Patents Examined by David C. Thomas
  • Patent number: 10975416
    Abstract: One or more temperature cycles are applied to the contents of a processing vial closed by an interlocked cap within a thermal cycler. The processing vial and the interlocked cap are transferred from the thermal cycler to a storage compartment within the instrument with a transfer mechanism with a probe engaged with the cap. In the storage compartment, the processing vial and interlocked cap are moved to an access opening in the instrument and are removed from the instrument through the access opening.
    Type: Grant
    Filed: June 22, 2018
    Date of Patent: April 13, 2021
    Inventors: David A. Buse, David Opalsky, Jason F. Rhubottom, Norbert D. Hagen, Jennifer L. Tidd
  • Patent number: 10975422
    Abstract: A system and method for capturing and analyzing a set of cells, comprising: an array including a set of parallel pores, each pore including a chamber including a chamber inlet and a chamber outlet, and configured to hold a single cell, and a pore channel fluidly connected to the chamber outlet; an inlet channel fluidly connected to each chamber inlet of the set of parallel pores; an outlet channel fluidly connected to each pore channel of the set of parallel pores; a set of electrophoresis channels fluidly coupled to the outlet channel, configured to receive a sieving matrix for electrophoretic separation; and a set of electrodes including a first electrode and a second electrode, wherein the set of electrodes is configured to provide an electric field that facilitates electrophoretic analysis of the set of cells.
    Type: Grant
    Filed: July 30, 2018
    Date of Patent: April 13, 2021
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Kalyan Handique, Priyadarshini Gogoi, Saedeh Sepehri Javdani, Yi Zhou
  • Patent number: 10954562
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
    Type: Grant
    Filed: January 27, 2020
    Date of Patent: March 23, 2021
    Assignee: 10X GENOMICS, INC.
    Inventors: Phillip Belgrader, Josephine Harada, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Serge Saxonov, John R. Stuelpnagel
  • Patent number: 10954560
    Abstract: Described herein are cell-based analytic methods, including a method of incorporating nucleic acid sequences into reaction products from a cell population, wherein the nucleic acid sequences are incorporated into the reaction products of each cell individually or in small groups of cells individually. Also described herein is a matrix-type microfluidic device that permits at least two reagents to be delivered separately to each cell or group of cells, as well as primer combinations useful in the method and device.
    Type: Grant
    Filed: December 10, 2018
    Date of Patent: March 23, 2021
    Inventors: Carolyn G. Conant, Tze Howe Charn, Jason A. A. West, Xiaohui Wang
  • Patent number: 10947586
    Abstract: An additive composition used in a loop mediated isothermal amplification (LAMP) reaction for reducing a threshold time for a positive sample includes but not limited to EDTA, EGTA, BSA, DMSO, nonionic surfactants, and polymers, and the additive composition used in LAMP reactions includes at least one of the above mentioned additives and may be any combination use of the additives.
    Type: Grant
    Filed: May 10, 2018
    Date of Patent: March 16, 2021
    Inventors: Junxin Liang, Casthri Krishnamurthy, Shuwen An, Kah Sin Loh, Weishi Zhang
  • Patent number: 10947588
    Abstract: The present invention relates to the technical field of nucleic acid amplification using a Polymerase Chain Reaction (PCR). Specifically, the present invention relates to Polymerase Chain Reaction (PCR) primers and Polymerase Chain Reaction (PCR) nucleic acid amplification mixture and the use thereof in (quantitative) Polymerase Chain Reactions (PCR).
    Type: Grant
    Filed: June 19, 2015
    Date of Patent: March 16, 2021
    Assignee: MULTIPLICOM N.V.
    Inventor: Jurgen Del Favero
  • Patent number: 10940473
    Abstract: Nucleic acid from cells and viruses sampled from a variety of environments may purified and expressed utilizing microfluidic techniques. Individual or small groups of cells or viruses may be isolated in microfluidic chambers by dilution, sorting, and/or segmentation. The isolated cells or viruses may be lysed directly in the microfluidic chamber, and the resulting nucleic acid purified by exposure to affinity beads. Subsequent elution of the purified nucleic acid may be followed by ligation and cell transformation, all within the same microfluidic chip. Cell isolation, lysis, and nucleic acid purification may be performed utilizing a highly parallelized microfluidic architecture to construct gDNA and cDNA libraries.
    Type: Grant
    Filed: April 26, 2019
    Date of Patent: March 9, 2021
    Assignee: California Institute of Technology
    Inventors: Jong Wook Hong, Vincent Studer, W. French Anderson, Stephen R. Quake, Jared Leadbetter
  • Patent number: 10941430
    Abstract: The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subjected to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer.
    Type: Grant
    Filed: January 31, 2020
    Date of Patent: March 9, 2021
    Assignee: President and Fellows of Harvard College
    Inventors: David A. Weitz, Jeremy Agresti, Liang-Yin Chu, Jin-Woong Kim, Amy Rowat, Morten Sommer, Gautam Dantas, George M. Church
  • Patent number: 10934585
    Abstract: Compositions, methods and systems are provided for the loading of extended polymerase-nucleic acid complexes onto substrates. Primed polymerase-template complex comprising a polymerase enzyme and a circular nucleic acid template comprising a double stranded region connected at each end by a single-stranded hairpin region are provides in which the circular nucleic acid template comprises at least one reversible pause point. Nucleic acid synthesis is carried out such that a nascent strand is synthesized up to the reversible stop point producing an extended polymerase-template complex. The extended polymerase-template complex is then attached to a substrate. Such attached complexes can be used for single molecule sequencing in which the nucleic acid synthesis is re-initiated such that nucleic acid synthesis continues past the reversible stop point.
    Type: Grant
    Filed: June 13, 2018
    Date of Patent: March 2, 2021
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Thang Pham, Arunashree Bhamidipati, Kevin Travers, Eric Olivares, Tyson A. Clark, Jonas Korlach
  • Patent number: 10927420
    Abstract: This document provides methods and materials for detecting target nucleic acid. For example, methods and materials for detecting the presence or absence of target nucleic acid, methods and materials for detecting the amount of target nucleic acid present within a sample, kits for detecting the presence or absence of target nucleic acid, kits for detecting the amount of target nucleic acid present within a sample, and methods for making such kits are provided.
    Type: Grant
    Filed: September 28, 2018
    Date of Patent: February 23, 2021
    Assignee: Cascade Biosystems, Inc.
    Inventors: Kenneth D. Smith, Nina Yazvenko, Mariya Smit
  • Patent number: 10927369
    Abstract: Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.
    Type: Grant
    Filed: July 18, 2018
    Date of Patent: February 23, 2021
    Assignee: Gen9, Inc.
    Inventors: Joseph Jacobson, Martin J. Goldberg, Li-Yun A. Kung, Daniel Schindler, Michael E. Hudson
  • Patent number: 10927402
    Abstract: A capsule to store and deliver lyophilized reagents is described. The lyophilized reagent capsule is configured to store a lyophilized reagent for at least five days, and is further configured to deliver a lyophilized reagent to a biological sample. The capsule includes a top, a bottom, and a lyophilized reagent. A method for delivering the lyophilized reagent via the capsule and without the use of pipettes to deliver the lyophilized reagents is described. The capsule may be part of a lyophilized reagent capsule kit.
    Type: Grant
    Filed: April 10, 2018
    Date of Patent: February 23, 2021
    Assignee: STEM Arts Projects, LLC
    Inventors: Abraham Oommen, Heather Piscatelli, Molly Manning, Alyssa Hangman
  • Patent number: 10920270
    Abstract: Methods and compositions are provided for improved nucleic acid amplification assays. In some embodiments, the nucleic acid amplification assay is a tagged amplicon primer extension (TAPE) nucleic acid amplification reaction.
    Type: Grant
    Filed: March 22, 2019
    Date of Patent: February 16, 2021
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Nicholas Heredia, Dianna Maar
  • Patent number: 10900068
    Abstract: The present invention provides methods and systems for the capture and enrichment of target nucleic acids and analysis of the enriched target nucleic acids. In particular, the present invention provides for the enrichment of targeted sequences in a solution based format.
    Type: Grant
    Filed: September 15, 2017
    Date of Patent: January 26, 2021
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Matthew Rodesch, Thomas Albert
  • Patent number: 10894983
    Abstract: Described herein is a method for amplifying a target nucleic acid sequence ta-tC-tV-tC?-tn? comprising a first amplification using a first primer pair with sequence ma-K-pC and ma-K?-pC?, and a subsequent second amplification using a second primer pair with sequence aL-aP-aK and aL?-aP?-aK?, wherein pC is the same sequence as sequence element tC. pC and pC? are 8 to 40 nucleotides in length, K comprises a 3?-terminal sequence k1-k2-s, s is a mismatch sequences preventing PCR bias, ak is the same sequence as sequence element k1, aP-aK hybridize to a contiguous sequence on sequence element ma-K, k1 is 2 to 9 nucleotides in length, aL and aL? can be any sequence, and tV is a variable region within the target nucleic acid sequence. Also described are collections of primer sets for use in the method of the invention.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: January 19, 2021
    Inventors: Julia-Marie Ritter, Volkhard Seitz, Steffen Hennig, Michael Hummel
  • Patent number: 10889851
    Abstract: A method for moving a processing vial between locations of an instrument. The method includes the steps of dispensing a fluid into a processing vial with a disposable pipette tip frictionally fitted onto a probe of a pipettor, stripping the disposable pipette tip from the probe of the pipettor, and then engaging a cap in a frictional fit with the probe of the pipettor. While the cap is engaged in a frictional fit with the probe of the pipettor, coupling the cap to the processing vial to form a cap/vial assembly, where the cap seals the processing vial. The pipettor moves the cap/vial assembly from a first location of an instrument to a second location of the instrument. At the second location of the instrument, the cap/vial assembly is ejected from the probe of the pipettor, thereby depositing the cap/vial assembly at the second location.
    Type: Grant
    Filed: March 25, 2020
    Date of Patent: January 12, 2021
    Assignee: Gen-Probe Incorporated
    Inventors: David A. Buse, Norbert D. Hagen, Byron J. Knight, Tyler Moore, David Opalsky, Anita Prasad, Bruce Richardson
  • Patent number: 10889863
    Abstract: FRET-based analytes detection and related methods and systems are described where a pair of FRET labeled primers and/or oligonucleotides are used that are specific for target sequences located at a distance up to four time the Förster distance of the FRET chromophores presented on the FRET labeled primers and/or oligonucleotides one with respect to the other in one or more polynucleotide analyte; in particular the pair of FRET labeled primers and/or oligonucleotides is combined with a sample and subjected to one or more polynucleotide amplification reactions before measuring FRET signals from at least one FRET chromophore.
    Type: Grant
    Filed: August 13, 2018
    Date of Patent: January 12, 2021
    Inventors: Emil P. Kartalov, Aditya Rajagopal, Axel Scherer, Mark D. Goldberg
  • Patent number: 10883984
    Abstract: A method for preparing a label-free aptamer electrochemical sensor of ?-interferon based on a dendrimer/gold nanoparticle/molybdenum disulfide nanocomposite is provided. The nanocomposite is drip-coated on a surface of an electrode to prepare a modified electrode, and a terminal sulfhydryl group of a ?-interferon aptamer chain is connected to the gold nanoparticle via Au—S bond to obtain a nanocomposite-aptamer modified electrode. When ?-interferon is present, the ?-interferon specifically binds to the aptamer chain on the sensor, resulting in the aptamer's hairpin structure being opened and stretched, which can effectively adsorb methylene blue MB in the electrolyte, causing significant enhancement of MB redox signal. A linear relationship between a current intensity of MB oxidation peak and a concentration of the ?-interferon is fitted to construct the label-free aptamer electrochemical sensor of ?-interferon.
    Type: Grant
    Filed: March 21, 2019
    Date of Patent: January 5, 2021
    Inventors: Hui Jin, Xiaohui Gao, Rijun Gui, Zonghua Wang
  • Patent number: 10876147
    Abstract: The present disclosure provides methods of generating supports (e.g., beads) comprising barcode molecules coupled thereto. A barcode molecule coupled to a support may comprise a barcode sequence and a functional sequence. A barcode molecule may be generated using two or more ligation reactions in a combinatorial fashion. A support comprising two or more different barcode molecules may be useful for analyzing or processing one or more analytes such as nucleic acid molecules, proteins, and/or perturbation agents.
    Type: Grant
    Filed: November 11, 2019
    Date of Patent: December 29, 2020
    Assignee: 10X GENOMICS, INC.
    Inventors: Zachary Bent, Elliott Meer, Daniel Riordan, Paul Ryvkin, Niranjan Srinivas, Jessica Terry
  • Patent number: 10876110
    Abstract: The invention relates to methods and devices for preparing synthetic nucleic acids.
    Type: Grant
    Filed: March 21, 2017
    Date of Patent: December 29, 2020
    Assignee: Codex DNA, Inc.
    Inventors: Peer F. Staehler, Raphael Carapito, Cord F. Staehler, Mark Matzas, Jack T. Leonard, Joachim Jaeger, Markus Beier