Patents Examined by Suryaprabha Chunduru
  • Patent number: 10202642
    Abstract: Provided herein is technology relating to sequencing nucleic acids and particularly, but not exclusively, to methods, compositions, systems, and kits for sequencing a nucleic acid using a degenerate two-base code. Particular embodiments provide: 1) that the two-base degenerate code relates a first element to a base comprising adenine (A) or guanine (G) and a second element to a base comprising cytosine (C) or thymine (T); 2) that the two-base degenerate code relates a first element to a base comprising A or C and a second element to a base comprising G or T; and 3) that the two-base degenerate code relates a first element to a base comprising G or C and a second element to a base comprising A or T.
    Type: Grant
    Filed: May 2, 2013
    Date of Patent: February 12, 2019
    Assignee: IBIS BIOSCIENCES, INC.
    Inventor: Mark W. Eshoo
  • Patent number: 10202608
    Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules using iterative activation of one or more vector-encoded traits to progressively assemble a longer nucleic acid insert. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using iterative activation of one or more vector-encoded traits.
    Type: Grant
    Filed: September 30, 2011
    Date of Patent: February 12, 2019
    Assignee: Gen9, Inc.
    Inventor: William J. Blake
  • Patent number: 10196692
    Abstract: A polynucleotide comprising at least the final six nucleotides of one of the following primer sequences, or a sequence complementary thereto: SEQ. ID NOS. 3 to 16, 18, 20 to 33, 35 or 37 to 39. A method of detecting the presence or absence of a mutation in the PIK3CA gene, wherein the mutation is one of H1047R, H1047L, E542K and E545K, and preferably ARMS primers are combined with Scorpion primers.
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: February 5, 2019
    Assignee: QIAGEN MANCHESTER LIMITED
    Inventors: Ruth Board, Jennifer Haworth, Paul Francis Ravetto, Nicola Jo Thelwell, David Whitcombe
  • Patent number: 10196684
    Abstract: The present invention relates to assays, including amplification assays, conducted in the presence of modulators. These assays can be used to detect the presence of particular nucleic acid sequences. In particular, these assays can allow for genotyping or other genetic analysis.
    Type: Grant
    Filed: October 16, 2014
    Date of Patent: February 5, 2019
    Assignee: California Institute of Technology
    Inventors: Rustem F. Ismagilov, Bing Sun, Jesus Rodriguez Manzano, Eugenia Khorosheva, Matthew S. Curtis
  • Patent number: 10190171
    Abstract: A polynucleotide comprising at least the final six nucleotides of one of the following primer sequences, or a sequence complementary thereto: SEQ. ID NOS. 3 to 16, 18, 20 to 33, 35 or 37 to 39. A method of detecting the presence or absence of a mutation in the PIK3CA gene, wherein the mutation is one of H1047R, H1047L, E542K and E545K, and preferably ARMS primers are combined with Scorpion primers.
    Type: Grant
    Filed: September 18, 2015
    Date of Patent: January 29, 2019
    Assignee: QIAGEN MANCHESTER LIMITED
    Inventors: Ruth Board, Jennifer Haworth, Paul Francis Ravetto, Nicola Jo Thelwell, David Whitcombe
  • Patent number: 10174386
    Abstract: An object of the present invention is to provide a method of quantitating or detecting a microorganism, capable of detecting a live microorganism at high sensitivity and more precisely. A method of quantitating a microorganism of interest, using as an index the amount of rRNA of the microorganism of interest is provided.
    Type: Grant
    Filed: January 30, 2006
    Date of Patent: January 8, 2019
    Assignee: KABUSHIKI KAISHA YAKULT HONSHA
    Inventors: Hirokazu Tsuji, Kazunori Matsuda, Takashi Asahara, Koji Nomoto, Mayumi Kiwaki
  • Patent number: 10161007
    Abstract: Methods for the detection of components from biological samples are provided. In certain aspects, the methods may be used to detect and/or quantify specific components in a biological sample, such as tumor cells (e.g., circulating tumor cells). Systems and devices for practicing the subject methods are also provided.
    Type: Grant
    Filed: August 12, 2013
    Date of Patent: December 25, 2018
    Assignee: The Regents of the University of California
    Inventors: Adam R. Abate, Dennis Jay Eastbum, Adam R. Sciambi
  • Patent number: 10144957
    Abstract: This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided. Paneling and multiplex analyses of more than one nucleic acid analyte using one sample are also provided.
    Type: Grant
    Filed: March 30, 2016
    Date of Patent: December 4, 2018
    Assignee: Enzo Life Sciences, Inc.
    Inventors: Elazar Rabbani, James J. Donegan, Dakai Liu
  • Patent number: 10144956
    Abstract: This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided.
    Type: Grant
    Filed: February 26, 2016
    Date of Patent: December 4, 2018
    Assignee: Enzo Biochem, Inc.
    Inventors: Elazar Rabbani, Jannis G. Stavrianopoulos, James J. Donegan, Jack Coleman, Dakai Liu
  • Patent number: 10131941
    Abstract: An application of thiolated single-stranded DNA enhances specific amplification of polymerase chain reaction, namely a method for enhancing specific amplification of polymerase chain reaction by utilizing thiolated single-stranded DNA, which includes the following step: adding an appropriate amount of the thiolated single-stranded DNA into a PCR system to perform PCR amplification, wherein the appropriate amount means that the final concentration of the thiolated single-stranded DNA in a 20 ?L reaction system is not less than 15 ?M. The thiolated single-stranded DNA meets the following conditions: the thiolated single-stranded DNA is one segment of any sequence which is non-complementary and non-homologous to a target sequence; the Tm value is not less than 37.7° C.; and at least one end contains a thiolalkyl group SH—C6H12—.
    Type: Grant
    Filed: August 21, 2014
    Date of Patent: November 20, 2018
    Assignee: INSTITUTE OF PLANT PROTECTION, SHANDONG ACADEMY OF AGRICULTURAL SCIENCES
    Inventors: Xingbo Lu, Guangyuan Zhang, Hongwei Sun, Fan Li, Shuke Yang, Rui Gao, Xiaohui Xu
  • Patent number: 10119114
    Abstract: A cartridge that can be positioned inside an air collection component and receive a component for recovering nucleic acids is described, the cartridge being substantially cylindrical and containing a microorganism retaining zone, the retaining zone containing a microorganism lysis mechanism. Also described is a device for collecting microorganisms contained in the air and a device for microorganism lysis.
    Type: Grant
    Filed: June 6, 2008
    Date of Patent: November 6, 2018
    Assignee: BIOMERIEUX
    Inventors: Hermanus Johannes Maria Kreuwel, Emiel Gerebern Maria Verwimp
  • Patent number: 10106837
    Abstract: This invention provides a single process that collects any and all target nucleic acids from a sample that can contain any of a number of biological species, including bacteria, viruses, or fungi, where the first step renders the sample nonhazardous and releases nucleic acids from cell structures, compartments, and molecular complexes that may hold them, the second step concentrates the target nucleic acids from even very highly dilute states, in the third step releases these in a form that, following dilution, makes them compatible with processes that amplify nucleic acids, both standard PCR as well as isothermal amplification protocols. The pre-amplification process involves ammonia solutions no more toxic than those found in the commercial product Windex, requires no electrical power, requires materials no more complex than water desalinization resin and salt, and can be used by inexperienced individuals.
    Type: Grant
    Filed: February 4, 2015
    Date of Patent: October 23, 2018
    Inventor: Steven A Benner
  • Patent number: 10106842
    Abstract: The present invention provides for novel methods and compositions for nucleic acid sequence detection. Unique, identifying cleavage fragments from probes, bound to target nucleic acids, are produced during PCR by the 5?-nuclease activity of the polymerase. The identity of the targets can be determined by identifying the unique cleavage fragments.
    Type: Grant
    Filed: September 17, 2014
    Date of Patent: October 23, 2018
    Assignee: Roche Molecular Systems, Inc.
    Inventor: Amar Gupta
  • Patent number: 10100292
    Abstract: Provided herein are mutant endonuclease V enzymes that are capable of nicking an inosine-containing DNA sequence. Nucleic acid assays and agents that employ such mutant endonuclease V enzymes to introduce a nick into a target DNA including one or more inosine, and uses a DNA polymerase to generate amplicons of a target DNA are also described.
    Type: Grant
    Filed: February 19, 2016
    Date of Patent: October 16, 2018
    Assignee: General Electric Company
    Inventors: John Richard Nelson, Robert Scott Duthie, Gregory Andrew Grossman, Anuradha Sekher
  • Patent number: 10093908
    Abstract: The present invention features novel, diverse, hybrid and engineered recombinase enzymes, and the utility of such proteins with associated recombination factors for carrying out DNA amplification assays. The present invention also features different recombinase ‘systems’ having distinct biochemical activities in DNA amplification assays, and differing requirements for loading factors, single-stranded DNA binding proteins (SSBs), and the quantity of crowding agent employed.
    Type: Grant
    Filed: December 19, 2013
    Date of Patent: October 9, 2018
    Assignee: Alere San Diego, Inc.
    Inventors: Olaf Piepenburg, Niall A. Armes, Mathew James David Parker
  • Patent number: 10072283
    Abstract: Certain embodiments provide a method for capturing a genomic fragment. The method may comprise: obtaining a substrate comprising a first population of surface-bound oligonucleotides and a second population of surface-bound oligonucleotides; hybridizing a first member of the first population of surface-bound oligonucleotides to a selection oligonucleotide comprising a region that hybridizes with the first member and a region that contains a genomic sequence; extending the first member of the first population of surface-bound oligonucleotides to produce a support-bound selection primer that comprises a sequence that is complementary to the genomic sequence; hybridizing the support-bound selection primer to a nucleic acid fragment comprising the genomic sequence; extending the support-bound selection primer to produce an extension product that contains a sequence that flanks the genomic sequence, e.g., in a genome; and amplifying the extension product on the substrate.
    Type: Grant
    Filed: June 9, 2014
    Date of Patent: September 11, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Samuel Myllykangas, Jason D. Buenrostro, Hanlee P. Ji
  • Patent number: 10072285
    Abstract: Methods of detecting and amplifying short RNAs are provided.
    Type: Grant
    Filed: August 17, 2015
    Date of Patent: September 11, 2018
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Man Cheng, Xiao-Song Gong, Yan Wang, Adam M. McCoy
  • Patent number: 10053728
    Abstract: Devices, containers, and methods are provided for performing biological analysis in a closed environment. Illustrative biological analyzes include high density nucleic acid amplification and detection and immune-PCR.
    Type: Grant
    Filed: July 16, 2015
    Date of Patent: August 21, 2018
    Assignee: BioFire Diagnostics, LLC
    Inventors: Kirk M. Ririe, Mark Aaron Poritz
  • Patent number: 10053729
    Abstract: The present disclosure relates to methods for testing a human for aneuploidy. In some aspects, a plurality of chromosomal sequences in a DNA sample from a human are amplified with a single pair of primers complementary to said chromosomal sequences to form a plurality of amplicons, wherein the plurality of amplicons are not identical, and wherein the plurality of amplicons include sequences on a query chromosome and sequences on a plurality of reference chromosomes. In some aspects, reactions are performed to determine the nucleotide sequence of at least 3 nucleotides of the plurality of amplicons. In some aspects, amplicon nucleotide sequences are matched in silico to genomic sequences at genomic loci. In some aspects, numbers of matching amplicons at individual genomic loci are counted. In some aspects, numbers of amplicons matched to genomic loci on the query chromosome are compared to numbers of amplicons matched to genomic loci on the reference chromosomes.
    Type: Grant
    Filed: March 22, 2013
    Date of Patent: August 21, 2018
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac G. Kinde
  • Patent number: 10041130
    Abstract: Disclosed are diagnostic methods for determining a subtype of methicillin-resistant Staphylococcus aureus (MRSA) in a biological sample of a mammal. Methods include providing a biological sample of the mammal, performing a PCR analysis of the biological sample, and analyzing the PCR amplicons with respect to their sizes so as to determine for type I, type II, type III, type IV or type V MRSA that may be present in the biological sample. Further example embodiments include using at least one mecA primer pair and/or using at least one Staphylococcus aureus nuc primer pair in the PCR analysis. Further disclosed are methods for screening populations for MRSA, and methods of treating a mammal testing positive for Type IV MRSA. Also disclosed are kits for determining a MRSA subtype in a mammal and isolated primers that may be used in the present methods and kits.
    Type: Grant
    Filed: March 18, 2014
    Date of Patent: August 7, 2018
    Assignee: Medical Diagnostic Laboratories, LLC
    Inventors: Scott Elliot Gygax, Christina Lim Overmyer, Lisa A. DeSalvia, Martin Adelson, Eli Mordechai