Patents Examined by Stephanie K. Mummert
  • Determination of nucleic acid methylation
    Patent number: 11021743
    Abstract: The invention relates to methods and kits for determining the methylation status of a target nucleic acid molecule in a sample comprising (a) bisulfite treatment of the target nucleic acid, (b) amplifying the treated target nucleic acid with methylation-specific primers, (c) contacting the amplicons with a methylation-specific plasmonic nanoprobe and (d) determining the methylation status based on melting temperature Tm of the hybrid probe and the target nucleic acid. In particular, a plasmonic gold nanoparticle covalently coupled to a morpholino oligonucleotide probe. Also claimed are methods and kits for determining methylation status of the Septin 9 (SEPT9) gene promoter.
    Type: Grant
    Filed: November 25, 2016
    Date of Patent: June 1, 2021
    Assignee: Agency for Science, Technology and Research
    Inventors: Yanbing Zu, Jackie Y. Ying
  • Assay for detecting hepatitis C virus (HCV)
    Patent number: 11021763
    Abstract: The disclosure is directed to methods, kits, and compositions, for amplifying and detecting a human hepatitis C virus (HCV) in a sample, which comprises a variety of combinations of forward oligonucleotide primers, reverse oligonucleotide primers, and oligonucleotide probes.
    Type: Grant
    Filed: October 3, 2018
    Date of Patent: June 1, 2021
    Assignee: ABBOTT MOLECULAR INC.
    Inventors: Dan Toolsie, Shihai Huang, Hong Su, Darren Drapp, William Caminiti, Kara Nordin, Sevim Arslan, Sara Jones
  • Method of preparing cell free nucleic acid molecules by in situ amplification
    Patent number: 11015213
    Abstract: Methods for in situ amplification (ISA) of cfNA, such as cfDNA, in a sample are provided wherein the cfNA in the sample is not subject to a nucleic acid purification step. The methods disclosed may be used to generate an analyzable pool of cfNA present in the sample. The analyzable pool may be used with a variety of analytical techniques to characterize the nucleic acid in the sample. Methods of diagnosis, determining a therapeutic intervention and monitoring of a subject are also provided.
    Type: Grant
    Filed: August 12, 2016
    Date of Patent: May 25, 2021
    Assignee: CIRCULOGENE THERANOSTICS, LLC
    Inventor: Chen-Hsiung Yeh
  • Maximizing DNA yield of blood specimens collected in rapid clot tubes
    Patent number: 11015186
    Abstract: The invention provides methods for isolating DNA from a blood sample collected into tubes containing a rapid clot activator, which involves the use of a lysis buffer comprising an alcohol.
    Type: Grant
    Filed: September 7, 2017
    Date of Patent: May 25, 2021
    Assignee: Abbott Molecular Inc.
    Inventors: Wai-Bing Mak, Dominik Duelli, Shihai Huang
  • Detection of colorectal cancer
    Patent number: 11001898
    Abstract: The present disclosure provides, among other things, methods for colorectal cancer detection (e.g., screening) and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include analysis of methylation status of one or more methylation biomarkers, and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer detection (e.g., screening) that include detecting (e.g., screening) methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include detecting (e.g., screening) methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA, using MSRE-qPCR.
    Type: Grant
    Filed: March 26, 2020
    Date of Patent: May 11, 2021
    Assignee: Universal Diagnostics, S.L.
    Inventors: Marko Bitene, Kristi Kruusmaa, Juan Martinez-Barea, Christian Hense, Pol Sola de los Santos, Pol Canal Noguer, Marko Chersicola, Primo{hacek over (z)} Knap
  • Methods of monitoring conditions by sequence analysis
    Patent number: 11001895
    Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
    Type: Grant
    Filed: December 17, 2018
    Date of Patent: May 11, 2021
    Assignee: Adaptive Biotechnologies Corporation
    Inventors: Malek Faham, Thomas Willis
  • Methods of utilizing thermostable mismatch endonuclease
    Patent number: 10975415
    Abstract: A polypeptide having a mismatch endonuclease activity of recognizing a mismatch and cleaving the mismatch; a mismatch-specific cleavage reaction using the polypeptide; a method for removing an error in a nucleic acid amplification reaction utilizing the polypeptide; a method for inhibiting the amplification of a nucleic acid comprising a specific nucleotide sequence during a nucleic acid amplification reaction; and a method for detecting a nucleic acid having a single-nucleotide polymorphism mutation utilizing the inhibition method.
    Type: Grant
    Filed: September 9, 2015
    Date of Patent: April 13, 2021
    Assignees: TAKARA BIO INC., KYUSHU UNIVERSITY, NATIONAL UNIVERSITY CORPORATION, EDUCATIONAL CORPORATION KANSAI BUNRI SOUGOUGAKUEN
    Inventors: Takashi Uemori, Yoshizumi Ishino, Takehiro Sagara, Sonoko Ishino, Takeshi Yamagami, Tsuyoshi Shirai
  • Methods for simultaneous amplification of target loci
    Patent number: 10975439
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Grant
    Filed: January 21, 2020
    Date of Patent: April 13, 2021
    Assignee: Natera, Inc.
    Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
  • Process for cognate nucleotide detection in a nucleic acid sequencing workflow
    Patent number: 10975427
    Abstract: Method and composition for identifying cognate nucleotides in a Sequencing By Binding™ procedure, wherein one or more labeled nucleotides are detected in ternary complexes but never incorporated. Labeled nucleotides can be incorporable nucleotides that contact preformed blocked primed template nucleic acids. Alternatively, labeled nucleotides are labeled non-incorporable nucleotides. Labeled nucleotides, including labeled non-incorporable nucleotides, can be detected in ternary complexes in the same reaction mixture that incorporates a reversible terminator nucleotide to create a blocked primed template nucleic acid. Detection of ternary complexes can take place in the presence of a catalytic metal ion.
    Type: Grant
    Filed: January 17, 2018
    Date of Patent: April 13, 2021
    Assignee: OMNIOME, INC.
    Inventors: Corey M. Dambacher, Joseph Rokicki, Keunho Ahn, Brittany Ann Rohrman, Michael Nguyen, Kandaswamy Vijayan
  • Method for evaluating efficacy of chemoradiotherapy against squamous cell carcinoma
    Patent number: 10969390
    Abstract: A method for evaluating an efficacy of a chemoradiotherapy against squamous cell carcinoma comprises the following steps (a) to (c): (a) detecting an expression level of at least one gene selected from a SIM2 gene and genes co-expressed with the SIM2 gene in a squamous cell carcinoma specimen isolated from a subject; (b) comparing the expression level detected in the step (a) with a reference expression level of the corresponding gene; and (c) determining that an efficacy of a chemoradiotherapy against squamous cell carcinoma in the subject is high if the expression level in the subject is higher than the reference expression level as a result of the comparison in the step (b).
    Type: Grant
    Filed: September 24, 2015
    Date of Patent: April 6, 2021
    Assignees: NATIONAL CANCER CENTER, KYOTO UNIVERSITY, OTSUKA PHARMACEUTICAL CO., LTD.
    Inventors: Hiroki Sasaki, Kazuhiko Aoyagi, Manabu Muto, Hiroo Takahashi
  • Method to identify subjects at higher risk to develop an autoimmune disease based on genetic and/or phenotypic screening for epistatic variants in DDX39B (RS2523506) and IL7R (RS6897932)
    Patent number: 10961581
    Abstract: The present invention includes a method, kits, and assays for identifying a human subject as having an increased risk of developing an autoimmune disease, or a human subject with multiple sclerosis caused by elevated soluble Interleukin 7 receptor (sIL7R), by obtaining a biological sample and detecting or measuring in the biological sample an amount of a soluble Interleukin-7 receptor (sIL7R) and an amount of an RNA Helicase DDX39B, whereby a lower expression of DDX39B and a higher secretion of sIL7R identifies the subject from which the biological sample was obtained as having an increased risk of developing an autoimmune disease, when compared to a human subject not having an autoimmune disease. The present invention also includes a method of modifying a treating of subjects based on the lower expression of RNA Helicase DDX39B alone or in combination with an increase in sIL7R.
    Type: Grant
    Filed: March 22, 2018
    Date of Patent: March 30, 2021
    Assignees: Board of Regents, The University of Texas System, Duke University, Case Western Reserve, The Regents of the University of California
    Inventors: Mariano A. Garcia-Blanco, Gaddiel Galarza-Munoz, Simon G. Gregory, Farren B. S. Briggs, Lisa F. Barcellos, Shelton S. Bradrick, Irina Evsyukova, Dennis C. Ko
  • Devices, systems, and methods for single molecule, real-time nucleic acid sequencing
    Patent number: 10954551
    Abstract: Methods, systems, and reagents for real-time single molecule sequencing of nucleic acids, particularly long DNA molecules, is described. Preferably, such methods and systems combine FRET (Förster Resonance Energy Transfer)-based proximity sensing of labeled nucleotides in or near a DNA polymerase's active site with FRET-based monitoring of the conformational changes in the polymerase that occur during nucleotide incorporation.
    Type: Grant
    Filed: March 7, 2018
    Date of Patent: March 23, 2021
    Assignee: Singular Genomics Systems, Inc.
    Inventor: Eli Glezer
  • Use of a porous capillary membrane for determining the amount of rolling circle amplification products
    Patent number: 10934579
    Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: (a) filtering a liquid sample containing rolling circle amplification (RCA) products using a porous capillary membrane, thereby producing an array of the RCA products on the membrane; wherein the sample contains at least a first population of RCA products and a second population of RCA products, wherein the first and second populations of labeled RCA products are distinguishably labeled; and (b) determining the amount of the first labeled population of RCA products and the amount of the second labeled population of RCA products in an area of the membrane.
    Type: Grant
    Filed: January 11, 2019
    Date of Patent: March 2, 2021
    Assignee: VANADIS DIAGNOSTICS
    Inventors: Ove Öhman, Fredrik Persson, Mathias Howell
  • Assay for detection of human parvovirus nucleic acid
    Patent number: 10934598
    Abstract: Nucleic acid oligomers specific for human parvovirus genomic DNA are disclosed. An assay for amplifying and detecting human parvovirus genotypes 1, 2 and 3 nucleic acid in biological specimens is disclosed. Compositions for amplifying and detecting the presence of human parvovirus genotypes 1, 2 and 3 genomic DNA in human biological specimens are disclosed.
    Type: Grant
    Filed: June 20, 2018
    Date of Patent: March 2, 2021
    Assignee: GEN-PROBE INCORPORATED
    Inventor: James M. Carrick
  • Isothermal amplification of oligonucleotides
    Patent number: 10920267
    Abstract: Processes are disclosed that create derivative DNA molecules in large numbers under isothermal conditions, where amplification of a looped structure derived from a target is achieved by a process that separately or in combination includes (a) a displaceable probe that (b) may be captured in a separate site, optionally containing (c) components of an artificially expanded genetic information system, where the primers optionally contain (d) components of a self-avoiding molecular recognition system, and optionally (e) involving direct transfer of DNA or RNA from a sample from a capture medium with immobilized quaternary ammonium salts.
    Type: Grant
    Filed: November 29, 2017
    Date of Patent: February 16, 2021
    Inventors: Steven A Benner, Ozlem Yaren, Patricia Moussatche
  • Devices and methods for assembling extremely long DNA molecules
    Patent number: 10907195
    Abstract: Provided among other things is a method of applying force to a macromolecule such as dsDNA to make an end more accessible, such as more accessible to ligation.
    Type: Grant
    Filed: February 16, 2017
    Date of Patent: February 2, 2021
    Assignee: PharmaSeq, Inc.
    Inventor: Wlodek Mandecki
  • Methods for targeted genomic analysis
    Patent number: 10907149
    Abstract: The invention provides a method for genetic analysis in individuals that reveals both the genetic sequences and chromosomal copy number of targeted and specific genomic loci in a single assay. The present invention further provide methods for the sensitive and specific detection of target gene sequences and gene expression profiles.
    Type: Grant
    Filed: January 17, 2018
    Date of Patent: February 2, 2021
    Assignee: Resolution Bioscience, Inc.
    Inventors: Christopher K. Raymond, Christopher D. Armour, Lee P. Lim
  • System and method for immobilization free electrochemiluminescence DNA detection using a luminophore dye for multi-species detection
    Patent number: 10889854
    Abstract: Present invention disclosed a novel method for detecting and quantifying target DNA from the biological sample. It provides a method of amplification of DNA sequences with loop-mediated isothermal amplification (LAMP) and its easy and accurate detection and quantification by electrochemiluminescence (ECL) technique. The target LAMP DNA is bound electrostatically with [Ru(bpy)3]+2 on the carbon electrode surface, and an ECL reaction is triggered by tripropylamine (TPrA) to yield luminescence. This is a highly sensitive strategy for the detection of sequence-specific DNA from different biological samples at picogram levels. The target DNA of Sus scrofa (pork) meat was detected as low as 1 pg/?L (3.43×10?1 copies/?L) and for Bacillus subtilis DNA samples the detection limit of 10 pg/?L (2.2×103 copies/?L) was achieved.
    Type: Grant
    Filed: August 8, 2017
    Date of Patent: January 12, 2021
    Assignee: UNIVERSITI BRUNEI DARUSSALAM
    Inventors: Sharmili Roy, Minhaz Uddin Ahmed
  • Method for sequencing a polynucleotide template
    Patent number: 10876158
    Abstract: The invention provides methods for pairwise sequencing of a double-stranded polynucleotide template, which methods result in the sequential determination of nucleotide sequences in two distinct and separate regions of the polynucleotide template.
    Type: Grant
    Filed: June 11, 2018
    Date of Patent: December 29, 2020
    Assignee: Illumina Cambridge Limited
    Inventors: Geoffrey Paul Smith, Jonathan Mark Boutell, Colin Lloyd Barnes, Roberto Rigatti, Niall Anthony Gormley, David Bentley, Tobias William Barr Ost, Vincent Peter Smith, Graham John Worsley, Eric Hans Vermaas
  • Methods for measuring enzyme activity useful in determining cell viability in non-purified samples
    Patent number: 10876173
    Abstract: An assay kit of reagents including a nucleic acid capable of acting as substrate for polymerase microorganism activity useful in a method of detecting polymerase activity as an indicator of the presence of a micro-organism in a sample are disclosed. The disclosed embodiments also relate to reagents for use in such methods, and to test kits comprising such reagents for carrying out the methods.
    Type: Grant
    Filed: August 12, 2015
    Date of Patent: December 29, 2020
    Inventors: Shawn Mark O'Hara, Daniel Zweitzig