Involving Nucleic Acid Patents (Class 435/6.1)
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Patent number: 12043828Abstract: The disclosure provides for methods to form compact cross-linked polynucleotide/protein structures that can then be labeled using a barcoded oligonucleotide array in order to reconstruct physical linkage and/or genomic proximity (and phase) of polynucleotide fragments.Type: GrantFiled: July 12, 2021Date of Patent: July 23, 2024Assignee: The Regents of the University of CaliforniaInventors: Daniel Rokhsar, Richard E. Green, Jr.
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Patent number: 12043832Abstract: Among the various aspects of the present disclosure is the provision of compositions and methods for selectively reducing pathogenic isoforms (e.g., DNAJB6) in a subject having a neuromuscular disorder. An aspect of the present disclosure provides for selectively reducing DNAJB6 in a subject having a neuromuscular disorder (e.g., limb-girdle muscular dystrophy D1 (LGMD-D1)) comprising administering an amount of a DNAJB6-targeting antisense oligonucleotide (ASO) sufficient to reduce the expression of DNAJB6 compared to the subject prior to being administered the DNAJB6-targeting ASO.Type: GrantFiled: September 16, 2022Date of Patent: July 23, 2024Assignee: Washington UniversityInventors: Andrew Findlay, Conrad Weihl
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Patent number: 12037636Abstract: The invention relates to new methods for synthesising polynucleotide molecules according to a predefined nucleotide sequence. The invention also relates to methods for the assembly of synthetic polynucleotides following synthesis, as well as systems and kits for performing the synthesis and/or assembly methods.Type: GrantFiled: July 19, 2019Date of Patent: July 16, 2024Assignee: Oxford Nanopore Technologies PLCInventors: John Milton, Sobia Nayyar, Jan Riedl, Ryosuke Ogaki
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Patent number: 12031175Abstract: The invention generally relates to droplet based digital PCR and methods for analyzing a target nucleic acid using the same. In certain embodiments, methods of the invention involve forming sample droplets containing, on average, a single target nucleic acid, amplifying the target in the droplets, excluding droplets containing amplicon from the target and amplicon from a variant of the target, and analyzing target amplicons.Type: GrantFiled: November 20, 2023Date of Patent: July 9, 2024Assignee: Bio-Rad Laboratories, Inc.Inventors: Jonathan William Larson, Qun Zhong, Darren Roy Link
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Patent number: 12031133Abstract: The invention relates to a double-stranded ribonucleic acid (dsRNA) targeting a G-alpha q subunit (GNAQ) of a heterotrimeric G gene, and methods of using the dsRNA to inhibit expression of GNAQ.Type: GrantFiled: February 9, 2021Date of Patent: July 9, 2024Assignee: Alnylam Pharmaceuticals, Inc.Inventors: Jared Gollob, Gregory Hinkle, Ivanka Toudjarska, David Bumcrot
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Patent number: 12023673Abstract: The present disclosure relates to devices and methods for the detection and/or sorting of nucleic acids. Further disclosed are methods for device fabrication.Type: GrantFiled: March 12, 2021Date of Patent: July 2, 2024Assignee: The Board of Trustees of The University of AlabamaInventor: Qiang Huang
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Patent number: 12018259Abstract: The present disclosure provides methods of treating subjects having a liver disease, and methods of identifying subjects having an increased risk of developing liver disease.Type: GrantFiled: December 22, 2021Date of Patent: June 25, 2024Assignee: Regeneron Pharmaceuticals, Inc.Inventors: Niek Verweij, Luca Andrea Lotta, Aris Baras, Mary Haas, Jonas Nielsen, Olukayode Sosina, Adam Locke
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Patent number: 12018334Abstract: The present invention features a method and kit for isolating microvesicles or extracting microvesicle nucleic acids from a biological sample by using a control particle. The present invention provides control particles that are viruses or virus-like particles, such as bacteriophages, that contain control nucleic acids that can be detected to assess the accuracy, reliability, and efficiency of the microvesicle isolation or nucleic acid extraction steps. The methods described herein may further comprise the analysis of the presence, absence, or level of at least one biomarker associated with a disease or medical condition for diagnosing, prognosing, or monitoring the disease or medical condition.Type: GrantFiled: August 25, 2021Date of Patent: June 25, 2024Assignee: Exosome Diagnostics, Inc.Inventors: Mikkel Noerholm, Susan Belzer, Charlotte Romain, Johan Karl Olov Skog, Leileata M. Russo, Wayne Comper
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Patent number: 12018329Abstract: Embodiments of this invention provide methods, systems, and apparatus for determining whether a fetal chromosomal aneuploidy exists from a biological sample obtained from a pregnant female. Nucleic acid molecules of the biological sample are sequenced, such that a fraction of the genome is sequenced. Respective amounts of a clinically-relevant chromosome and of background chromosomes are determined from results of the sequencing. The determination of the relative amounts may count sequences of only certain length. A parameter derived from these amounts (e.g. a ratio) is compared to one or more cutoff values, thereby determining a classification of whether a fetal chromosomal aneuploidy exists. Prior to sequencing, the biological sample may be enriched for DNA fragments of a particular sizes.Type: GrantFiled: March 23, 2011Date of Patent: June 25, 2024Assignee: The Chinese University of Hong KongInventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan
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Patent number: 12018323Abstract: Described herein are methods useful for incorporating one or more adaptors and/or nucleotide tag(s) and/or barcode nucleotide sequence(s) one, or typically more, target nucleotide sequences. In particular embodiments, nucleic acid fragments having adaptors, e.g., suitable for use in high-throughput DNA sequencing are generated. In other embodiments, information about a reaction mixture is encoded into a reaction product. Also described herein are methods and kits useful for amplifying one or more target nucleic acids in preparation for applications such as bidirectional nucleic acid sequencing. In particular embodiments, methods of the invention entail additionally carrying out bidirectional DNA sequencing. Also described herein are methods for encoding and detecting and/or quantifying alleles by primer extension.Type: GrantFiled: September 20, 2021Date of Patent: June 25, 2024Assignee: FLUIDIGM CORPORATIONInventors: Megan Anderson, Peilin Chen, Brian Fowler, Robert C. Jones, Fiona Kaper, Ronald Lebofsky, Andrew May
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Patent number: 12018044Abstract: Methods for purifying RNA from a sample, comprising one or more steps of tangential flow filtration, hydroxyapatite chromatography, core bead flow-through chromatography, or any combinations thereof. These techniques are useful individually, but show very high efficiency when used in combination, or when performed in particular orders. The methods can purify RNA in a highly efficient manner without unduly compromising potency or stability, to provide compositions in which RNA is substantially cleared of contaminants. Moreover, they can be performed without the need for organic solvents.Type: GrantFiled: January 25, 2021Date of Patent: June 25, 2024Assignee: GLAXOSMITHKLINE BIOLOGICALS SAInventors: Francesco Berlanda Scorza, Yingxia Wen, Andrew Geall, Frederick Porter
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Patent number: 12000827Abstract: The present disclosure provides a system comprising a communication interface and computer for assigning a label to the biomolecule fingerprint, wherein the label corresponds to a biological state. The present disclosure also provides a sensor arrays for detecting biomolecules and methods of use. In some embodiments, the sensor arrays are capable of determining a disease state in a subject.Type: GrantFiled: December 27, 2022Date of Patent: June 4, 2024Assignee: THE BRIGHAM AND WOMEN'S HOSPITAL, INC.Inventors: Omid Farokhzad, Morteza Mahmoudi, Claudia Corbo
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Patent number: 11999948Abstract: Provided are methods of producing size-selected nucleic acid libraries. The methods include contacting a nucleic acid sample and a nucleic acid binding reagent including an affinity tag, under conditions in which nucleic acids of less than a desired length are substantially bound to the nucleic acid binding reagent and nucleic acids of the desired length are substantially not bound to the nucleic acid binding reagent. The conditions include the duration of the contacting, the concentration of the nucleic acid binding reagent, or both. The methods further include separating, using the affinity tag, the nucleic acids of less than the desired length bound to the nucleic acid binding reagent from the nucleic acids of the desired length not bound to the nucleic acid binding reagent, to produce a size-selected nucleic acid library. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure, are also provided.Type: GrantFiled: May 3, 2018Date of Patent: June 4, 2024Assignee: The Regents of the University of CaliforniaInventors: Hugh E. Olsen, Miten Jain, Mark A. Akeson
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Patent number: 11999999Abstract: Disclosed herein, inter alia, are compounds, compositions, and methods of use thereof in the sequencing of a nucleic acid.Type: GrantFiled: July 12, 2021Date of Patent: June 4, 2024Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORKInventors: Jingyue Ju, Xiaoxu Li, Xin Chen, Zengmin Li, Shiv Kumar, Shundi Shi, Cheng Guo, Jianyi Ren, Min-Kang Hsieh, Minchen Chien, Chuanjuan Tao, Ece Erturk, Sergey Kalachikov, James J. Russo
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Patent number: 11993801Abstract: Disclosed herein include methods and compositions for nucleic acid synthesis using a terminal deoxynucleotidyl transferase with deoxyribonucleotide trisphosphates each comprising a modified base with a photocleavable carbon chain moiety that enables single incorporations when present.Type: GrantFiled: July 20, 2021Date of Patent: May 28, 2024Assignees: Illumina Singapore Pte. Ltd., Nanyang Technological UniversityInventors: Pin Koon Ee, Yin Nah Teo, Shunsuke Chiba
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Patent number: 11987851Abstract: The present disclosure relates to oligonucleotide sequences for amplification primers and their use in performing nucleic acid amplifications of HCV, in particular regions that encode the NS3 polypeptide. In some embodiments the primers are used in nested PCR methods for the detection or sequencing of HCV NS3. The oligonucleotide sequences are also provided assembled as kits that can be used to amplify and detect or sequence HCV NS3.Type: GrantFiled: March 17, 2021Date of Patent: May 21, 2024Assignee: Siemens Healthcare Diagnostics Inc.Inventors: Arejas Uzgiris, Sunil Pandit, Lance Palmer
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Patent number: 11986827Abstract: A method includes flowing a first fluid through a first channel of a microfluidic apparatus and flowing a second fluid through a second channel of the microfluidic apparatus. The first fluid comprises biological material and a matrix material and is immiscible with the second fluid. The first and second fluids are combined at a junction to form droplets of the first fluid dispersed in the second fluid in a third channel. Multiple exposures of a droplet in the third channel are captured in a single image, comprising: illuminating a region of the third channel with multiple successive illumination pulses during a single frame of the imaging device; identifying the droplet and determining a velocity or a size of the droplet based on an analysis of the captured exposures; and controlling the flow of the first fluid or second fluid to obtain droplets of a target size or velocity.Type: GrantFiled: October 11, 2023Date of Patent: May 21, 2024Assignee: Xilis, Inc.Inventors: Bradley Scott Thomas, Timothy A. Miller, David Stafford
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Patent number: 11987848Abstract: A method of processing a fecal sample from a human subject comprising combining a first portion of a collected fecal sample with a stabilizing buffer that maintains DNA integrity in a fecal sample, and combining a second portion of the sample with a solution that prevents denaturation or degradation of blood proteins found in a fecal sample. Embodiments comprise testing DNA extracted from the first portion of the fecal sample for the presence of a human DNA, and testing the second portion of the fecal sample for the presence of human blood.Type: GrantFiled: March 7, 2023Date of Patent: May 21, 2024Assignee: Exact Sciences CorporationInventor: Joost Louwagie
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Patent number: 11987815Abstract: The invention provides methods for reprogramming somatic cells to generate multipotent or pluripotent cells. Such methods are useful for a variety of purposes, including treating or preventing a medical condition in an individual. The invention further provides methods for identifying an agent that reprograms somatic cells to a less differentiated state.Type: GrantFiled: October 28, 2019Date of Patent: May 21, 2024Assignee: Whitehead Institute for Biomedical ResearchInventors: Rudolf Jaenisch, Konrad Hochedlinger
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Patent number: 11981898Abstract: The present disclosure provides compositions and methods for targeted insertion of a gene of interest in the genome of a cell using single-stranded DNA or double-stranded DNA with 3 overhang. Also provided are methods of generating single-stranded DNA or double-stranded DNA with 3? over-hang that can be used for targeted insertion.Type: GrantFiled: June 18, 2018Date of Patent: May 14, 2024Assignee: APPLIED STEMCELL, INC.Inventors: Lingjie Kong, Alfonso Farruggio, Andrew Hilmer, Padmaja Tummala, Ruby Yanru Tsai
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Patent number: 11981961Abstract: Methods for constructing consecutively connected copies of nucleic acid molecules are disclosed. Consecutively connected copies of nucleic acid molecules can be used to perform sequencing of the same nucleic acid molecules several times, improving overall accuracy of sequencing. Connected copies of nucleic acid molecules can be constructed by circularizing nucleic acid molecules, performing rolling circle amplification and debranching with nicking and polymerases comprising 5?-3? exonuclease and/or flap endonuclease activity.Type: GrantFiled: January 21, 2018Date of Patent: May 14, 2024Assignee: Vastogen, Inc.Inventor: Dimitra Tsavachidou
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Patent number: 11981896Abstract: Compositions of matter comprising RNA silencing molecules capable of mediating cleavage of p21 mRNA are disclosed. Methods of eradicating senescent cells or cancer cells, as well as methods of treating senescence-associated diseases or disorders, cancer, and fibrotic diseases and disorders are also disclosed.Type: GrantFiled: June 28, 2023Date of Patent: May 14, 2024Assignee: 1E Therapeutics Ltd.Inventors: Noam Pilpel, Yossi Ovadya, Dina Raichlin, Etti Katz-Kadosh, Alaa Knany, Ella Gillis, Noam Borovsky, Anastasia Shapiro, Ido Bachelet
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Patent number: 11976322Abstract: 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: GrantFiled: September 14, 2018Date of Patent: May 7, 2024Assignee: ILLUMINA, INC.Inventors: Jeffrey G. Mandell, Kevin L. Gunderson, Michael Gregory Keehan, Erin Christine Garcia
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Patent number: 11977040Abstract: Certain disclosed methods include: transmitting an excitation signal into the MUT and transmitting a reference signal to a set of magnitude and phase (M/P) detectors; receiving the response signal; separately comparing a magnitude and phase for each of the excitation signal and the reference signal with corresponding detection ranges for a first one of the M/P detectors; separately comparing a magnitude and phase for each of the response signal and the reference signal with corresponding detection ranges for a second one of the M/P detectors; iteratively adjusting the excitation signal until the response signal has both a magnitude and a phase within the corresponding detection ranges for the second M/P detector; and iteratively adjusting the reference signal until the reference signal has both a magnitude and a phase within the corresponding detection ranges for the first and the second M/P detectors.Type: GrantFiled: February 15, 2023Date of Patent: May 7, 2024Assignee: TRANSTECH SYSTEMS, INC.Inventors: Adam D. Blot, Manfred Geier, Andrew J. Westcott
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Patent number: 11970734Abstract: 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: GrantFiled: May 8, 2020Date of Patent: April 30, 2024Assignee: Illumina, Inc.Inventors: Kevin L Gunderson, Jeffrey G. Mandell
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Patent number: 11970746Abstract: A method of processing a fecal sample from a human subject comprising combining a first portion of a collected fecal sample with a stabilizing buffer, combining a second portion of the sample with a solution that prevents denaturation or degradation of blood proteins found in a fecal sample. Embodiments comprise testing nucleic acid extracted from the first portion of the fecal sample for an amount of a human nucleic acid, and testing the second portion of the fecal sample for the presence of human blood.Type: GrantFiled: March 7, 2023Date of Patent: April 30, 2024Assignee: Exact Sciences CorporationInventor: Joost Louwagie
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Patent number: 11971404Abstract: The present disclosure provides a system comprising a communication interface and computer for assigning a label to the biomolecule fingerprint, wherein the label corresponds to a biological state. The present disclosure also provides a sensor arrays for detecting biomolecules and methods of use. In some embodiments, the sensor arrays are capable of determining a disease state in a subject.Type: GrantFiled: December 27, 2022Date of Patent: April 30, 2024Assignee: THE BRIGHAM AND WOMEN'S HOSPITAL, INC.Inventors: Omid Farokhzad, Morteza Mahmoudi, Claudia Corbo
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Patent number: 11965162Abstract: In one aspect, compositions are provided for the early diagnosis and treatment of pancreatic ductal adenocarcinoma and include microRNAs, e.g. miR-21 and inhibitors thereof. The treatment compositions can be useful for early detection, and for intercepting developing premalignant pancreatic lesions and other KRAS-driven premalignancies.Type: GrantFiled: April 16, 2021Date of Patent: April 23, 2024Assignee: The Johns Hopkins UniversityInventors: Elizabeth A. Jaffee, Nina Chu, Jacquelyn Winifred Zimmerman
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Patent number: 11965901Abstract: A management system including a processor, the processor is configured to acquire an image obtained by imaging an outer surface of each of plural sample containers and a boundary container, the sample container containing a sample and in which subject information of a subject from whom the sample is collected is given to the outer surface, the boundary container in which group boundary information indicating a boundary between plural groups of subjects is given to the outer surface, recognize the subject information and the group boundary information based on the image, and associate a test result related to the sample contained in each of the sample containers with a test order which includes the subject information and in which the group is divided corresponding to the group boundary information, based on a result of the recognition and the test order.Type: GrantFiled: July 12, 2021Date of Patent: April 23, 2024Assignee: FUJIFILM CORPORATIONInventors: Yoshihiro Seto, Haruyasu Nakatsugawa
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Patent number: 11958888Abstract: Nucleotide sequences including a micro-dystrophin gene are provided. The micro-dystrophin genes may be operatively linked to a regulatory cassette. Methods of treating a subject having, or at risk of developing, muscular dystrophy, sarcopenia, heart disease, or cachexia are also provided. The methods may include administering a pharmaceutical composition including the micro-dystrophin gene and a delivery vehicle to a subject. Further, the methods may include administering the pharmaceutical composition a subject having Duchenne muscular dystrophy or Becker muscular dystrophy.Type: GrantFiled: October 4, 2019Date of Patent: April 16, 2024Assignee: University of WashingtonInventors: Jeffrey S. Chamberlain, Julian Ramos, Stephen D. Hauschka
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Patent number: 11959143Abstract: Provided herein are methods for miRNA profiling for the diagnosis, prognosis, and management of melanoma and differentiation of melanoma from nevi.Type: GrantFiled: November 24, 2020Date of Patent: April 16, 2024Assignee: Quest Diagnostics Investments LLCInventors: Kevin Qu, Anthony Sferruzza, Ke Zhang, Yan Liu, Renius Owen
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Patent number: 11959126Abstract: The present technology provides for an apparatus for detecting polynucleotides in samples, particularly from biological samples. The technology more particularly relates to microfluidic systems that carry out PCR on nucleotides of interest within microfluidic channels, and detect those nucleotides. The apparatus includes a microfluidic cartridge that is configured to accept a plurality of samples, and which can carry out PCR on each sample individually, or a group of, or all of the plurality of samples simultaneously.Type: GrantFiled: October 7, 2021Date of Patent: April 16, 2024Assignee: Handylab, Inc.Inventors: Kalyan Handique, Sundaresh N. Brahmasandra, Karthik Ganesan, Jeff Williams
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Patent number: 11957704Abstract: The present disclosure provides methods of treating a subject having metabolic disorders and/or cardiovascular diseases, methods of identifying subjects having an increased risk of developing a metabolic disorder and/or a cardiovascular disease, and methods of detecting human Inhibin Subunit Beta E variant nucleic acid molecules and variant polypeptides.Type: GrantFiled: August 31, 2022Date of Patent: April 16, 2024Assignee: Regeneron Pharmaceuticals, Inc.Inventors: Luca Andrea Lotta, Parsa Akbari, Olukayode Sosina, Manuel Allen Revez Ferreira, Aris Baras
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Patent number: 11953464Abstract: A device for base calling is provided. The device includes a receptacle configured to hold a biosensor having a sample surface holding a plurality of clusters during a sequence of sampling events, an array of sensors sensing information from clusters disposed in corresponding pixel areas of the sample surface during the sampling events and generate sequences of pixel signals and a communication port configured to output the sequences of pixel signals. The device also includes a signal processor coupled to the communication port and configured to receive and process at least one pixel signal in the sequences of pixel signals that mixes light gathered from at least two clusters in a corresponding pixel area, and to base call each of the at least two clusters using the at least one pixel signal.Type: GrantFiled: June 2, 2022Date of Patent: April 9, 2024Assignee: Illumina, Inc.Inventors: Dietrich Dehlinger, Ali Agah, Tracy Helen Fung, Emrah Kostem
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Patent number: 11952616Abstract: The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.Type: GrantFiled: December 5, 2022Date of Patent: April 9, 2024Assignee: Guardant Health, Inc.Inventors: Andrew Kennedy, Stefanie Ann Ward Mortimer, Helmy Eltoukhy, AmirAli Talasaz, Diana Abdueva
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Patent number: 11952630Abstract: There is disclosed a composition of an aqueous solution comprising, consisting or consisting essentially of a flap endonuclease, a bulking agent and an organic buffer, wherein the aqueous solution has an inorganic salt concentration of 5 mM or less and wherein the composition is substantially free of glycerol.Type: GrantFiled: May 17, 2022Date of Patent: April 9, 2024Assignee: GEN-PROBE INCORPORATEDInventors: Patrick Peterson, Tony Luu, Matthias Jost
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Patent number: 11944676Abstract: Generally, the inventive technology relates to novel strategies for disease control in animal systems. Specifically, the inventive technology relates to novel methods, systems and compositions for the biocontrol of pathogens in aquatic systems. Specifically, the invention may comprise novel techniques, systems, and methods for the biocontrol of disease-transmitting pathogens affecting shrimp in aquaculture systems.Type: GrantFiled: August 7, 2018Date of Patent: April 2, 2024Assignee: Pebble Labs Inc.Inventors: Richard Sayre, Tatiana Vinogradova-Shah, Elena Sineva
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Patent number: 11946929Abstract: The invention generally relates to performing sandwich assays in droplets. In certain embodiments, the invention provides methods for detecting a target analyte that involve forming a compartmentalized portion of fluid including a portion of a sample suspected of containing a target analyte and a sample identifier, a first binding agent having a target identifier, and a second binding agent specific to the target analyte under conditions that produce a complex of the first and second binding agents with the target analyte, separating the complexes, and detecting the complexes, thereby detecting the target analyte.Type: GrantFiled: July 18, 2023Date of Patent: April 2, 2024Assignee: Bio-Rad Laboratories, Inc.Inventors: Michael L. Samuels, Darren Roy Link
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Patent number: 11941534Abstract: A system is provided that includes a bit vector-based distance counter circuitry configured to generate one or more bit vectors encoded with information about potential matches and edits between a read and a reference genome, wherein the read comprises an encoding of a fragment of deoxyribonucleic acid (DNA) encoded via bases G, A, T, C. The system further includes a bit vector-based traceback circuitry configured to divide the reference genome into one or more windows and to use the plurality of bit vectors to generate a traceback output for each of the one or more windows, wherein the traceback output comprises a match, a substitution, an insert, a delete, or a combination thereof, between the read and the one or more windows.Type: GrantFiled: December 28, 2019Date of Patent: March 26, 2024Assignee: Intel CorporationInventors: Gurpreet Singh Kalsi, Anant V. Nori, Christopher Justin Hughes, Sreenivas Subramoney, Damla Senol
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Patent number: 11939622Abstract: Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.Type: GrantFiled: July 21, 2020Date of Patent: March 26, 2024Assignee: Becton, Dickinson and CompanyInventor: Hye-Won Song
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Patent number: 11939628Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.Type: GrantFiled: February 22, 2021Date of Patent: March 26, 2024Assignee: New England Biolabs, Inc.Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
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Patent number: 11938187Abstract: The syntheses of two phosphoramidite building blocks based on BNSF and BNSMB structures are disclosed. Furthermore, some common molecular intermediates have been designed and linked to the central biphenyl core of the two molecules, resulting in a versatile and cost-effective design. These compounds can be effectively introduced to DNA oligonucleotides via the well-established standard cyanoethylphosphoramidite chemistry on the nucleic acid synthesizer. Fragmentation of these BNSF- and BNSMB-functionalized DNA strands is achieved by both one-photon and two-photon photolysis of photoliable bonds of [2-(2-nitrophenyl)propoxy]carbonyl groups on BNSF and BNSMB molecules respectively, resulting in two short pieces of single-stranded DNAs.Type: GrantFiled: June 10, 2021Date of Patent: March 26, 2024Assignee: CITY UNIVERSITY OF HONG KONGInventors: Peggy Pik Kwan Lo, Ling Sum Liu, Dick Yan Tam
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Patent number: 11932846Abstract: A system for expressing a chloramphenicol split protein is disclosed. Uses thereof are also disclosed.Type: GrantFiled: August 8, 2018Date of Patent: March 19, 2024Assignee: Technology Innovation Momentum Fund (Israel) Limited PartnershipInventor: Gali Prag
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Patent number: 11931737Abstract: Disclosed herein are platforms, systems, and methods including a cell culture system that includes a cell culture container comprising a cell culture, the cell culture receiving input cells, a cell imaging subsystem configured to acquire images of the cell culture, a computing subsystem configured to perform a cell culture process on the cell culture according to the images acquired by the cell imaging subsystem, and a cell editing subsystem configured to edit the cell culture to produce output cell products according to the cell culture process.Type: GrantFiled: September 7, 2022Date of Patent: March 19, 2024Assignee: CELLINO BIOTECH, INC.Inventors: Matthias Wagner, Suvi Aivio, Mariangela Amenduni, Catherine Pilsmaker, Arnaldo Pereira, Ananya Zutshi, Ozge Whiting, George Harb, Steven Nagle, Anthia Toure, Matthew Sullivan, Maya Berlin-Udi, Lukas Vasadi, Alexander Stange, Sangkyun Lee, Stefanie Morgan, Nick Seay, Scott Luro
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Patent number: 11926824Abstract: Methods for diagnosis and treatment of cancers by use of exosomes comprising miRNAs and precursors thereof. For example, in some aspects, a cancer may be diagnosed or evaluated by determining the miRNA content of exosomes in a sample from a subject or by detecting miRNA processing in exosomes.Type: GrantFiled: March 23, 2020Date of Patent: March 12, 2024Assignees: Board of Regents, The University of Texas System, Beth Israel Deaconess Medical Center, Inc.Inventors: Raghu Kalluri, Sónia Melo
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Patent number: 11920201Abstract: Provided herein are methods of determining one or more modification(s) of the nucleic acid sequence of at least one nucleic acid and at least one epigenetic alteration of the at least one nucleic acid in a sample of a subject. The sample is derived from a body fluid of the subject. The methods link the one or more modification(s) to a specific cell type.Type: GrantFiled: January 23, 2018Date of Patent: March 5, 2024Assignee: Siemens Healthcare GMBHInventors: Carsten Dietrich, Andreas Emanuel Posch
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Patent number: 11920151Abstract: Provided are: a composition for DNA double-strand breaks (DSBs), comprising (1) a cytosine deaminase and an inactivated target-specific endonuclease, (2) a guide RNA, and (3) a uracil-specific excision reagent (USER); a method for producing DNA double-strand breaks by means of a cytosine deaminase using the composition; a method for analyzing a DNA nucleic acid sequence to which base editing has been introduced by means of a cytosine deaminase; and a method for identifying (or measuring or detecting) base editing, base editing efficiency at an on-target site, an off-target site, and/or target specificity by means of a cytosine deaminase.Type: GrantFiled: September 13, 2017Date of Patent: March 5, 2024Assignees: TOOLGEN INCORPORATED, SEOUL NATIONAL UNIVERSITY R&Db FOUNDATION, INSTITUTE FOR BASIC SCIENCEInventor: Daesik Kim
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Patent number: 11921103Abstract: A sequence of polymer units in a polymer (3), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore (1), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units (4). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units.Type: GrantFiled: June 21, 2019Date of Patent: March 5, 2024Assignee: Oxford Nanopore Technologies PLCInventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, James Anthony Clarke, Andrew John Heron
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Patent number: 11919006Abstract: A generic point of care based portable device and method thereof as a platform technology for detecting pathogenic infection via nucleic acid based testing achieving sample-to-result integration, comprising the following interconnected stand-alone modules: a thermal unit for executing piece-wise isothermal reactions in a pre-programmable concomitant fashion without necessitating in-between operative intervention; a colorimetric detection unit seamlessly interfaced with smartphone-app based analytics for detecting the target analyte.Type: GrantFiled: March 16, 2021Date of Patent: March 5, 2024Assignee: INDIAN INSTITUTE OF TECHNOLOGY, KHARAGPURInventors: Nandita Kedia, Sujay Kumar Biswas, Saptarshi Banerjee, Aditya Bandopadhyay, Arindam Mondal, Suman Chakraborty
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Patent number: 11920181Abstract: Some aspects of this disclosure provide strategies, methods, and reagents for determining nuclease target site preferences and specificity of site-specific endonucleases. Some methods provided herein utilize a novel “one-cut” strategy for screening a library of concatemers comprising repeat units of candidate nuclease target sites and constant insert regions to identify library members that can been cut by a nuclease of interest via sequencing of an intact target site adjacent and identical to a cut target site. Some aspects of this disclosure provide strategies, methods, and reagents for selecting a site-specific endonuclease based on determining its target site preferences and specificity. Methods and reagents for determining target site preference and specificity are also provided.Type: GrantFiled: January 27, 2021Date of Patent: March 5, 2024Assignee: President and Fellows of Harvard CollegeInventors: David R. Liu, Vikram Pattanayak