Patents Examined by Jennifer Dunston
  • Patent number: 10731181
    Abstract: The present invention provides RNA-guided endonucleases, which are engineered for expression in eukaryotic cells or embryos, and methods of using the RNA-guided endonuclease for targeted genome modification in eukaryotic cells or embryos. Also provided are fusion proteins, wherein each fusion protein comprises a CRISPR/Cas-like protein or fragment thereof and an effector domain. The effector domain can be a cleavage domain, an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. Also provided are methods for using the fusion proteins to modify a chromosomal sequence or regulate expression of a chromosomal sequence.
    Type: Grant
    Filed: June 21, 2016
    Date of Patent: August 4, 2020
    Assignee: Sigma, Aldrich Co. LLC
    Inventors: Fuqiang Chen, Gregory D. Davis
  • Patent number: 10731167
    Abstract: Computer programs, algorithms, and methods for identifying TALE-activator binding sites, and methods for generation and use of TALE-activators that bind to these sites.
    Type: Grant
    Filed: January 10, 2017
    Date of Patent: August 4, 2020
    Assignee: The General Hospital Corporation
    Inventors: J. Keith Joung, Morgan Maeder
  • Patent number: 10699800
    Abstract: Provided herein are methods, processes and apparatuses for non-invasive assessment of genetic variations that make use of decision analyses. The decision analyses sometimes include segmentation analyses and/or odds ratio analyses.
    Type: Grant
    Filed: May 23, 2014
    Date of Patent: June 30, 2020
    Assignee: Sequenom, Inc.
    Inventors: Chen Zhao, Zeljko Dzakula, Cosmin Deciu, Sung Kyun Kim, Amin R. Mazloom, Gregory Hannum, Mathias Ehrich
  • Patent number: 10697967
    Abstract: The present invention provides compositions and methods for detecting the expression and/or activation levels of components of signal transduction pathways in tumor cells such as triple-negative metastatic breast tumor cells. Information on the expression and/or activation levels of components of signal transduction pathways derived from use of the present invention can be used for cancer diagnosis, prognosis, and in the design of cancer treatments.
    Type: Grant
    Filed: September 20, 2016
    Date of Patent: June 30, 2020
    Assignee: Société des Produits Nestlé S.A.
    Inventors: Xinjun Liu, Phillip Kim, Richard Kirkland, Tani Lee, Belen Ybarrondo, Sharat Singh
  • Patent number: 10676734
    Abstract: Provided are methods, compositions, reagents, kits that are useful for detecting a specific nucleic acid region in genome with high efficiency and high sensitivity.
    Type: Grant
    Filed: July 11, 2017
    Date of Patent: June 9, 2020
    Assignee: LIFE TECHNOLOGIES CORPORATION
    Inventor: Pei-Zhong Tang
  • Patent number: 10675302
    Abstract: Disclosed herein are methods and compositions for targeted cleavage of a genomic sequence, targeted alteration of a genomic sequence, and targeted recombination between a genomic region and an exogenous polynucleotide homologous to the genomic region. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain and polynucleotides encoding same. Methods for targeted cleavage include introduction of such fusion proteins, or polynucleotides encoding same, into a cell. Methods for targeted recombination additionally include introduction of an exogenous polynucleotide homologous to a genomic region into cells comprising the disclosed fusion proteins.
    Type: Grant
    Filed: June 30, 2017
    Date of Patent: June 9, 2020
    Assignee: Sangamo Therapeutics, Inc.
    Inventors: Michael C. Holmes, Fyodor Urnov
  • Patent number: 10676749
    Abstract: Computer programs, algorithms, and methods for identifying TALE-activator binding sites, and methods for generation and use of TALE-activators that bind to these sites.
    Type: Grant
    Filed: February 7, 2014
    Date of Patent: June 9, 2020
    Assignee: The General Hospital Corporation
    Inventors: J. Keith Joung, Morgan Maeder
  • Patent number: 10669557
    Abstract: Disclosed herein are methods and compositions for targeted deletion of double-stranded DNA. The compositions include fusion proteins comprising a cleavage domain (or cleavage half-domain) and an engineered zinc finger domain, and polynucleotides encoding same. Methods for targeted deletion include introduction of such fusion proteins, or polynucleotides encoding same, into a cell such that two targeted cleavage events occur. Subsequent cellular repair mechanisms result in deletion of sequences between the two cleavage sites.
    Type: Grant
    Filed: May 31, 2017
    Date of Patent: June 2, 2020
    Assignee: Sangamo Therapeutics, Inc.
    Inventors: Dmitry Guschin, Fyodor Urnov
  • Patent number: 10655162
    Abstract: The present disclosure, in some aspects, provides compositions, systems and methods for proximity-based detection of target biomolecules of interest.
    Type: Grant
    Filed: March 3, 2017
    Date of Patent: May 19, 2020
    Assignee: The Broad Institute, Inc.
    Inventors: Alon Goren, Robert Nicol, Harris Nusbaum
  • Patent number: 10650312
    Abstract: Methods and systems for encoding digital information in nucleic acid (e.g., deoxyribonucleic acid) molecules without base-by-base synthesis, by encoding bit-value information in the presence or absence of unique nucleic acid sequences within a pool, comprising specifying each bit location in a bit-stream with a unique nucleic sequence and specifying the bit value at that location by the presence or absence of the corresponding unique nucleic acid sequence in the pool But, more generally, specifying unique bytes in a bytestream by unique subsets of nucleic acid sequences. Also disclosed are methods for generating unique nucleic acid sequences without base-by-base synthesis using combinatorial genomic strategies (e.g., assembly of multiple nucleic acid sequences or enzymatic-based editing of nucleic acid sequences).
    Type: Grant
    Filed: December 21, 2017
    Date of Patent: May 12, 2020
    Assignee: CATALOG TECHNOLOGIES, INC.
    Inventors: Nathaniel Roquet, Hyunjun Park, Swapnil P. Bhatia
  • Patent number: 10604752
    Abstract: Compositions and methods for using nucleosome interacting protein domains to increase accessibility of programmable DNA modification proteins to target chromosomal sequences, thereby increasing efficiency of targeted genome/epigenetic modification in eukaryotic cells.
    Type: Grant
    Filed: July 10, 2018
    Date of Patent: March 31, 2020
    Assignee: Sigma-Aldrich Co. LLC
    Inventors: Fuqiang Chen, Xiao Ding, Yongmei Feng, Gregory D. Davis
  • Patent number: 10603390
    Abstract: A method includes: (1) applying stimulations to a system, wherein applying the stimulations includes modulating, over time, characteristics of the stimulations; (2) measuring a time-varying response of the system to the stimulations; (3) fitting the time-varying response of the system into a model of the system; and (4) using the model of the system, identifying an optimized combination of characteristics of the stimulations to yield a desired response of the system.
    Type: Grant
    Filed: July 29, 2014
    Date of Patent: March 31, 2020
    Assignee: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
    Inventors: Yong Chen, Chih-Ming Ho
  • Patent number: 10544472
    Abstract: A protein reporter system comprising at least one reporter including a response element responsive to the binding of a transcription factor, a secreted enzyme backbone and a recognition region for specific binding of an antibody. Multiplexed assays for binding, assaying and quantifying the activity of transcription factors are also described, in which the assays use protein reporters in sets, libraries or other groupings, as necessary to achieve desired quantification.
    Type: Grant
    Filed: January 9, 2015
    Date of Patent: January 28, 2020
    Assignee: ATTAGENE, INC.
    Inventors: Sergei S. Makarov, Ming Zheng
  • Patent number: 10533224
    Abstract: Methods for diagnosis of sepsis are disclosed. In particular, the invention relates to the use of biomarkers for aiding diagnosis, prognosis, and treatment of sepsis, and to a panel of biomarkers that can be used to distinguish sepsis from noninfectious sources of inflammation, such as caused by traumatic injury, surgery, autoimmune disease, thrombosis, or systemic inflammatory response syndrome (SIRS).
    Type: Grant
    Filed: March 12, 2016
    Date of Patent: January 14, 2020
    Assignee: THE BOARD OF TRUSTEE OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Purvesh Khatri, Timothy E. Sweeney
  • Patent number: 10526639
    Abstract: The present invention relates to the field of analysis of the three-dimensional structure of the genome, i.e., for genome architecture mapping (GAM). The invention provides a method of determining spatial proximity of a plurality of nucleic acid loci in a compartment such as the cell nucleus, by exploiting their co-segregation amongst fractions of that compartment, identified upon separation of the nucleic acid loci from each other depending on their localization in the compartment to obtain a collection of fractions, e.g., by cryo-sectioning or cryo-milling the compartment; determining the presence or absence of the plurality of loci in the fractions; and determining the co-segregation of the plurality of loci. Co-segregation may then be analysed with statistical methods to determine spatial proximity. The method can be used e.g., for determining physical distance between a plurality of loci; and mapping loci and/or genome architecture, e.g.
    Type: Grant
    Filed: December 11, 2015
    Date of Patent: January 7, 2020
    Assignees: MAX-DELBRÜCK-CENTRUM FÜR MOLEKULARE MEDIZIN IN DER HELMHOLTZ-GEMEINSCHAFT, CAMBRIDGE ENTERPRISE LTD.
    Inventors: Ana Pombo, Paul Edwards, Mario Nicodemi, Antonio Scialdone, Robert Beagrie
  • Patent number: 10501794
    Abstract: Unbiased, genomewide and highly sensitive methods for detecting mutations, e.g., off-target mutations, induced by engineered nucleases.
    Type: Grant
    Filed: October 12, 2017
    Date of Patent: December 10, 2019
    Assignee: The General Hospital Corporation
    Inventors: J. Keith Joung, Shengdar Tsai
  • Patent number: 10460829
    Abstract: In one embodiment, a method of encoding variation data for a population comprises receiving, by a variant encoding engine executing on a processor, information describing genetic variation of a population of individuals. The information comprises a plurality of variable sites within the reference genome of the population and the genotypes of a plurality of individuals in the population with respect to those variable sites. The method further comprises selecting an encoding strategy for the information based on the characteristics of the genetic variation across the population, and encoding the information according to the selected encoding strategy. In certain embodiments, selecting an encoding strategy may comprise determining the variability of a variable site within the population, and encoding information associated with the variable site based on the variability.
    Type: Grant
    Filed: January 26, 2016
    Date of Patent: October 29, 2019
    Assignee: SEVEN BRIDGES GENOMICS INC.
    Inventor: Benjamin Murray
  • Patent number: 10450561
    Abstract: The present invention relates to a method for determining an uterine receptivity profile in order to increase implantation success in assisted fertilization.
    Type: Grant
    Filed: July 19, 2013
    Date of Patent: October 22, 2019
    Assignee: MATRICELAB INNOVE
    Inventors: Nathalie Ledee, Marie Petitbarat
  • Patent number: 10450585
    Abstract: The present disclosure is in the field of genome engineering, particularly targeted modification of the genome of a cell.
    Type: Grant
    Filed: July 13, 2016
    Date of Patent: October 22, 2019
    Assignee: Sangamo Therapeutics, Inc.
    Inventors: Gary K. Lee, Brigit E. Riley, Susan J. St. Martin, Thomas Wechsler
  • Patent number: 10441653
    Abstract: The present invention relates to a nucleic acid of the general formula (I): GIXmGn, which may be modified by a lipid. The invention relates further to a pharmaceutical composition containing an immune-stimulating agent according to the invention in combination with a pharmaceutically active carrier/vehicle (and, optionally, further auxiliary substances, additives and/or further adjuvants). The present invention can relate to a vaccine, which corresponds to a pharmaceutical composition of the invention, wherein the pharmaceutically active component induces a specific immune response (e.g. an antigen). The present invention can relate to the use of a nucleic acid of the invention or a pharmaceutical composition according to the invention for the treatment of infectious diseases, autoimmune disease, allergies or cancer diseases.
    Type: Grant
    Filed: June 8, 2012
    Date of Patent: October 15, 2019
    Assignee: CureVac AG
    Inventors: Ingmar Hoerr, Jochen Probst, Thomas Ketterer, Birgit Scheel