Patents Examined by Jezia Riley
  • Patent number: 10480025
    Abstract: Nucleosides and nucleotides are disclosed that are linked to detectable labels via a cleavable linker group.
    Type: Grant
    Filed: July 5, 2016
    Date of Patent: November 19, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Shankar Balasubramanian, Colin Lloyd Barnes, Xiaohai Liu, John Milton, Xiaolin Wu, Harold Swerdlow
  • Patent number: 10472382
    Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable Media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.
    Type: Grant
    Filed: November 16, 2018
    Date of Patent: November 12, 2019
    Assignee: QIAGEN SCIENCES, LLC
    Inventors: Steven Gordon, Jerzy Olejnik
  • Patent number: 10465182
    Abstract: Methods and reagents are provided for the rapid extraction of nucleic acids from a cell or tissue sample. In certain embodiments the sample comprises a formalin fixed paraffin embedded sample (e.g., a FFPET sample), or a fine needle aspirate and/or a cell/tissue smear. In some embodiments, the methods comprise incubating one or more sections of said tissue sample in a lysis solution comprising a buffer sufficient to maintain the pH of said solution at a pH ranging from about pH 4 to about pH 9; a chaotropic agent; a chelating agent; and a detergent; where the incubating is at a temperature ranging from about 50° C. to about 100° C.; and recovering the nucleic acid from said lysis solution.
    Type: Grant
    Filed: July 12, 2016
    Date of Patent: November 5, 2019
    Assignee: CEPHEID
    Inventor: Kenneth E. Ho
  • Patent number: 10457984
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: October 2, 2018
    Date of Patent: October 29, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10456415
    Abstract: Oligonucleotide analogues are provided that incorporate 5-aza-cytosine in the oligonucleotide sequence, e.g., in the form of 5-aza-2?-deoxycytidine (decitabine) or 5-aza-cytidine. In particular, oligonucleotide analogues rich in decitabine-deoxyguanosine islets (DpG and GpD) are provided to target the CpG islets in the human genome, especially in the promoter regions of genes susceptible to aberrant hypermethylation. Such analogues can be used for modulation of DNA methylation, such as effective inhibition of methylation of cytosine at the C-5 position. Methods for synthesizing these oligonucleotide analogues and for modulating nucleic acid methylation are provided. Also provided are phosphoramidite building blocks for synthesizing the oligonucleotide analogues, methods for synthesizing, formulating and administering these compounds or compositions to treat conditions, such as cancer and hematological disorders.
    Type: Grant
    Filed: September 28, 2016
    Date of Patent: October 29, 2019
    Assignee: ASTEX PHARMACEUTICALS, INC.
    Inventors: Pasit Phiasivongsa, Sanjeev Redkar
  • Patent number: 10450558
    Abstract: The present invention relates to a new method for enriching and/or isolating nucleic acids from microbial cells which comprises filtering a liquid sample through a nucleic acid-binding matrix which has a pore size small enough to retain microbial cells, lysing the microbial cells on the matrix to release the nucleic acids from the microbial cells, binding the nucleic acids to the matrix and subsequently eluting the DNA. The invention also relates to a method for enriching and/or isolating nucleic acids from microbial cells which are present in a liquid sample that comprises microbial cells and higher eukaryotic cells and/or tissues. The invention also provides a cartridge for carrying out the methods of the invention. Finally, the invention relates to kits for carrying out the methods of the invention.
    Type: Grant
    Filed: May 7, 2015
    Date of Patent: October 22, 2019
    Assignee: Molzym GmbH & Co. KG
    Inventor: Michael Lorenz
  • Patent number: 10443086
    Abstract: The present invention relates generally to the use of a class of surfactants for emulsion and droplet polymerase chain reaction (“PCR”) mixtures. The class of surfactants consists of those having the chemical formula R—(OCH2CH2)n—OH, wherein R is an alkyl group consisting of 12 to 18 carbons and n is 2 to 25. The present invention also relates to methods, devices, systems, and kits incorporating the above-described class of surfactants.
    Type: Grant
    Filed: December 30, 2014
    Date of Patent: October 15, 2019
    Assignee: University of Maryland, College Park
    Inventors: Ian M. White, Kunal Pandit, Srinivasa Raghavan
  • Patent number: 10443096
    Abstract: This disclosure is related to a method of sequencing a single-stranded DNA using deoxynucleotide polyphosphate analogues and translocation of tags from incorporated deoxynucleotide polyphosphate analogues through a nanopore.
    Type: Grant
    Filed: December 16, 2011
    Date of Patent: October 15, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Shiv Kumar, Zengmin Li, Chuanjuan Tao, Minchen Chien, James J. Russo, Sergey Kalachikov, Ken Shepard, Jacob Karl Rosenstein
  • Patent number: 10444224
    Abstract: The present invention relates to novel nucleic acid molecules, called aptamers, that bind specifically to a small molecule fluorophore and thereby enhance the fluorescence signal of the fluorophore upon exposure to radiation of suitable wavelength. Molecular complexes formed between the novel fluorophores, novel nucleic acid molecules, and their target molecules are described, and the use of multivalent aptamer constructs as fluorescent sensors for target molecules of interest are also described.
    Type: Grant
    Filed: February 26, 2019
    Date of Patent: October 15, 2019
    Assignee: Cornell University
    Inventors: Samie R. Jaffrey, Jeremy Paige
  • Patent number: 10435742
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: October 2, 2018
    Date of Patent: October 8, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10428380
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: October 2, 2018
    Date of Patent: October 1, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10428379
    Abstract: Provided herein is technology relating to sequencing nucleic acids, but not exclusively, to compositions, methods, systems, and kits related to nucleotides comprising an electrochemically detectable moiety and one or more photolabile synthesis-inhibiting moieties.
    Type: Grant
    Filed: March 12, 2014
    Date of Patent: October 1, 2019
    Assignee: IBIS BIOSCIENCES, INC.
    Inventors: Mark A. Hayden, Jeffrey Huff, Mark W. Eshoo, John Picuri
  • Patent number: 10428371
    Abstract: The present invention is intended to provide a novel fluorescent labeled single-stranded nucleic acid, by which the background of an exciton oligomer can be further reduced and the novel use thereof. The present invention relates to a labeled single-stranded nucleic acid having at least two fluorescent atomic group pairs that exhibit an exciton effect. The labeled single-stranded nucleic acid is characterized in that the emission peak wavelength of one of the fluorescent atomic group pairs (fluorescent atomic group pair A) is shorter than the excitation peak wavelength of the other fluorescent atomic group pair (fluorescent atomic group pair B), and the fluorescent atomic group pairs A and B have a Förster resonance energy transfer (FRET) effect. This fluorescent labeled single-stranded nucleic acid is usable as a primer for amplifying a target nucleic acid or a probe to be hybridized with a target nucleic acid.
    Type: Grant
    Filed: March 27, 2015
    Date of Patent: October 1, 2019
    Assignee: KABUSHIKI KAISHA DNAFORM
    Inventors: Takeshi Hanami, Yoshihide Hayashizaki, Takahiro Soma, Yasumasa Kimura
  • Patent number: 10415088
    Abstract: Disclosed are processes that use DNA polymerases to extend primers annealed to templates, wherein a standard nucleotide in the template guiding the extension directs the incorporation of a nonstandard nucleotide analog into the product duplex opposite that standard template nucleotide, and processes wherein a nonstandard nucleotide in the template guiding the extension directs the incorporation of a standard nucleotide analog opposite the nonstandard template nucleotide. Conditions, including the pH of the mixture where the primer extension is done and the composition of triphosphate mixtures where the primary extensions done, are disclosed.
    Type: Grant
    Filed: June 4, 2018
    Date of Patent: September 17, 2019
    Inventors: Steven A Benner, Zunyi Yang
  • Patent number: 10407721
    Abstract: Some embodiments described herein relate to modified nucleotide and nucleoside molecules with novel 3?-hydroxy protecting groups. Also provided herein are methods to prepare such modified nucleotide and nucleoside molecules and sequencing by synthesis processes using such modified nucleotide and nucleoside molecules.
    Type: Grant
    Filed: February 28, 2017
    Date of Patent: September 10, 2019
    Assignee: Illumina Cambridge Limited
    Inventors: Xiaohai Liu, Xiaolin Wu, Geoffrey Paul Smith
  • Patent number: 10407713
    Abstract: The present invention provides a special reagent for the pretreatment of sample materials. The pretreatment with the reagent according to the invention enables the isolation of nucleic acids by a uniform method from very diverse sample materials, in particular different bioprocess samples, even if the nucleic acids are only present in small amounts in the sample materials. The reagent used for the pretreatment comprises, as key component, at least one compound comprising an amino group. The invention further relates to methods of purification of nucleic acids, in which the sample material is pretreated correspondingly, and suitable kits.
    Type: Grant
    Filed: July 4, 2012
    Date of Patent: September 10, 2019
    Assignee: QIAGEN GmbH
    Inventor: Peter Porschewski
  • Patent number: 10407459
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: October 1, 2018
    Date of Patent: September 10, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10407458
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analog after the nucleotide analog is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogs which comprise unique labels attached to the nucleotide analog through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: October 1, 2018
    Date of Patent: September 10, 2019
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10392418
    Abstract: The present disclosure provides a solid phase method of making oligonucleotides via sequential coupling cycles including at least one coupling of a dinucleotide dimer subunit to a free 3?-terminal group of a growing chain. The oligonucleotides include at least two nucleoside subunits joined by a N3??P5? phosphoramidate linkage. The method may include the steps of (a) deprotecting the protected 3? amino group of a terminal nucleoside attached to a solid phase support, said deprotecting forming a free 3? amino group; (b) contacting the free 3? amino group with a 3?-protected amino-dinucleotide-5?-phosphoramidite dimer in the presence of a nucleophilic catalyst to form an internucleoside N3??P5? phosphoramidite linkage; and (c) oxidizing (e.g., sulfurizing) the linkage. The compositions produced by the subject methods may include a reduced amount of one or more (N?x) oligonucleotide products. Also provided are pharmaceutical compositions including the subject oligonucleotide compositions.
    Type: Grant
    Filed: September 14, 2017
    Date of Patent: August 27, 2019
    Assignee: Geron Corporation
    Inventor: Premchandran H. Ramiya
  • Patent number: 10392659
    Abstract: The invention provides a novel class of cyanine dyes that are functionalized with sulfonic acid groups and a linker moiety that facilitates their conjugation to other species and substituent groups which increase the water-solubility, and optimize the optical properties of the dyes. Also provided are conjugates of the dyes, methods of using the dyes and their conjugates and kits including the dyes and their conjugates.
    Type: Grant
    Filed: September 12, 2016
    Date of Patent: August 27, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Yue, Gene Shen, Wei-Chuan (David) Sun