Patents Examined by Narayan K Bhat
  • Single-cell RNA sequencing using click-chemistry
    Patent number: 11519027
    Abstract: The present disclosure relates to a method of sequencing nascent RNA in a cell. In some embodiments, the nascent RNA is conjugated to DNA using copper-catalyzed azide-alkyne cycloaddition (CuAAC). Methods of the present disclosure can be used to generate genomic libraries of a cell and measure gene expression and enhancer and/or super-enhancer activity.
    Type: Grant
    Filed: March 29, 2019
    Date of Patent: December 6, 2022
    Assignee: Massachusetts Institute of Technology
    Inventors: Phillip A. Sharp, Dig Mahat
  • Single molecule detection or quantification using DNA nanotechnology
    Patent number: 11513076
    Abstract: The present invention relates to a method and a DNA nanostructure for detecting a target structure. In particular, the present invention relates to a DNA nanostructure, which ensures a preferably linear dependence on the number of marker molecules and the measurement signal regardless of the physical arrangement of a plurality of such DNA nanostructures by virtue of the skilled selection of the shape of the DNA nanostructure and the placement of the marker molecules attached to it. The invention additionally relates to the use of said DNA nanostructures and other nanoreporters, preferably in combination with adapters which bind specifically to target molecules, in a method for quantifying a plurality of target molecules, preferably in a simultaneous manner, using a multiplex method.
    Type: Grant
    Filed: June 14, 2017
    Date of Patent: November 29, 2022
    Assignee: LUDWIG-MAXIMILIANS-UNIVERSITÄT MÜNCHEN
    Inventors: Heinrich Grabmayr, Johannes Benedikt Woehrstein
  • Mitigating adverse impacts of detection systems on nucleic acids and other biological analytes
    Patent number: 11499189
    Abstract: A method for sequencing a population of nucleic acids, which includes (a) binding the population of nucleic acids with a fractionally labeled mixture of nucleotides, thereby forming a fractionally labeled population of nucleic acids, wherein the mixture includes nucleotide cognates for a common base type in the templates, and wherein a fraction of the nucleotide cognates for the common base type in the mixture are exogenously labeled nucleotides that produce a signal that is not produced by other nucleotide cognates for the common base type in the mixture; (b) detecting the signal from the fractionally labeled population of nucleic acids; and (c) repeating (a) and (b) using a second mixture of the fractionally labeled nucleotides, wherein the fraction of the exogenously labeled nucleotides is higher in the second mixture.
    Type: Grant
    Filed: February 6, 2020
    Date of Patent: November 15, 2022
    Assignee: PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
    Inventor: Min-Jui Richard Shen
  • Nucleotide sequence generation by barcode bead-colocalization in partitions
    Patent number: 11479816
    Abstract: Comparison of common sequencing reads from sequencing based on partition-based barcoding can be used to improve sequencing results. Increased loading of barcodes per partition can also improve sequencing results.
    Type: Grant
    Filed: August 20, 2019
    Date of Patent: October 25, 2022
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Ronald Lebofsky, Andrew Kohlway, Jennifer Chew, Zachary Burkett, Man Cheng
  • Methods, carrier assemblies, and systems for imaging samples for biological or chemical analysis
    Patent number: 11479808
    Abstract: Method includes positioning a first carrier assembly on a system stage. The carrier assembly includes a support frame having an inner frame edge that defines a window of the support frame. The first carrier assembly includes a first substrate that is positioned within the window and surrounded by the inner frame edge. The first substrate has a sample thereon. The method includes detecting optical signals from the sample of the first substrate. The method also includes replacing the first carrier assembly on the system stage with a second carrier assembly on the system stage. The second carrier assembly includes the support frame and an adapter plate held by the support frame. The second carrier assembly has a second substrate held by the adapter plate that has a sample thereon. The method also includes detecting optical signals from the sample of the second substrate.
    Type: Grant
    Filed: March 5, 2020
    Date of Patent: October 25, 2022
    Assignee: ILLUMINA CAMBRIDGE LIMITED
    Inventors: Stephen Rawlings, Venkatesh Mysore Nagaraja Rao, Beng Keong Ang, Nitin Udpa
  • Diagnostic applications using nucleic acid fragments
    Patent number: 11479825
    Abstract: Various embodiments are directed to applications (e.g., classification of biological samples) of the analysis of the count, the fragmentation patterns, and size of cell-free nucleic acids, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, such as viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).
    Type: Grant
    Filed: April 24, 2020
    Date of Patent: October 25, 2022
    Assignees: The Chinese University of Hong Kong, GRAIL, Inc.
    Inventors: Yuk-Ming Dennis Lo, Rossa Wai Kwun Chiu, Kwan Chee Chan, Peiyong Jiang, Wai Kei Lam
  • Metal nanoshell-coated barcodes
    Patent number: 11473152
    Abstract: The present invention relates to barcodes coated with metal nanoshells and to methods of making the metal nanoshell-coated barcodes. The metal nanoshell-coated barcodes of the present invention have applications in detection systems, including multiplex detection systems.
    Type: Grant
    Filed: February 14, 2014
    Date of Patent: October 18, 2022
    Inventors: Warren Che War Chan, Leo Y. T. Chou, Kun Chen
  • Spatial sequencing of nucleic acids using DNA origami probes
    Patent number: 11473139
    Abstract: A method of sequencing nucleic acids is provided using DNA origami as a barcode for a nucleic acid probe.
    Type: Grant
    Filed: March 26, 2020
    Date of Patent: October 18, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Richard C. Terry, Frederic Vigneault
  • Detection of co-occurring receptor-coding nucleic acid segments
    Patent number: 11466310
    Abstract: Methods for identifying co-occurrence of nucleic acid segments in a nucleic acid sample from a specimen including obtaining a nucleic acid sample from a specimen, determining sequences of first and second nucleic acid segments in nucleic acid fragments of the sample to generate a first and second sets of sequences, generating a first and second sets of probes from the first and second sets of sequences, exposing a detection sample to a member of the first set of probes and a member of the second set of probes, performing a hybridization analysis to determine whether the members of the first and second sets of probes hybridize to the detection sample, and determining whether the first and second nucleic acid segments co-occur in a common cell of the specimen.
    Type: Grant
    Filed: October 21, 2019
    Date of Patent: October 11, 2022
    Assignee: Akoya Biosciences, Inc.
    Inventor: Steven Daniel
  • Methods and systems for characterizing analytes using nanopores
    Patent number: 11466317
    Abstract: Methods of characterizing an analyte using a nanopore. One aspect features methods for characterizing a double-stranded polynucleotide using a nanopore, e.g., without using a hairpin connecting a template and a complement of the double-stranded polynucleotide. Another aspect features methods for characterizing an analyte using a tag-modified nanopore with increased sensitivity and/or higher throughput. Compositions and systems including, e.g., adaptors for attachment to double-stranded polynucleotides and tag-modified nanopores, which can be used in the methods are also provided.
    Type: Grant
    Filed: November 29, 2017
    Date of Patent: October 11, 2022
    Assignee: Oxford Nanopore Technologies PLC
    Inventors: James Clarke, James White, Richard Muscat, Jessica Mary May Knott, Ramiz Iqbal Nathani, Andrew John Heron, Mark John Bruce, Lakmal Nishantha Jayasinghe, Domenico Caprotti, David Jackson Stoddart, Rebecca Victoria Bowen, Christopher James Wright, Paul Richard Moody
  • Multi-Z imaging and dispensing with multi-well devices
    Patent number: 11460405
    Abstract: Provided are methods, devices, assemblies, and systems for dispensing into the wells of a multi-well device and imaging such wells from multiple Z-planes. Multi-Z imaging of the present methods and systems may allow for the detection of wells of a multi-well device that contain a desired number of cells. Also provided are methods, devices, assemblies, and systems for processing cell-containing wells of a multi-well device identified through the use of multi-Z imaging.
    Type: Grant
    Filed: July 20, 2017
    Date of Patent: October 4, 2022
    Assignee: Takara Bio USA, Inc.
    Inventors: Patricio A. Espinoza Vallejos, Syed A. Husain, Chun-Wah Lin, Hermann Hubschle
  • Method for processing polynucleotide-containing samples
    Patent number: 11441171
    Abstract: Methods and systems for processing polynucleotides (e.g., DNA) are disclosed. A processing region includes one or more surfaces (e.g., particle surfaces) modified with ligands that retain polynucleotides under a first set of conditions (e.g., temperature and pH) and release the polynucleotides under a second set of conditions (e.g., higher temperature and/or more basic pH). The processing region can be used to, for example, concentrate polynucleotides of a sample and/or separate inhibitors of amplification reactions from the polynucleotides. Microfluidic devices with a processing region are disclosed.
    Type: Grant
    Filed: March 27, 2020
    Date of Patent: September 13, 2022
    Assignee: HANDYLAB, INC.
    Inventors: Betty Wu, John S. Althaus, Nikhil Phadke, Sundaresh N. Brahmasandra, Kalyan Handique, Aaron Kehrer, Gene Parunak, Cecelia Haley, Ted Springer
  • Methods of detecting modified and unmodified DNA
    Patent number: 11427858
    Abstract: Methods and kits for detecting the presence of at least one target DNA sequence with or without a modification in a DNA molecule are provided.
    Type: Grant
    Filed: July 31, 2018
    Date of Patent: August 30, 2022
    Assignees: TECHNION RESEARCH & DEVELOPMENT FOUNDATION LIMITED, RAMOT AT TEL-AVIV UNIVERSITY LTD.
    Inventors: Amit Meller, Tal Gilboa, Chen Torfstein, Yuval Ebenstein, Elmar Weinhold, Yael Michaeli-Hoch, Assaf Grunwald
  • Compositions and methods for quantifying a nucleic acid sequence in a sample
    Patent number: 11427863
    Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time. These methods are compatible with target oligonucleotides amplified using a NEAR reaction.
    Type: Grant
    Filed: August 9, 2011
    Date of Patent: August 30, 2022
    Assignee: Envirologix Inc.
    Inventor: Stephen A. Judice
  • Method of improved sequencing by strand identification
    Patent number: 11427866
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants, as well as methods of determining copy number of a genetic locus in a sample. Systems and kits for performing methods of the disclosure, as well as compositions produced by or useful in methods of the disclosure are also provided. In some embodiments, methods comprise extending 3? ends of polynucleotides by adding one or more pre-determined nucleotides. In some embodiments, methods comprise use of a strand-tagging sequence.
    Type: Grant
    Filed: May 16, 2017
    Date of Patent: August 30, 2022
    Assignee: ACCURAGEN HOLDINGS LIMITED
    Inventors: Malek Faham, Shengrong Lin, Ling Fung Tang, Yontao Lu, Zhaohui Sun, Yingyu Wang, Li Weng
  • Barcode-free single vesicle multiplexed protein and RNA analysis
    Patent number: 11414699
    Abstract: According to various embodiments, a system and method for characterizing protein and nucleic acid content of a plurality of individual particles. The method includes encapsulating individual particles into compartments also containing analyte specific binding complements with oligonucleotide tags comprising a unique molecular identifier sequence, a sequence to identify the analyte specific binding complement, and a homology domain sequence. Allowing the oligonucleotide tags to hybridize on homology domain to form initial tag pairs, amplifying the tag pairs, using an enzyme to cut at the homology domain, allowing tags to re-hybridize, pooling the compartments, and sequencing. Finally, predicting co-encapsulated analytes by computational identification of clusters based on more frequently found oligonucleotide tag pairs.
    Type: Grant
    Filed: May 15, 2019
    Date of Patent: August 16, 2022
    Assignee: MANTRA BIO, INC.
    Inventors: Terry Alden Gaige, Chi-Chih (Ginny) Kang, Catherine RoseMary Planey, Dragan Sebisanovic
  • Analysis of a polymer
    Patent number: 11401549
    Abstract: A biochemical analysis system analyses polymers by taking measurements of a polymer from a sensor element comprising a nanopore during translocation of the polymer through the nanopore. When a polymer has partially translocated, the series of measurements is analysed using reference data derived from a reference sequence to provide a measure of similarity. Responsive to the measure of similarity, the sensor element may be selectively operated to eject the polymer and thereby make the nanopore available to receive a further polymer. Where the biochemical analysis system comprises an array of sensor elements and is takes measurements from sensor elements selected in a multiplexed manner, responsive to the measure of similarity, the biochemical analysis system ceases taking measurements from the currently selected sensor element and to starts taking measurements from a newly selected sensor element.
    Type: Grant
    Filed: May 12, 2020
    Date of Patent: August 2, 2022
    Assignee: Oxford Nanopore Technologies PLC
    Inventors: Stuart William Reid, Gavin Harper, Clive Gavin Brown, Daniel John Turner, Andrew John Heron, Christopher James Wright
  • Spatially encoded biological assays
    Patent number: 11401545
    Abstract: The present invention provides assays and assay systems for use in spatially encoded biological assays. The invention provides an assay system comprising an assay capable of high levels of multiplexing where reagents are provided to a biological sample in defined spatial patterns; instrumentation capable of controlled delivery of reagents according to the spatial patterns; and a decoding scheme providing a readout that is digital in nature.
    Type: Grant
    Filed: December 20, 2021
    Date of Patent: August 2, 2022
    Assignee: Prognosys Biosciences, Inc.
    Inventor: Mark S. Chee
  • Method and system for recovering products from an emulsion
    Patent number: 11396017
    Abstract: The present invention relates to a method for selecting and recovering products, comprising the following steps: providing an emulsion (6) comprising a plurality of drops (4) contained in a carrier fluid (10), each drop comprising an internal fluid (8), measuring at least one physical parameter for several drops (4) of the emulsion (6), classifying at least some of the drops (4) of the emulsion in a class based on measurements obtained during the measuring step, tagging at least some of the classified drops (4) based on the class of the drop (4), selectively recovering the drop (4) or part of the drop (4) using the tag of the drop or part of the drop (4).
    Type: Grant
    Filed: April 14, 2017
    Date of Patent: July 26, 2022
    Assignee: ECOLE SUPERIEURE DE PHYSIQUE ET DE CHIMIE INDUSTRIELLES DE LA VILLE DE PARIS
    Inventors: Jean Baudry, Jérôme Bibette, Laurent Boitard, Klaus Eyer, Krzysztof Langer
  • Gene chip and gene detection device
    Patent number: 11391749
    Abstract: This disclosure provides a gene chip comprising a substrate and at least one positioning device fixed on an upper surface of the substrate, wherein the at least one positioning device is provided with a receiving cavity for receiving a bead, the receiving cavity being arranged on a surface of the at least one positioning device facing away from the substrate, and a cross-sectional area of the receiving cavity is gradually decreased in a direction toward the upper surface of the substrate. This disclosure further provides a gene detection device comprising the gene chip.
    Type: Grant
    Filed: June 24, 2019
    Date of Patent: July 19, 2022
    Assignee: BOE TECHNOLOGY GROUP CO., LTD.
    Inventors: Song Yang, Ming Zhu, Shiyu Zhang, Jiahui Han, Zheng Fang, Ge Shi, Haijun Niu, Yujie Liu, Yuyao Wang