Patents Assigned to University of Washington through its Center for Commercialization
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Patent number: 11566285Abstract: 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: January 31, 2023Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 11566288Abstract: 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: January 31, 2023Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 11566286Abstract: 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: June 28, 2021Date of Patent: January 31, 2023Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Publication number: 20230023536Abstract: Provided herein, among other aspects, are methods and apparatuses for analyzing particles in a sample. In some aspects, the particles can be analytes, cells, nucleic acids, or proteins and contacted with a tag, partitioned into aliquots, detected by a ranking device, and isolated. The methods and apparatuses provided herein may include a microfluidic chip. In some aspects, the methods and apparatuses may be used to quantify rare particles in a sample, such as cancer cells and other rare cells for disease diagnosis, prognosis, or treatment.Type: ApplicationFiled: September 16, 2022Publication date: January 26, 2023Applicant: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. CHIU, Mengxia ZHAO, Wyatt NELSON, Perry G. SCHIRO
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Patent number: 11555220Abstract: 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: January 17, 2023Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Patent number: 11549144Abstract: 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: January 10, 2023Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
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Publication number: 20220356512Abstract: 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: July 19, 2022Publication date: November 10, 2022Applicant: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. CHIU, Jason E. KREUTZ, Gloria S. YEN, Bryant S. FUJIMOTO
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Patent number: 11480575Abstract: Provided herein, among other aspects, are methods and apparatuses for analyzing particles in a sample. In some aspects, the particles can be analytes, cells, nucleic acids, or proteins and contacted with a tag, partitioned into aliquots, detected by a ranking device, and isolated. The methods and apparatuses provided herein may include a microfluidic chip. In some aspects, the methods and apparatuses may be used to quantify rare particles in a sample, such as cancer cells and other rare cells for disease diagnosis, prognosis, or treatment.Type: GrantFiled: December 3, 2019Date of Patent: October 25, 2022Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Mengxia Zhao, Wyatt Nelson, Perry G. Schiro
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Publication number: 20220331418Abstract: Compositions and methods are provided that enable activation of innate immune responses through RIG-I like receptor signaling. The compositions and methods incorporate synthetic nucleic acid pathogen associated molecular patterns (PAMPs) that comprise elements initially characterized in, and derived from, the hepatitis C virus genome.Type: ApplicationFiled: April 4, 2022Publication date: October 20, 2022Applicant: University of Washington through its Center for CommercializationInventors: Michael J. Gale, JR., Gretja Schnell, Yueh-Ming Loo
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Publication number: 20220315918Abstract: Contiguity information is important to achieving high-quality de novo assembly of mammalian genomes and the haplotype-resolved resequencing of human genomes.Type: ApplicationFiled: April 8, 2022Publication date: October 6, 2022Applicant: 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: 11427857Abstract: 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: March 6, 2020Date of Patent: August 30, 2022Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Jason E. Kreutz, Gloria S. Yen, Bryant S. Fujimoto
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Patent number: 11411435Abstract: An integrated circuit, such as included as a portion of a sensor node, can include a regulator circuit having an input coupleable to an energy harvesting transducer. The integrated circuit can include a wireless receiver circuit coupled to the regulator circuit and configured to wirelessly receive at least enough operating energy to establish operation of the sensor node without requiring the energy harvesting transducer. The integrated circuit can include a digital processor circuit coupled to the regulator circuit and a power management processor circuit. The digital processor circuit or one or more other circuits can include a subthreshold operational mode established by the power management processor circuit based on the selected energy consumption level. For example, establishing the subthreshold operational mode can include adjusting or selecting a supply voltage so as to establish subthreshold operation of a field effect transistor (FET) in the digital processor circuit or other circuits.Type: GrantFiled: November 25, 2019Date of Patent: August 9, 2022Assignees: University of Virginia Patent Foundation, University of Washington through its Center for CommercializationInventors: Benton H. Calhoun, Brian Otis
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Patent number: 11408884Abstract: Lyophilized chromophoric polymer dot compositions are provided. Also disclosed are methods of making and using the lyophilized compositions, methods of dispersing the lyophilized compositions in aqueous solutions and kits supplying the compositions.Type: GrantFiled: December 3, 2019Date of Patent: August 9, 2022Assignee: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Wei Sun, Jiangbo Yu, Changfeng Wu, Fangmao Ye
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Patent number: 11401547Abstract: Methods and systems for digital measurements are provided. In an embodiment, the method includes producing a plurality of droplets, wherein at least one of the droplets of the plurality of droplets contains an analyte molecule from a sample; measuring at least a first portion of the plurality of droplets to determine individual volumes of droplets in the first portion of the plurality of droplets; analyzing at least a second portion of the plurality of droplets to determine a number of droplets in the second portion of the plurality of droplets that contain the analyte molecule; and using individual volumes of the droplets in the first portion of the plurality of droplets and the number of droplets in the second portion of the plurality of droplets that contain the analyte molecule to determine the concentration of the analyte molecule in the sample.Type: GrantFiled: February 5, 2020Date of Patent: August 2, 2022Assignee: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Bryant S. Fujimoto, Alexander R. Gansen, Gloria S. Yen, Robert M. Lorenz
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Patent number: 11365943Abstract: A baffled ram accelerator system includes a ram accelerator tube with an inner surface and an outer surface and a plurality of baffles disposed on the inner surface. The plurality of baffles forms a sequential series of propellant chambers along the longitudinal axis of the ram accelerator tube. An accelerator gun is also disposed on an input end of the ram accelerator tube, and the accelerator gun is positioned to fire a projectile into the ram accelerator tube.Type: GrantFiled: September 16, 2020Date of Patent: June 21, 2022Assignee: University of Washington through its Center for CommercializationInventors: Carl Knowlen, Adam P. Bruckner, Andrew J. Higgins, Viggo Hansen
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Patent number: 11324817Abstract: Compositions and methods are provided that enable activation of innate immune responses through RIG-I like receptor signaling. The compositions and methods incorporate synthetic nucleic acid pathogen associated molecular patterns (PAMPs) that comprise elements initially characterized in, and derived from, the hepatitis C virus genome.Type: GrantFiled: October 7, 2019Date of Patent: May 10, 2022Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Michael J. Gale, Jr., Gretja Schnell, Yueh-Ming Loo
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Patent number: 11330170Abstract: Methods and systems for acquiring and/or projecting images from and/or to a target area are provided. Such a method or system can include an optical fiber assembly which may be driven to scan the target area in a scan pattern. The optical fiber assembly may provide multiple effective light sources (e.g., via a plurality of optical fibers) that are axially staggered with respect to an optical system located between the optical fiber and the target area. The optical system may be operable to focus and/or redirect the light from the multiple light sources onto separate focal planes. A composite image may be generated based on light reflected from and/or projected onto the separate focal planes. The composite image may have an extended depth of focus or field spanning over a distance between the separate focal planes while maintaining or improving image resolution.Type: GrantFiled: December 10, 2019Date of Patent: May 10, 2022Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Eric J. Seibel, Brian T. Schowengerdt
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Patent number: 11299730Abstract: 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: October 28, 2019Date of Patent: April 12, 2022Assignee: 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: 20220097043Abstract: Devices, systems and apparatuses for the discretization and manipulation of sample volumes are provided. Related methods are also provided.Type: ApplicationFiled: November 23, 2021Publication date: March 31, 2022Applicant: University of Washington through its Center for CommercializationInventors: Daniel T. Chiu, Thomas Schneider, Jason E. Kreutz
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Publication number: 20220082566Abstract: The present disclosure provides encoded chromophoric polymer particles that are capable of, for example, optical and/or biomolecular encoding of analytes. The present disclosure also provides suspensions comprising a plurality of encoded chromophoric polymer particles. The present disclosure also provides methods of using the encoded chromophoric polymer particles and systems for performing multiplex analysis with encoded chromophoric polymer particles.Type: ApplicationFiled: November 30, 2021Publication date: March 17, 2022Applicant: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATIONInventors: Daniel T. Chiu, Changfeng Wu, Jiangbo Yu