Patents Assigned to University of Washington through its Center for Commercialization
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Patent number: 12258629Abstract: 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: GrantFiled: July 3, 2019Date of Patent: March 25, 2025Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 12241123Abstract: 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: GrantFiled: August 2, 2021Date of Patent: March 4, 2025Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 12216124Abstract: 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: GrantFiled: November 23, 2022Date of Patent: February 4, 2025Assignee: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Changfeng Wu, Xuanjun Zhang, Jiangbo Yu, Fangmao Ye
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Publication number: 20250035636Abstract: 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: ApplicationFiled: October 10, 2024Publication date: January 30, 2025Applicant: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Changfeng Wu, Xuanjun Zhang, Jiangbo Yu, Fangmao Ye
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Patent number: 12167864Abstract: 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: GrantFiled: January 6, 2023Date of Patent: December 17, 2024Assignee: University of Washington through its Center for CommercializationInventors: Adam D. Maxwell, Bryan W. Cunitz, Wayne Kreider, Oleg A. Sapozhnikov, Ryan S. Hsi, Michael R. Bailey
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Publication number: 20240360502Abstract: 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: ApplicationFiled: July 11, 2024Publication date: October 31, 2024Applicants: University of Washington through its Center for Commercialization, Illumina, Inc.Inventors: Jens H. Gundlach, Andrew Laszlo, Ian Derrington, Jeffrey G. Mandell
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Publication number: 20240294980Abstract: 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: ApplicationFiled: October 12, 2023Publication date: September 5, 2024Applicant: University of Washington through its Center for CommercializationInventors: Jens H. Gundlach, Andrew Laszlo
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Publication number: 20240287507Abstract: 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: ApplicationFiled: April 29, 2024Publication date: August 29, 2024Applicant: University of Washington through its Center for CommercializationInventors: Jay Ashok Shendure, Jerrod Joseph Schwartz, Andrew Colin Adey, Cho li Lee, Joseph Brian Hiatt, Jacob Otto Kitzman, Akash Kumar
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Publication number: 20240263214Abstract: 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: ApplicationFiled: February 20, 2024Publication date: August 8, 2024Applicant: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. CHIU, Jason E. KREUTZ, Gloria S. YEN, Bryant S. FUJIMOTO
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Publication number: 20240254288Abstract: 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: ApplicationFiled: May 15, 2023Publication date: August 1, 2024Applicant: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Changfeng Wu, Yu Rong, Yong Zhang, Yi-Che Wu, Yang-Hsiang Chan, Xuanjun Zhang, Jiangbo Yu, Wei Sun
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Patent number: 12042531Abstract: 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: GrantFiled: October 20, 2021Date of Patent: July 23, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Mary L. Disis, Denise Cecil, Meredith Slota
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Patent number: 12024747Abstract: 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: GrantFiled: July 3, 2019Date of Patent: July 2, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 12006545Abstract: 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: GrantFiled: August 2, 2021Date of Patent: June 11, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 11999951Abstract: 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: GrantFiled: April 8, 2022Date of Patent: June 4, 2024Assignee: University of Washington through its Center for CommercializationInventors: Jay Ashok Shendure, Jerrod Joseph Schwartz, Andrew Colin Adey, Cho li Lee, Joseph Brian Hiatt, Jacob Otto Kitzman, Akash Kumar
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Patent number: 11993815Abstract: 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: GrantFiled: August 2, 2021Date of Patent: May 28, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Publication number: 20240158846Abstract: 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: ApplicationFiled: October 12, 2023Publication date: May 16, 2024Applicant: University of Washington through its Center for CommercializationInventors: Jens Gundlach, Ian M. Derrington, Andrew Laszlo, Elizabeth Manrao
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Patent number: 11982678Abstract: 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: GrantFiled: October 26, 2018Date of Patent: May 14, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Perry G. Schiro, Jason S. Kuo
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Patent number: 11970740Abstract: 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: GrantFiled: August 2, 2021Date of Patent: April 30, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 11959133Abstract: 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: GrantFiled: March 19, 2020Date of Patent: April 16, 2024Assignee: University of Washington Through Its Center for CommercializationInventors: Jens Gundlach, Ian M. Derrington, Andrew Laszlo, Elizabeth Manrao
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Patent number: 11939626Abstract: 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: GrantFiled: July 19, 2022Date of Patent: March 26, 2024Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Jason E. Kreutz, Gloria S. Yen, Bryant S. Fujimoto