Patents Examined by Kenneth Horlick
  • Patent number: 9970063
    Abstract: There is disclosed a PCR-based test kit and PCR process for identification of multiple clonal sub-species lineages of infectious bacteria, such as uropathogenic E. coli causing cystitis. pyelonephritis and urosepsis, for the purposes of predicting antibiotic resistance of the bacteria. More specifically, there is further disclosed a SNP (single nucleotide polymorphism) identification process that simultaneously detect compilations of the presence of absence of predictive SNPs within mutated loci of infectious bacterial clonal subspecies variants, such as the fumC/fimH loci of the E. coli bacterium. This disclosure provides a PCR detection kit incorporating a SNP compilation that forms a BFC (Binary Footprint Code) that allows for rapid identification of multiple infectious bacterial clonotypes based on their SNP footprint. More specifically there is disclosed a clonotyping method for clonal typing E.
    Type: Grant
    Filed: February 26, 2016
    Date of Patent: May 15, 2018
    Assignee: ID Genomics, Inc.
    Inventor: Sujay Chattopdhyay
  • Patent number: 9926609
    Abstract: Disclosed are compositions, assays, methods, diagnostic methods, kits and diagnostic kits for the specific and differential detection of Mycobacterium avium subsp. paratuberculosis from samples including veterinary samples, clinical samples, food samples, forensic sample, an environmental sample (e.g., soil, dirt, garbage, sewage, air, or water), including food processing and manufacturing surfaces, or a biological sample.
    Type: Grant
    Filed: December 22, 2015
    Date of Patent: March 27, 2018
    Assignee: Life Technologies Corporation
    Inventors: Yongmei Ji, Pius Brzoska, Angela Burrell, Craig Cummings, Catherine O'Connell
  • Patent number: 9926594
    Abstract: A method for the amplification of nucleic acids, in which nanoparticles in a reaction volume transfer heat to their environment through excitation. The method comprises a step of providing nanoparticles with the nucleic acids in a reaction volume and one or more heating steps. In at least one of the heating steps, the heating is achieved at least partially through the excitation of the nanoparticles. The interval of the excitation is chose to be shorter or equal to a critical excitation time.
    Type: Grant
    Filed: June 7, 2016
    Date of Patent: March 27, 2018
    Assignee: GNA Biosolutions GmbH
    Inventors: Joachim Stehr, Federico Buersgens, Lars Ullerich
  • Patent number: 9914973
    Abstract: Described herein are methods and kits for detecting the presence or absence of gene dysregulations such as those arising from gene fusions and/or chromosomal abnormalities, e.g. translocations, insertions, inversions and deletions. The methods, compositions and kits are useful for detecting mutations that cause the differential expression of a 5? portion of a target gene relative to the 3? region of the target gene. The average expression of the 5? portion of the target gene is compared with the average expression of the 3? portion of the target gene to determine an intragenic differential expression (IDE). The IDE can then be used to determine if a dysregulation or a particular disease (or susceptibility to a disease) is present or absent in a subject or sample.
    Type: Grant
    Filed: March 24, 2015
    Date of Patent: March 13, 2018
    Assignee: Quest Diagnostics Investments Incorporated
    Inventor: Shih-Min Cheng
  • Patent number: 9902993
    Abstract: The present invention relates to a proximity probe based detection assay (“proximity assay”) for an analyte in a sample, specifically a proximity probe extension assay (PEA), an in particular to an improvement in the method to reduce non-specific “background” signals, wherein the improvement comprises the use in such assays of a hyperthermophilic polymerase, said method comprising: (a) contacting said sample with at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte; (b) allowing the nucleic acid domains of the proximity probes to interact with each other upon binding of said proximity probes to said analyte, wherein said interaction comprises the formation of a duplex; (c) extending the 3? end of at least one nucleic acid domain of said duplex to generate an extension product, wherein the extension reaction comprises increasing the temperature of assay above room temperature and
    Type: Grant
    Filed: January 29, 2013
    Date of Patent: February 27, 2018
    Assignee: OLINK PROTEOMICS AB
    Inventors: Simon Fredriksson, Martin Lundberg, Anna Eriksson, Emma Rennel-Dickens
  • Patent number: 9862998
    Abstract: This disclosure provides a method of determining a sequence of nucleotides for a nucleic acid template. The method can include the steps of contacting the nucleic acid template with a conformationally labeled polymerase and at least four different nucleotide species under conditions wherein the conformationally labeled polymerase catalyzes sequential addition of the nucleotide species to form a nucleic acid complement of the nucleic acid template, wherein the sequential addition of each different nucleotide species produces a conformational signal change from the conformationally labeled polymerase and wherein the rate or time duration for the conformational signal change is distinguishable for each different nucleotide species; detecting a series of changes in the signal from the conformationally labeled polymerase under the conditions; and determining the rates or time durations for the changes in the signal, thereby determining the sequence of nucleotides for the nucleic acid template.
    Type: Grant
    Filed: April 19, 2016
    Date of Patent: January 9, 2018
    Assignee: ILLUMINA, INC.
    Inventors: Molly He, Cheng-Yao Chen, Eric Kool, Mostafa Ronaghi, Michael Previte, Rigo Pantoja
  • Patent number: 9856527
    Abstract: Disclosed are compositions and methods for making differentiable amplicon species at unequal ratios using a single amplification system in a single vessel. The number of differentiable amplicons and their ratios to one another are chosen to span the required linear dynamic range for the amplification reaction and to accommodate limitations of the measuring system used to determine the amount of amplicon generated. Unequal amounts of distinguishable amplicon species are generated by providing unequal amounts of one or more amplification reaction components (e.g., distinguishable amplification oligomers, natural and unnatural NTP in an NTP mix, or the like). The amount of target nucleic acid present in a test sample is determined using the linear detection range generated from detection of one or more amplicon species having an amount within the dynamic range of detection.
    Type: Grant
    Filed: May 23, 2016
    Date of Patent: January 2, 2018
    Assignee: GEN-PROBE INCORPORATED
    Inventors: Daniel L. Kacian, Kenneth A. Browne
  • Patent number: 9840743
    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: March 23, 2017
    Date of Patent: December 12, 2017
    Assignee: Guardant Health, Inc.
    Inventor: AmirAli Talasaz
  • Patent number: 9840733
    Abstract: An apparatus for monitoring amplification of a nucleic acid by providing a pH sensor or pH indicator, a nucleic acid in an amplification mixture, and an isothermal amplification enzyme.
    Type: Grant
    Filed: September 30, 2016
    Date of Patent: December 12, 2017
    Assignee: DNAE GROUP HOLDINGS LIMITED
    Inventors: Maurizio Lamura, Angel Chan-Ju Wang, Alpesh Patel
  • Patent number: 9834816
    Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.
    Type: Grant
    Filed: March 6, 2017
    Date of Patent: December 5, 2017
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: R. Scott Kuersten
  • Patent number: 9834822
    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: April 20, 2017
    Date of Patent: December 5, 2017
    Assignee: Guardant Health, Inc.
    Inventor: AmirAli Talasaz
  • Patent number: 9834818
    Abstract: The method includes obtaining a sample including a target nucleic acid, contacting the sample with a quantification primer, adding a quantity of blocking primer to the sample, and repeating the contacting and adding steps until the total quantity of blocking primer present in the sample meets or exceeds the amount of target present in the sample. Each repetition utilizes a quantification primer having a different unique identifying feature assigned to sequentially increasing quantification levels, and the quantity of blocking primer added at each repetition establishes numerical spacing between the quantification levels. The method further includes identifying the unique identifying feature present in any bound quantification primers that remain in the sample, where the presence of a unique identifying feature assigned to a particular quantification level indicates the approximate amount of the target present in the sample.
    Type: Grant
    Filed: October 23, 2013
    Date of Patent: December 5, 2017
    Assignee: Siemens Healthcare Diagnostics Inc.
    Inventor: Adrian Nielsen Fehr
  • Patent number: 9834823
    Abstract: Disclosed are primers, probes, and single nucleotide polymorphisms (SNP) specific to a distinct subclones of the E. coli sequence type 131 (ST131). Also disclosed are methods and assay kits useful in detecting the presence of the distinct subtype of E. coli and methods of treating a subject suffering from an infection from a subclone of ST131.
    Type: Grant
    Filed: July 2, 2013
    Date of Patent: December 5, 2017
    Inventors: Lance B. Price, Evgeni V. Sokurenko, James R. Johnson
  • Patent number: 9822411
    Abstract: In some embodiments, methods for obtaining sequence information from a nucleic acid template linked to a support include hybridizing a first primer to a template strand linked to a support, sequencing a portion of the nucleic acid template, thereby forming an extended first primer product that is complementary to a portion of the nucleic acid template, In some embodiments, the method further includes introducing a nick into a portion of the template strand that is hybridized to the extended first primer product, degrading a portion of the template strand from the nick using a degrading agent, where a portion of the extended first primer remains hybridized to an undegraded portion of the template strand, and sequencing at least some of the single-stranded portion of the extended first primer by synthesis.
    Type: Grant
    Filed: February 3, 2017
    Date of Patent: November 21, 2017
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventors: Jason Myers, Zhoutao Chen, Devin Dressman, Theo Nikiforov
  • Patent number: 9816088
    Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. In some aspects, such methods may comprise steps of: (a) forming a plurality of first vessels each comprising: (i) a single cell, and (ii) a single solid support; (b) copying onto the single solid support: (i) a first copy of a first cell polynucleotide from the single cell, and (ii) a second copy of a second cell polynucleotide from the single cell; (c) forming a plurality of second vessels each comprising (i) a single solid support from the plurality of first vessels, and (ii) a barcoded polynucleotide; and (d) amplifying (i) the first copy and the second copy with a first primer set, and (ii) the barcode with a second primer set, wherein a primer of the first primer set is complementary to a primer of the second set; and (e) forming first and second single cell barcoded sequences.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: November 14, 2017
    Assignee: AbVitro LLC
    Inventors: Francois Vigneault, Adrian Wrangham Briggs
  • Patent number: 9809863
    Abstract: This disclosure relates to Theiler's disease-associated virus (“TDAV”), reagents relating thereto, and methods for detecting, using, and/or treating diseases associated with TDAV.
    Type: Grant
    Filed: October 31, 2013
    Date of Patent: November 7, 2017
    Assignees: ELANCO TIERGESUNDHEIT AG, CORNELL UNIVERSITY
    Inventors: Sanjay Chandriani, Peter Skewes-Cox, Amy Kistler, Bud Tennant, Thomas Divers
  • Patent number: 9809861
    Abstract: A method of evaluating inhibitory effect on damp-dry malodor, containing the steps of: bringing microorganisms which produce damp-dry malodor-causing substances and a test substance into contact with each other in the presence of a sebaceous dirt component; detecting expression of at least one kind of gene selected from a fatty acid desaturase gene and a ? oxidation-related enzyme gene derived from the microorganisms; and thereby evaluating a damp-dry malodor inhibitory function of the test substance based on a change in expression amount of the at least one kind of gene.
    Type: Grant
    Filed: May 28, 2013
    Date of Patent: November 7, 2017
    Assignee: Kao Corporation
    Inventors: Asako Mitani, Hiromi Kubota, Yu Niwano, Kohei Takeuchi, Atsushi Tanaka, Noriko Yamaguchi
  • Patent number: 9797007
    Abstract: A micro-liquid phase reaction method based on a substrate with a hydrophilic-hydrophobic patterned surface, including the following: applying a liquid phase system containing a hydrotropic substance and/or an amphipathic substance to a hydrophobic smooth plane in a sample-spotting manner to form an array of tiny droplets, subsequently removing the solvent in each droplet to bond the hydrotropic substance and/or amphipathic substance in each droplet to the hydrophobic smooth plane so as to form an array of hydrophilic bonding points, then moving an aqueous phase system or hydrophilic liquid phase system containing more than one reactants over the hydrophobic smooth plane, thereby forming island-like tiny reaction droplets at each hydrophilic bonding point, and finally under the set reaction conditions, reacting the reactants in each tiny reaction droplet.
    Type: Grant
    Filed: November 30, 2012
    Date of Patent: October 24, 2017
    Assignee: Suzhou Institute of Nano-Tech and Nano-Bionics of Chinese Academy of Science
    Inventors: Jiong Li, Kexiao Zheng
  • Patent number: 9797001
    Abstract: Methods for the high-throughput analysis of transgenic events are herein disclosed. The methods use libraries of sheared genomic DNA ligated to specialized adapters and pooled for sequence analysis and comparison to known genomic and insert sequence. The method finds use in detecting characterizing insertion site, transgene integrity, and transgene copy number.
    Type: Grant
    Filed: April 17, 2014
    Date of Patent: October 24, 2017
    Assignee: PIONEER HI-BRED INTERNATIONAL, INC.
    Inventors: Mary Beatty, Kevin Hayes, Jenna Hoffman, Haining Lin, Gina Zastrow-Hayes
  • Patent number: 9797014
    Abstract: The invention relates to a method of identifying VDJ recombination products which comprises the use of sequence specific enrichment and specific restriction endonuclease enzymes or other DNA-shearing approaches to provide high resolution and high throughput interrogation of antigen receptor repertoires.
    Type: Grant
    Filed: March 1, 2013
    Date of Patent: October 24, 2017
    Assignee: The Babraham Institute
    Inventors: Andrew Wood, Daniel Bolland, Louise Matheson, Anne Corcoran