Patents Examined by Kenneth R. Horlick
  • Patent number: 11373730
    Abstract: A method in which a microorganism operational taxonomic unit (OTU) in a sample is defined based on a DNA sequence of a system generation information gene of microorganism in the sample. In the method, qualified sequence segments are obtained by means of processing and reading of an original sequence; the segments are sorted according to a relative abundance value of each segment; and only the qualified sequences with the high abundance values are used to obtain the temporary OTU. The qualified sequences with the low abundance values are reallocated; and the qualified sequence can be distributed to the proper temporary OTU respectively when a sequence similarity degree between the qualified sequence and an OTU sequence reaches at least 97%. The present disclosure also provides a sequence-assisted microorganism separation method.
    Type: Grant
    Filed: November 16, 2018
    Date of Patent: June 28, 2022
    Assignee: Perfect (China) Co., Ltd.
    Inventors: Liping Zhao, Jing Wang, Menghui Zhang
  • Patent number: 11371094
    Abstract: Provided herein are compositions, systems and methods for tagging molecular events, reactions, species, etc., but without the need for complex, highly diverse libraries of tagging molecules. Provided are tagging moieties that can have a smaller number, a few, or even a single original “tagging” structure that may be transformed or transformable, in situ, into a collection of larger numbers of unique tagging or “barcode” moieties.
    Type: Grant
    Filed: March 13, 2020
    Date of Patent: June 28, 2022
    Assignee: 10X Genomics, Inc.
    Inventors: Paul Ryvkin, Jason Underwood, Michael Schnall-Levin, Tarjei Mikkelsen, Benjamin Hindson
  • Patent number: 11371076
    Abstract: Disclosed herein include systems, methods, compositions, and kits for PCR normalization. In some embodiments, after barcoding copies of a higher abundance target (e.g., a cDNA species), the barcoded copies are amplified using a pair of forward primers comprising one or more mismatches and a reverse primer. The amplified copies can be further linearly amplified using a forward primer comprising the sequence of one of the pair of forward primers, and a reverse primer.
    Type: Grant
    Filed: January 15, 2020
    Date of Patent: June 28, 2022
    Assignee: Becton, Dickinson and Company
    Inventors: Katherine Lazaruk, Eleen Shum, Christina Chang
  • Patent number: 11359227
    Abstract: Disclosed are methods and systems for determining the three-dimensional structure of chromatin in eukaryotic cells. More specifically, disclosed are methods and systems for obtaining chromatin structural information by surface immobilization that includes tethering crosslinked protein:DNA complexes and/or ligated DNA complexes to media such as beads, gels, and or matrices during the conformation capture assay.
    Type: Grant
    Filed: December 8, 2017
    Date of Patent: June 14, 2022
    Assignee: University of Southern California
    Inventor: Lin Chen
  • Patent number: 11352663
    Abstract: The invention provides a method and kit for preventing inhibition of a thermal cycling reaction by protein coagulation in a sample.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: June 7, 2022
    Assignee: Genedrive Diagnostics Ltd
    Inventors: Shaun Ainsworth, Ben Cobb, Gino Miele
  • Patent number: 11352675
    Abstract: The disclosure relates generally to molecular diagnostic devices configured to amplifying a single nucleotide polymorphism (SNP) locus and discriminate between two or more allelic variants of the SNP, indicating presence or absence of a target allele. In some embodiments, the molecular diagnostic devices are capable of detecting, at point-of-care, SNPs associated with resistance or susceptibility to antibiotic treatment of organism infections. In other aspects, the disclosure provides methods of treatment for disease or disorders (e.g. organism infections) where treatment is guided by presence or absence of an allele at a SNP locus as determined by such molecular diagnostic devices.
    Type: Grant
    Filed: December 31, 2020
    Date of Patent: June 7, 2022
    Assignee: VISBY MEDICAL, INC.
    Inventors: Brian Ciopyk, Paul Dentinger, Teresa Abraham, Brandon Ma, Kamal Kajouke, Mackenzie Hunt, Austin Phung
  • Patent number: 11345955
    Abstract: The invention is a novel method of making and using a library such as a sequencing library of single stranded circular nucleic acid templates via splint ligation. In particular, disclosed are methods of making circular target nucleic acid molecules and libraries of such molecules for downstream analysis such as nucleic acid sequencing. The method comprises the steps of adding universal sequences to nucleic acid molecules, rendering single-stranded these nucleic acid molecules with universal sequences on their ends by contacting with a probe complementary to at least a portion of the universal sequences, and allowing the hybridized probe to enable circularization and formation of single-stranded circular (sscDNA) molecules.
    Type: Grant
    Filed: March 9, 2020
    Date of Patent: May 31, 2022
    Assignees: ROCHE SEQUENCING SOLUTIONS, INC., KAPA BIOSYSTEMS, INC.
    Inventors: Daleen Badenhorst, Richard Dannebaum, Ashley Hayes, Monica Herrera, Severine Margeridon, Martin Ranik
  • Patent number: 11345957
    Abstract: The present disclosure relates to methods for treating glioblastoma in a subject in need thereof using gene signatures in exosomal RNA derived from the subject. The gene signatures comprise: at least one of FAM229B, ZNF35, CTD-2647L4.4, CABP5, CYP20A1, CEP126, DTX2P1-UPK3BP1-PMS2P11, RP11-507K12.1, KRBA2, CALD1, LRFN1, RP2, SLC2A13, CDKL3, SLC8A3, ANTXR2, TIGD5, AC074289.1 RP11-932O9.7; at least one of tRNA-Lys-CTT-2-2, tRNA-Pro-AGG-2-7, LAMTOR2, RAD51AP1, DENND2A, A1BG, THSD1, CSF1, RP11-332M2.1, ZNF717, ZNF860, ORC6, Clorf50, PSPH, HIST1H4C, CYP2U1, THAP8, TMEM192, NAA20; or at least one of CREBBP, CXCR2 and S100A9. The treatment methods comprise measuring the expression level of at least one of the aforementioned genes in exosomal RNA from a subject and administering to the subject a glioblastoma treatment based on the expression level(s).
    Type: Grant
    Filed: July 18, 2018
    Date of Patent: May 31, 2022
    Assignee: Exosome Diagnostics, Inc.
    Inventors: Robert Kitchen, Michael Valentino, Johan Skog, Vasisht Tadigotla, Dalin Chan, Sudipto Chakrabortty, James Hurley
  • Patent number: 11326205
    Abstract: The invention relates to a method for the duplication of nucleic acids by means of a polymerase chain reaction, in the case of which a cycle consisting of the steps of denaturing, annealing and elongation is repeatedly performed. In one embodiment, in at least one passage of the cycle, the quotient of the duration of effect tA and the reaction volume Vr irradiated by the energy source is less than 1 seconds per microliter. In another embodiment, in at least one passage of the cycle, the ratio of the duration of effect (tA) and the duration of the PCR cycle (tc) is less than 20%. In certain embodiments, the yield (g) of nucleic acids at the end of at least one of the passages of the cycle is less than 80% of the nucleic acids present at the start of the passage.
    Type: Grant
    Filed: December 6, 2019
    Date of Patent: May 10, 2022
    Assignee: GNA Biosolutions GmbH
    Inventors: Federico Buersgens, Joachim Stehr, Lars Ullerich
  • Patent number: 11319597
    Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
    Type: Grant
    Filed: July 8, 2021
    Date of Patent: May 3, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 11319590
    Abstract: Disclosed are methods for sequencing immune cell receptor repertoires from immune cell populations, the methods comprising isolating RNA from immune cells, generating cDNA from the RNA, ligating adapter sequences to the cDNA, and sequencing the cDNA. Also provided are kits containing primer mixtures for the sequencing of immune cell receptor repertoires.
    Type: Grant
    Filed: January 30, 2018
    Date of Patent: May 3, 2022
    Assignee: Ludwig Institute for Cancer Research Ltd.
    Inventor: Raphael Genolet
  • Patent number: 11319589
    Abstract: A method for detecting the presence or absence of a target polynucleotide in a sample is described.
    Type: Grant
    Filed: February 26, 2020
    Date of Patent: May 3, 2022
    Inventors: John D. Curry, Heather Koshinsky, Amanda K. Lindholm-Perry, Richard M. Thallman
  • Patent number: 11319598
    Abstract: The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
    Type: Grant
    Filed: July 27, 2021
    Date of Patent: May 3, 2022
    Assignee: GUARDANT HEALTH, INC.
    Inventor: AmirAli Talasaz
  • Patent number: 11312999
    Abstract: A set of genes for the molecular classifying of medulloblastoma is disclosed, including the following 24 genes: EPHA7 gene, OTX2 gene, ROBO1 gene, TTR gene, LGR5 gene, IGF2BP3 gene, TBR1 gene, ZFPM2 gene, TRDC gene, TRAC gene, PEX5L gene, NKD1 gene, RALYL gene, GABRA5 gene, GAD1 gene, TNC gene, KCNA1 gene, EOMES gene, MAB21L2 gene, WIF1 gene, DKK2 gene, PDLIM3 gene, IMPG2 gene, and KHDRBS2 gene. In addition, the present invention also discloses the use of the genome in the preparation of a kit and a gene chip for the molecular classifying of medulloblastoma. After validation, the present invention can accurately differentiate medulloblastoma WNT subgroup, SHE subgroup, Group3 subgroup, and Group4 subgroup, and has important clinical significance for the precise treatment of patients due to the objective results, high accuracy, and short experimental period.
    Type: Grant
    Filed: September 6, 2019
    Date of Patent: April 26, 2022
    Assignee: HANGZHOU CANHELP GENOMICS TECHNOLOGY CO. LTD.
    Inventors: Qinghua Xu, Chengshu Chen, Yifeng Sun, Jinying Chen, Qifeng Wang, Kaibin Song
  • Patent number: 11306352
    Abstract: The present invention relates generally to an improved method of amplifying a nucleic acid region of interest and to primers for use therein. More particularly, the present invention is directed to an improved method of amplifying a nucleic acid region which has resulted from the recombination of two or more immunoglobulin or T cell receptor gene segments and primers for use therein. The method of the present invention is based on the determination that performing the amplification step at an annealing temperature determined relative to the critical annealing temperature unique to a given reaction and/or using optimised primers enables higher levels of sensitivity than have previously been achievable in the context of prior art methods of amplifying rearranged immunological or T cell receptor genes. The method of the present invention is particularly useful where the subject recombination target comprises only one N region.
    Type: Grant
    Filed: June 7, 2019
    Date of Patent: April 19, 2022
    Assignee: Monoquant Pty Ltd.
    Inventor: Alexander Alan Morley
  • Patent number: 11299789
    Abstract: A method and system are disclosed for detecting microbial pathogens in a sample suspected of containing the pathogens. The method includes combining loop-mediated isothermal amplification (LAMP) reagents and a polymer gel, such as a hydrogel, together with the sample to form a mixture. The gel polymerizes over a short time to immobilize the viral particles within the mixture. If target DNA/RNA are present in the sample, amplicons are produced. The target microorganisms are detected by visually detecting the presence or absence of the amplicons. The target microorganism concentrations may be determined based on the number of fluorescent amplicon dots after the reaction using a smartphone or a fluorescent microscope. The method may be employed for rapidly and inexpensively quantifying microbial pathogens in environmental water samples with high sensitivity.
    Type: Grant
    Filed: December 31, 2018
    Date of Patent: April 12, 2022
    Assignee: California Institute of Technology
    Inventors: Xiao Huang, Michael R. Hoffmann
  • Patent number: 11268142
    Abstract: A disposable assay platform for detecting a target nucleic acid comprising multiple chambers and a method for operating the assay platform. Solutions containing the target nucleic acid move from one chamber to the next chamber by opening a vent pocket. The resulting pressure change enables the solution to flow to the next chamber. The platform comprises an electronic layer and one or more fluid layers bonded together. All heating operations can be performed by using resistive heating elements in the platform. All cooling operations are preferably passive. The platform is preferably operated when in a vertical orientation and can be docked to an external docking station that controls the operation of the platform.
    Type: Grant
    Filed: November 8, 2019
    Date of Patent: March 8, 2022
    Assignee: Mesa Biotech, Inc.
    Inventors: Marc Dejohn, Robert B. Cary, Nathan J. Cobb
  • Patent number: 11268149
    Abstract: This invention provides methods of diagnosis, predicting and diagnosing susceptibility to, predicting disease progression and treatment of inflammatory bowel disease (IBD), including Crohn's disease and/or subtypes of Crohn's disease (CD) and/or Ulcerative Colitis (UC). In one embodiment, a method of the invention is practiced by determining the presence or absence of the genetic variants NOD2, TLR8, TLR2, CARD8, CARD15 and/or JAK3 to diagnose, predict and diagnose susceptibility and predict disease progression in an individual. In another embodiment, a method of the invention is practiced by determining the presence or absence of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA in an individual. In another embodiment, the invention further associates the presence or absence of the risk variants with the expression of anti-Cbir1, anti-OmpC, ASCA, anti-I2 and/or pANCA for the diagnosis, prediction of susceptibility, prediction of disease progression and/or treatment of IBD, including CD and/or UC.
    Type: Grant
    Filed: November 13, 2019
    Date of Patent: March 8, 2022
    Assignee: Cedars-Sinai Medical Center
    Inventors: Stephan R. Targan, Marla C. Dubinsky, Carol J. Landers, Ling Mei, Jerome I. Rotter, Kent D. Taylor
  • Patent number: 11254982
    Abstract: Provided are compositions and methods for the conversion of thiolated nucleotides, and subsequent detection of the converted nucleotides in RNA or DNA. Also provided herein are compositions and methods for the metabolic labeling of RNA and DNA by incorporation of thiolated nucleotides, and their subsequent conversion and detection.
    Type: Grant
    Filed: August 7, 2019
    Date of Patent: February 22, 2022
    Assignees: UNIVERSITY OF INNSBRUCK, MEDICAL UNIVERSITY OF INNSBRUCK
    Inventors: Ronald Micura, Alexandra Lusser, Christian Riml, Thomas Amort, Catherina Gasser, Isabel Delazer
  • Patent number: 11230730
    Abstract: A reagent solution includes water, a nucleotide, and tris(2-carboxyethyl)phosphine in a range of 0.5 ?M to 1000 ?M. The reagent solution can further include a non-ionic surfactant in an amount of 0.001% to 1% or a biocidal agent in an amount of 0.001% to 1%. The reagent solution can include salts, such as sodium chloride or magnesium sulfate.
    Type: Grant
    Filed: October 16, 2019
    Date of Patent: January 25, 2022
    Assignee: Life Technologies Corporation
    Inventors: Jamsheed Ghadiri, Karta Atehortua-Khalsa