Grant
    Filed: March 19, 2020
    Date of Patent: April 16, 2024
    Assignee: University of Washington Through Its Center for Commercialization
    Inventors: Jens Gundlach, Ian M. Derrington, Andrew Laszlo, Elizabeth Manrao
  • Patent number: 11939626
    Abstract: Methods, devices, and systems for performing digital assays are provided. In certain aspects, the methods, devices, and systems can be used for the amplification and detection of nucleic acids. In certain aspects, the methods, devices, and systems can be used for the recognition, detection, and sizing of droplets in a volume. Also provided are compositions and kits suitable for use with the methods and devices of the present disclosure.
    Type: Grant
    Filed: July 19, 2022
    Date of Patent: March 26, 2024
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Daniel T. Chiu, Jason E. Kreutz, Gloria S. Yen, Bryant S. Fujimoto