Biochemical Method (e.g., Using An Enzyme Or Whole Viable Micro-organism, Etc.) Patents (Class 506/26)
  • Patent number: 11499182
    Abstract: A method for generating amplicon constructs of a target sequence is disclosed, the method comprising providing a target sequence; an oligonucleotide probe, comprising a universal sequence and further comprising, at or towards its 5? end, a target specific sequence capable of hybridising to the reverse complement of a sequence at, or flanking one of the 3? ends of the target sequence; a universal primer, comprising at its 3? end a sequence capable of hybridising to the universal sequence of the oligonucleotide probe and performing a Polymerase Chain Reaction (PCR).
    Type: Grant
    Filed: March 3, 2016
    Date of Patent: November 15, 2022
    Assignee: Salisbury NHS Foundation Trust
    Inventors: Daniel Leonard Ward, Christopher John Mattocks
  • Patent number: 11499192
    Abstract: An example of a sequencing kit includes a flow cell, an encapsulation matrix precursor composition, and a radical initiator. The flow cell includes a plurality of chambers and primers attached within each of the plurality of chambers. The encapsulation matrix precursor composition consists of a fluid, a monomer or polymer including a radical generating and chain elongating functional group, a radical source, and a crosslinker. The radical initiator is part of the encapsulation matrix precursor composition or is a separate component.
    Type: Grant
    Filed: January 23, 2020
    Date of Patent: November 15, 2022
    Assignee: Illumina, Inc.
    Inventors: Xi-Jun Chen, Yir-Shyuan Wu, Tarun Kumar Khurana, Liangliang Qiang, Andrew J. Price, Elisabet Rosas
  • Patent number: 11466321
    Abstract: An example of an array includes a support including a plurality of discrete wells, a gel material positioned in each of the discrete wells, a sequencing primer grafted to the gel material, and a non-sequencing entity grafted to the gel material. Each of the sequencing primer and the non-sequencing entity is in its as-grafted form.
    Type: Grant
    Filed: December 20, 2017
    Date of Patent: October 11, 2022
    Assignee: Illumina, Inc.
    Inventors: James Tsay, Yuxiang Huang
  • Patent number: 11453913
    Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.
    Type: Grant
    Filed: May 19, 2021
    Date of Patent: September 27, 2022
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
  • Patent number: 11428699
    Abstract: A sensor including a surface plasmon resonance detector with a reservoir for containing a liquid sample. The sensor further includes a sensing metallic film positioned within the reservoir so that at least a majority of a surface of the sensing metallic film is to be in contact with the liquid sample being housed within the reservoir. The sensory also includes a semiconductor device having a contact in electrical communication with the sensing metal containing film that is positioned within the reservoir. The semiconductor device measures the net charges of molecules within the liquid sample within a Debye length from the sensing metallic film.
    Type: Grant
    Filed: April 30, 2019
    Date of Patent: August 30, 2022
    Assignee: INTERNATIONAL BUSINESS MACHINES CORPORATION
    Inventors: Bobby E. Feller, Jianqiang Lin, Robert D. Miller, Ramachandran Muralidhar, Tak H. Ning, Sufi Zafar
  • Patent number: 11428696
    Abstract: The invention relates to a method for determining the presence of at least one distinct polypeptide in a biological sample comprising contacting the biological sample with a hydrolyzing agent, wherein the hydrolyzing agent is capable of hydrolyzing the distinct polypeptide in a sequence-specific manner such that at least one distinct peptide having a predetermined peptide measured accurate mass would result if the at least one distinct polypeptide were present in the biological sample, to obtain a hydrolyzed sample; bringing the hydrolyzed sample in contact with a substrate comprising at least one immobilized binding partner, wherein the at least one immobilized binding partner is capable of specifically binding the distinct peptide; removing the hydrolyzed sample from the substrate in a manner such that the distinct peptide would remain bound to the immobilized binding partner; contacting the substrate with an elution solution, wherein the distinct peptide would dissociate from the immobilized binding partne
    Type: Grant
    Filed: June 2, 2020
    Date of Patent: August 30, 2022
    Assignee: Cell Signaling Technology, Inc.
    Inventors: Albrecht Moritz, John Edward Rush, II, Roberto Polakiewicz
  • Patent number: 11384382
    Abstract: Methods of preparing double-stranded nucleic acids with single-stranded overhangs for amplification and sequencing are disclosed. Contacting a blunt-ended double-stranded nucleic acid molecules with Taq results in non-templated directed addition of a single nucleotide to the 3? ends of the nucleic acid with A added most frequently followed by G followed by C and T. G tailing is sufficiently frequent that the efficiency of ligation of nucleic acid molecules to adapters can be significantly increased by including adapters tailed with T and C. The ligation efficiency can be increased even further with blunted-ended adapters to ligate to blunt-ended nucleic acid molecules that failed to undergo tailing.
    Type: Grant
    Filed: April 13, 2018
    Date of Patent: July 12, 2022
    Inventors: Andrew Kennedy, Stefanie Ann Ward Mortimer
  • Patent number: 11365438
    Abstract: The present disclosure provides methods and systems for nucleic acid preparation and analysis. Nucleic acid molecules may be derived from one or more cells. Preparation of nucleic acid molecules may comprise generation of one or more mutations, such as strand-specific mutations. Nucleic acid molecules may be prepared for and analyzed by sequencing. Sequences may be identified with nucleic acid orientation information.
    Type: Grant
    Filed: May 12, 2020
    Date of Patent: June 21, 2022
    Assignee: 10X GENOMICS, INC.
    Inventors: Daniel P. Riordan, Preyas Shah, Michael Schnall-Levin
  • Patent number: 11359238
    Abstract: Provided herein are methods for sequencing both strands of a double stranded nucleic acid fragment that improves fidelity and accuracy of a sequence determination compared to traditional next generation sequencing methods. Compositions and kits for use in the methods are also provided.
    Type: Grant
    Filed: March 5, 2021
    Date of Patent: June 14, 2022
    Inventors: Eli N. Glezer, Martin Maria Fabani, Sabrina Shore, Daan Witters
  • Patent number: 11326201
    Abstract: The present disclosure relates to a method for removing a non-target RNA from an RNA sample, including: performing reverse transcription on an RNA sample by using a reverse transcription primer, and removing an RNA template, to obtain a non-target first-strand cDNA and a target first-strand cDNA; hybridizing the non-target first-strand cDNA with a specific probe to obtain a non-target first-strand cDNA-probe complex; and digesting the non-target first-strand cDNA-probe complex by using a duplex-specific nuclease to obtain the target first-strand cDNA. The non-target first-strand cDNA-probe complex can be further extended to obtain a double-stranded DNA region that can be completely digested by the duplex-specific nuclease, then the duplex-specific nuclease is added for digestion.
    Type: Grant
    Filed: April 25, 2018
    Date of Patent: May 10, 2022
    Assignee: BEIJING TRANSGEN BIOTECH CO., LTD.
    Inventors: Liang Geng, Wen Xin
  • Patent number: 11274343
    Abstract: The present invention is directed to methods, compositions and systems for analyzing sequence information from targeted regions of a genome. Such targeted regions may include regions of the genome that are poorly characterized, highly polymorphic, or divergent from reference genome sequences.
    Type: Grant
    Filed: February 24, 2016
    Date of Patent: March 15, 2022
    Assignee: 10X GENOMICS, INC.
    Inventors: Mirna Jarosz, Michael Schnall-Levin
  • Patent number: 11268072
    Abstract: The present disclosure provides compositions including recombinant K1E bacteriophages, methods for making the same, and uses thereof. The recombinant K1E bacteriophages disclosed herein are useful for the identification and/or antibiotic susceptibility profiling of specific bacterial strains/species present in a sample.
    Type: Grant
    Filed: July 12, 2019
    Date of Patent: March 8, 2022
    Assignee: THE CHARLES STARK DRAPER LABORATORY, INC.
    Inventors: Sarah Gruszka, Jason Holder
  • Patent number: 11268084
    Abstract: Glycerol-free enzyme formulations are described. In some embodiments, a glycerol-free enzyme formulation is stabilized by high salt concentration. The glycerol free enzyme formulation may comprise a reverse transcriptase enzyme.
    Type: Grant
    Filed: August 2, 2018
    Date of Patent: March 8, 2022
    Assignee: Thermo Fisher Scientific Baltics, UAB
    Inventors: Juozas Siurkus, Darius Kavaliauskas, Daumantas Matulis, Lina Baranauskiene
  • Patent number: 11236319
    Abstract: This invention relates to, in part, compositions of beta-lactamases and methods of using these enzymes in, for example, gastrointestinal tract (GI tract) disorders such as C. difficile infection (CDI).
    Type: Grant
    Filed: July 24, 2020
    Date of Patent: February 1, 2022
    Assignee: Synthetic Biologies, Inc.
    Inventors: Michael Kaleko, Sheila Connelly
  • Patent number: 11155868
    Abstract: Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.
    Type: Grant
    Filed: January 22, 2021
    Date of Patent: October 26, 2021
    Assignee: ULTIMA GENOMICS, INC.
    Inventors: Gilad Almogy, Nathan Beckett, Jacob A. Wolf, Nathan Caswell, Joseph Anthony, Jose Martin Sosa, Phillip Lee, Stephanie Kubecka
  • Patent number: 11142786
    Abstract: Presented are methods and compositions for preparing samples for amplification and sequencing. Particular embodiments relate to methods of preparing nucleic acid-continuing cellular samples for library amplification, wherein the methods include lysing cells of the sample to form a lysate, amplifying the nucleic acids from the lysed samples, exposing the amplified nucleic acids to a solid surface, and clonally amplifying the amplified nucleic acids to generate clusters.
    Type: Grant
    Filed: August 27, 2020
    Date of Patent: October 12, 2021
    Inventors: Louise Fraser, Paula Kokko-Gonzales, Andrew Slatter
  • Patent number: 11098357
    Abstract: The present invention provides methods, compositions and kits for detecting duplicate sequencing reads. In some embodiments, the duplicate sequencing reads are removed.
    Type: Grant
    Filed: January 15, 2020
    Date of Patent: August 24, 2021
    Assignee: TECAN GENOMICS, INC.
    Inventors: Douglas A. Amorese, Jonathan Scolnick, Ben Schroeder
  • Patent number: 10988761
    Abstract: Presented herein is a high-throughput (HTP) genomic engineering platform for improving the production of therapeutic proteins in Chinese hamster ovary (CHO) cells. The disclosed HTP genomic engineering platform is computationally driven and integrates molecular biology, automation, and advanced machine learning protocols. The platform utilizes a unique suite of HTP genetic engineering tools to explore the genomic landscape associated with therapeutic protein production pathways, in order to unravel the biological drivers and disentangle the uncharacterized genetic architecture responsible for optimizing therapeutic protein production in CHO cells.
    Type: Grant
    Filed: July 20, 2020
    Date of Patent: April 27, 2021
    Assignee: Zymergen Inc.
    Inventors: Kate Caves, Amarjeet Singh
  • Patent number: 10968447
    Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduces sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.
    Type: Grant
    Filed: January 17, 2018
    Date of Patent: April 6, 2021
    Assignee: MYRIAD WOMEN'S HEALTH, INC.
    Inventors: Henry H. Lai, Clement S. Chu
  • Patent number: 10865410
    Abstract: Provided herein is technology relating to next-generation sequencing and particularly, but not exclusively, to methods and compositions for preparing a next-generation sequencing library comprising short overlapping DNA fragments and using the library to sequence one or more target nucleic acids.
    Type: Grant
    Filed: June 29, 2018
    Date of Patent: December 15, 2020
    Assignee: ABBOTT MOLECULAR INC.
    Inventor: Dae Hyun Kim
  • Patent number: 10814299
    Abstract: Methods, compositions, and systems for distributing nucleic acids into array regions are provided. The methods, compositions, and systems utilize nucleic acid condensing agents to increase efficiency of distribution of the nucleic acids into the array regions. Various methods for facilitating distribution of the nucleic acids to the array regions are provided.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: October 27, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lei Sun, Jaime Juan Benitez-Marzan, Natasha Popovich, Sassan Sheikholeslami, Steven Lin, Aparna Vedula
  • Patent number: 10808277
    Abstract: An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.
    Type: Grant
    Filed: December 15, 2017
    Date of Patent: October 20, 2020
    Assignees: ILLUMINA, INC., ILLUMINA CAMBRIDGE LIMITED
    Inventors: Shaun Hunter, Peter McInerney, Jonathan Boutell, Claire Bevis-Mott
  • Patent number: 10774374
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: April 4, 2016
    Date of Patent: September 15, 2020
    Assignee: Spatial Transcriptomics AB and Illumina, Inc.
    Inventors: Jonas Frisén, Patrik Ståhl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 10767171
    Abstract: This invention relates to, in part, compositions of beta-lactamases and methods of using these enzymes in, for example, gastrointestinal tract (GI tract) disorders such as C. difficile infection (CDI).
    Type: Grant
    Filed: January 24, 2020
    Date of Patent: September 8, 2020
    Assignee: Synthetic Biologics, Inc.
    Inventors: Michael Kaleko, Sheila Connelly
  • Patent number: 10760121
    Abstract: Methods, devices and systems for analyzing precious samples of cells, including single cells are provided. The methods, devices, and systems in various embodiments of the invention are used to assess genomic heterogeneity, which has been recognized as a central feature of many cancers and plays a critical role in disease initiation, progression, and response to treatment. The methods devices and systems are also used to analyze embryonic biopsies for preimplantation genetic diagnosis (PGD). In one embodiment, the devices, systems and methods provided herein allow for the construction of genomic and RNA-seq libraries without a pre-amplification step.
    Type: Grant
    Filed: February 4, 2016
    Date of Patent: September 1, 2020
    Assignee: The University of British Columbia
    Inventors: Carl Lars Genghis Hansen, Hans Zahn, Jens Huft, Marinus Theodorus Johannes Van Loenhout, Kaston Leung, Bill Kengli Lin, Anders Klaus, Samuel Alves Jana Rodrigues Aparicio, Sohrab Prakash Shah, Adi Steif
  • Patent number: 10752949
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing. Such polynucleotide processing may be useful for a variety of applications, including polynucleotide sequencing.
    Type: Grant
    Filed: December 6, 2018
    Date of Patent: August 25, 2020
    Assignee: 10X GENOMICS, INC.
    Inventors: Benjamin Hindson, Christopher Hindson, Michael Schnall-Levin, Kevin Ness, Mirna Jarosz, Serge Saxonov, Paul Hardenbol
  • Patent number: 10731211
    Abstract: The present disclosure provides methods, compositions, and systems for distributing polymerase compositions into array regions. In particular, the described methods, compositions, and systems utilize density differentials and/or additives to increase efficiency in the distribution of polymerase compositions to a surface as compared to methods utilizing only diffusion control.
    Type: Grant
    Filed: November 17, 2016
    Date of Patent: August 4, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Sassan Sheikholeslami, Michael Hunkapiller, Natasha Popovich, Lei Sun, Erik Miller, Satwik Kamtekar
  • Patent number: 10725027
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications. 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) and chromatin (e.g., accessible chromatin).
    Type: Grant
    Filed: April 4, 2019
    Date of Patent: July 28, 2020
    Assignee: 10X GENOMICS, INC.
    Inventors: Jason Bell, Geoffrey McDermott, Francesca Meschi, Michael Schnall-Levin, Xinying Zheng
  • Patent number: 10711296
    Abstract: Processes, oligonucleotides, and kits for amplifying RNA. In particular, the processes generate and amplify cDNA libraries in which the orientation of the input RNA molecule is preserved in the products. Among the various aspects of the present disclosure is the provision of process for directionally amplifying RNA. The process comprises reverse transcribing at least one RNA molecule in the presence of a plurality of first synthesis primers to generate a plurality of first strands of complementary DNA (cDNA), wherein each of the first synthesis primers comprises a 3? sequence having complementarity to a portion of the RNA molecule, a non-complementary 5? sequence corresponding to one or more amplification primers, and optionally an internal tag sequence comprising a first tag sequence.
    Type: Grant
    Filed: March 24, 2016
    Date of Patent: July 14, 2020
    Assignee: Sigma-Aldrich Co. LLC
    Inventors: Kenneth B Heuermann, Carol A Kreader, Jaime K Robert, Brian W Ward
  • Patent number: 10683495
    Abstract: The present invention relates to improved yeast transformation of yeast cells and yeast cell libraries transformed thereby. More specifically, the present invention relates to the transformation of yeast by electroporation.
    Type: Grant
    Filed: November 15, 2017
    Date of Patent: June 16, 2020
    Assignee: IMMATICS BIOTECHNOLOGIES GMBH
    Inventors: Sebastian Bunk, Dominik Maurer, Felix Unverdorben
  • Patent number: 10647775
    Abstract: Provided herein are de novo binding domain containing polypeptides (DBDpp) that specifically bind a target of interest. Nucleic acids encoding the DBDpp, and vectors and host cells containing the nucleic acids are also provided. Libraries of DBDpp, methods of producing and screening such libraries and the DBDpp identified from such libraries and screens are also encompassed. Methods of making and using the DBDpp are additionally provided. Such uses include, without limitation, affinity purification, and diagnostic and therapeutic applications.
    Type: Grant
    Filed: April 4, 2016
    Date of Patent: May 12, 2020
    Assignees: Subdomain LLC, Arcellx, Inc.
    Inventors: David William Lafleur, David M. Hilbert
  • Patent number: 10633651
    Abstract: The present invention relates to nucleic acid samples for massively parallel sequencing. More particularly, the present invention relates to assay methods, compositions and kits for detecting contamination of nucleic acid identifiers such as sample barcodes.
    Type: Grant
    Filed: July 10, 2017
    Date of Patent: April 28, 2020
    Assignee: AGILENT TECHNOLOGIES, INC.
    Inventors: Katie Leigh Zobeck, Paige Anderson, Javelin Chi, Henrik Johansson
  • Patent number: 10625234
    Abstract: The present disclosure provides a fabrication process that results in creating large arrays of living cells, such as stem cells, which are subsequently exposed to nanoliter quantities of compounds to test the efficacy on cellular metabolism.
    Type: Grant
    Filed: August 28, 2015
    Date of Patent: April 21, 2020
    Assignee: StemoniX Inc.
    Inventor: Robert John Petcavich
  • Patent number: 10619207
    Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.
    Type: Grant
    Filed: May 21, 2019
    Date of Patent: April 14, 2020
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
  • Patent number: 10619199
    Abstract: Processes and kits for preparing a plurality of amplification products with reduced non-specific amplification artifacts.
    Type: Grant
    Filed: March 4, 2016
    Date of Patent: April 14, 2020
    Assignee: Sigma-Aldrich Co. LLC
    Inventors: Timothy Seebeck, Fuqiang Chen, Brian W Ward
  • Patent number: 10604804
    Abstract: 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: Grant
    Filed: May 13, 2019
    Date of Patent: March 31, 2020
    Assignee: UNIVERSITY OF WASHINGTON THROUGH ITS CENTER FOR COMMERCIALIZATION
    Inventors: Jesse Salk, Lawrence A. Loeb, Michael Schmitt
  • Patent number: 10590465
    Abstract: Assays can be used to detect mutations found in neoplasms of the pancreas, as well as for other neoplasms and other uses. Nucleic acids can be captured from body fluids such as cyst fluids. Thousands of oligonucleotides can be synthesized in parallel, amplified and ligated together. The ligated products can be further amplified. The amplified, ligated products are used to capture complementary DNA sequences, which can be analyzed, for example by massively parallel sequencing.
    Type: Grant
    Filed: May 30, 2017
    Date of Patent: March 17, 2020
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Jian Wu
  • Patent number: 10584326
    Abstract: This invention relates to, in part, compositions of beta-lactamases and methods of using these enzymes in, for example, gastrointestinal tract (GI tract) disorders such as C. difficile infection (CDI).
    Type: Grant
    Filed: May 16, 2019
    Date of Patent: March 10, 2020
    Assignee: Synthetic Biologics, Inc.
    Inventors: Michael Kaleko, Sheila Connelly
  • Patent number: 10562004
    Abstract: The present disclosure provides a fabrication process that results in creating large arrays of living cells, such as stem cells, which are subsequently exposed to nanoliter quantities of compounds to test the efficacy on cellular metabolism.
    Type: Grant
    Filed: August 28, 2015
    Date of Patent: February 18, 2020
    Assignee: StemoniX Inc.
    Inventor: Robert John Petcavich
  • Patent number: 10563257
    Abstract: The invention provides in situ nucleic acid sequencing to be conducted in biological specimens that have been physically expanded. The invention leverages the techniques for expansion microscopy (ExM) to provide new methods for in situ sequencing of nucleic acids as well as new methods for fluorescent in situ sequencing (FISSEQ) in a new process referred to herein as “expansion sequencing” (ExSEQ).
    Type: Grant
    Filed: August 23, 2018
    Date of Patent: February 18, 2020
    Assignees: Massachusetts Institute of Technology, President and Fellows of Harvard College
    Inventors: Edward Stuart Boyden, Fei Chen, Shahar Alon, George Church, Paul Warren Tillberg, Adam Henry Marblestone, Evan R. Daugharthy
  • Patent number: 10545494
    Abstract: A method for determining performance characteristics of a fermenter batch in a biofuel production plant based on stoichiometry of fermentation reactions, comprising determining a cell mass of a sample of the fermenter batch; a glucose equivalent total (GET) based at least on the cell mass of the sample of the fermenter batch, and a starch to glucose conversion factor (SGCF) based at least on the GET; a total amount of glucose based at least on the SGCF, a volume of ethanol based at least on the total amount of glucose and the GET; at least one of a fermenter yield based at least on the volume of ethanol, and a fermenter efficiency based on the fermenter yield or the volume of ethanol; and generating an output based on the fermenter yield and/or the fermenter efficiency.
    Type: Grant
    Filed: June 18, 2010
    Date of Patent: January 28, 2020
    Assignee: Rockwell Automation Technologies, Inc.
    Inventors: Srinivas Budaraju, James F. Bartee
  • Patent number: 10538594
    Abstract: Provided herein are methods and compositions for analyzing epigenetic modifications of genomes. The methods and compositions are suited for complete epigenome sequencing of any modification for which an antibody or an affinity binding agent has been developed. In one aspect, provided herein is a method for analyzing epigenetic modification of a genome. In some embodiments of aspects provided herein, the method further comprises sequencing a sequencing library to generate sequence reads, and assembling the sequence reads with aid of a positional barcode sequence information. In some embodiments of aspects provided herein, the method further comprises determining a location of at least two different epigenetic modifications of the nucleic acid. Another aspect of the present disclosure provides a kit for analyzing an epigenetic modification of a nucleic acid.
    Type: Grant
    Filed: April 6, 2016
    Date of Patent: January 21, 2020
    Assignee: Centrillion Technology Holdings Corporation
    Inventors: Wei Zhou, Jeremy Edwards, Justin Costa
  • Patent number: 10538812
    Abstract: The present invention provides a means for efficiently amplifying the exons of PKD1 and PKD2 genes, and a primer set that can amplify all the exons of PKD1 and PKD2 genes under a single set of PCR conditions.
    Type: Grant
    Filed: November 13, 2015
    Date of Patent: January 21, 2020
    Assignee: OTSUKA PHARMACEUTICAL CO., LTD.
    Inventors: Kiyonori Katsuragi, Moritoshi Kinoshita, Daisuke Koga, Ryo Higashiyama
  • Patent number: 10457982
    Abstract: It is an object of the present invention to provide a method for amplifying a nucleic acid, using RNA as a template, which can realize elimination of the risk of non-specific amplification caused by DNA mixed from reagents and/or working environment, an increase in the detection sensitivity of trace RNA, and a reduction in amplification bias. According to the present invention, there is provided a method for amplifying a nucleic acid, which comprises a step of incubating a mixture comprising template RNA, a primer, a degrading enzyme specific to DNA in RNA-DNA hybrid, an RNase H minus reverse transcriptase, and a substrate.
    Type: Grant
    Filed: September 30, 2015
    Date of Patent: October 29, 2019
    Assignee: RIKEN
    Inventors: Tetsutaro Hayashi, Yohei Sasagawa, Itoshi Nikaido
  • Patent number: 10300452
    Abstract: The present invention provides methods, compositions, and systems for distributing single polymerase molecules into array regions. In particular, the methods, compositions, and systems of the present invention result in a distribution of single polymerase molecules into array regions at a percentage that is larger than the percentage expected to be occupied under a Poisson distribution.
    Type: Grant
    Filed: March 23, 2016
    Date of Patent: May 28, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Lei Sun, Natasha Popovich, Gene Shen, Thang Pham, Stephen Turner
  • Patent number: 10294511
    Abstract: Embodiments provided herein relate to methods and compositions for preparing nucleic acid libraries. Some embodiments include preparing libraries from nucleic acids obtained from degraded samples, such as ancient samples and fixed samples.
    Type: Grant
    Filed: October 16, 2014
    Date of Patent: May 21, 2019
    Assignee: ILLUMINA, INC.
    Inventors: Raquel Maria Sanches-Kuiper, Vincent Peter Smith, Sean Humphray
  • Patent number: 10240196
    Abstract: Provided herein, among other things, are a variety of methods for transposase-mediated tagging and amplification of short DNA fragments, e.g., between about 150 bp and 1.5 Kb in length. In some aspects, the method includes tagging the DNA fragments with a first primer sequence using barcoded transposases followed by a primer extension reaction to introduce a second primer sequence, e.g., using random or gene-specific primers. Kits for performing this method are also provided.
    Type: Grant
    Filed: May 27, 2016
    Date of Patent: March 26, 2019
    Assignee: AGILENT TECHNOLOGIES, INC.
    Inventors: Bahram Arezi, Michael Borns, Holly Hogrefe, Connie Hansen
  • Patent number: 10208338
    Abstract: The present disclosure describes a method of adapter ligation to the ends of fragmented double-stranded DNA molecules.
    Type: Grant
    Filed: March 3, 2015
    Date of Patent: February 19, 2019
    Assignee: SWIFT BIOSCIENCES, INC.
    Inventors: Vladimir Makarov, Julie Laliberte
  • Patent number: 10150991
    Abstract: Improvements on the basic method used for BEAMing increase sensitivity and increase the signal-to-noise ratio. The improvements have permitted the determination of intrinsic error rates of various DNA polymerases and have permitted the detection of rare and subtle mutations in DNA isolated from plasma of cancer patients.
    Type: Grant
    Filed: June 6, 2016
    Date of Patent: December 11, 2018
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Frank Diehl, Kenneth W. Kinzler, Meng Li
  • Patent number: RE49207
    Abstract: Provided herein, among other things, are a variety of methods for transposase-mediated tagging and amplification of short DNA fragments, e.g., between about 150 bp and 1.5 Kb in length. In some aspects, the method includes tagging the DNA fragments with a first primer sequence using barcoded transposases followed by a primer extension reaction to introduce a second primer sequence, e.g., using random or gene-specific primers. Kits for performing this method are also provided.
    Type: Grant
    Filed: November 8, 2019
    Date of Patent: September 13, 2022
    Assignee: Agilent Technologies, Inc.
    Inventors: Bahram Arezi, Michael Borns, Holly Hogrefe, Connie Hansen