Patents Examined by Kenneth R. Horlick
  • Patent number: 10689686
    Abstract: A method for preserving and processing cell-free nucleic acids located within a blood sample is disclosed, wherein a blood sample containing cell-free nucleic acids is treated to reduce both blood cell lysis and nuclease activity within the blood sample. The treatment of the sample aids in increasing the amount of cell-free nucleic acids that can be identified and tested while maintaining the structure and integrity of the nucleic acids.
    Type: Grant
    Filed: April 8, 2019
    Date of Patent: June 23, 2020
    Assignee: Streck, Inc.
    Inventor: M. Rohan Fernando
  • Patent number: 10683538
    Abstract: The present invention provides a method of determining integrity and/or quantity of cell free DNA (cfDNA) in a bio logical sample comprising amplifying target sequences with at least a first primer/probe set and at least a second primer probe/set, amplifying the target sequences of differing lengths, and monitoring for detection of the labels of the oligonucleotide probes, and determining the integrity and/or quantity of the cfDNA based on the level of detection of the label of the oligonucleotide probe from the first primer/probe set compared to the level detection of the label of the oligonucleotide probe from the second primer/probe set. The present invention also provides methods for generating a library with the cfDNA for sequencing and analysis.
    Type: Grant
    Filed: April 18, 2016
    Date of Patent: June 16, 2020
    Assignee: The Translational Genomics Research Institute
    Inventors: Muhammed Murtaza, Tania Contente-Cuomo
  • Patent number: 10683546
    Abstract: An ex vivo method and a kit for predicting the response to a treatment with glucocorticoids (GC) in patients affected by inflammatory diseases, based on quantification of fold change ratio in GR isoform levels.
    Type: Grant
    Filed: May 24, 2016
    Date of Patent: June 16, 2020
    Assignee: UNIVERSIDAD DE CHILE
    Inventors: Cristhian Alejandro Urzua Salinas, Irmgadt Annelise Goecke Sariego
  • Patent number: 10669536
    Abstract: The invention provides methods for isolating RNA from whole urine and urine fractions for the diagnosis of prostate cancer and/or benign prostate hyperplasia. An exemplary method for diagnosing prostate cancer in an individual, said method comprises: (a) determining the amount of RNA encoding one or more diagnostic genes in the soluble urine fraction of a urine sample obtained from said individual; (b) comparing the amount of said RNA to a reference value for said one or more diagnostic genes, wherein said reference value is derived from the amount of RNA encoding said one or more diagnostic genes in one or more individuals that do not have prostate cancer; and (c) diagnosing said individual as having prostate cancer when the amount of said RNA is greater than said reference value.
    Type: Grant
    Filed: April 13, 2018
    Date of Patent: June 2, 2020
    Assignee: Quest Diagnostics Investments LLC
    Inventor: Heather R. Sanders
  • Patent number: 10655188
    Abstract: A method for detecting and characterizing a microorganism in a clinical sample includes introducing a clinical sample to a first culture vessel containing the culture medium; removing a test aliquot; separating DNA from the test aliquot; and performing nucleic acid tests on the DNA to identify the microorganism and to detect the presence or absence of one or more genetic antimicrobial resistance markers in the microorganism. If a microorganism is identified, an antimicrobial susceptibility test is performed wherein microbial growth in the antimicrobial susceptibility test is monitored by accessing growth or markers for growth and wherein the type and concentration of antimicrobial agents used in the antimicrobial susceptibility test is determined by the identity of the microorganism and the antimicrobial resistance markers detected. A device for performing the method is also provided.
    Type: Grant
    Filed: June 12, 2015
    Date of Patent: May 19, 2020
    Assignee: Q-Linea AB
    Inventors: Jonas Jarvius, Jan Grawe
  • Patent number: 10648030
    Abstract: The disclosure provides a method of determining the presence or absence of a plurality of target polynucleotides in a sample including combining a sample that may comprise one or more of the plurality of target polynucleotides with a plurality of sets of complementary polynucleotides; incubating the polynucleotides under conditions that allow hybridization of complementary sequences; joining the first and second complementary polynucleotides to form one or more product polynucleotides; and detecting the presence or absence of one or more product polynucleotides to determine the presence or absence of one or more of the plurality of target polynucleotides in the sample.
    Type: Grant
    Filed: January 14, 2013
    Date of Patent: May 12, 2020
    Assignee: Affymetrix, Inc.
    Inventors: John D. Curry, Heather Koshinsky, Amanda Kay Lindholm-Perry, Richard Mark Thallman
  • Patent number: 10626444
    Abstract: This disclosure provides methods, kits, and compositions to amplify sample DNA of low quantity by adding an amount of buffer DNA before amplification. The method protects the sample DNA against degradation and PCR bias. The method disclosed herein are useful to amplify DNA of low amount, such as genomic DNA from a single cell and therefore are especially useful for genetic diagnostic tests and precision medicine.
    Type: Grant
    Filed: October 11, 2017
    Date of Patent: April 21, 2020
    Assignee: Acudx Inc.
    Inventors: Xitong Li, Zhuanfen Cheng
  • Patent number: 10619151
    Abstract: A method for extracting a nucleic acid from a sample liquid comprises providing a heating element and providing an extraction nucleic acid that is bound to the heating element and/or providing the extraction nucleic acid such that the extraction nucleic acid binds to the heating element. The extraction nucleic acid is at least partly complementary to the nucleic acid. The method further comprises bringing the heating element into contact with the sample liquid such that the nucleic acid at least partly binds to the extraction nucleic acid, and separating the heating element from the sample liquid such that the nucleic acid bound to the extraction nucleic acid remains at the heating element. Additionally, the method comprises bringing the heating element into contact with a reaction solution, and heating the heating element to at least a denaturing temperature of the nucleic acid.
    Type: Grant
    Filed: February 12, 2019
    Date of Patent: April 14, 2020
    Assignee: GNA BIOSOLUTIONS GmbH
    Inventors: Joachim Stehr, Lars Ullerich, Federico Bürsgens, Domenik Zistl, Simon Schmidbauer, Daniel Grodd, Cecilia Rebuffo-Scheer, Lidiya Osinkina
  • Patent number: 10619204
    Abstract: Embodiments of the present disclosure relate to methods for capturing and amplifying target polynucleotides on a solid surface, in particular in a well in a microarray, wherein the microarray may comprise a) a substrate comprising at least one well, a surface surrounding the well and an inner well surface; b) a first layer covering the inner well surface and comprising at least one first capture primer pair; and c) a second layer covering the first layer and the surface surrounding the well.
    Type: Grant
    Filed: November 11, 2015
    Date of Patent: April 14, 2020
    Assignee: Illumina Cambridge Limited
    Inventors: Kevin L. Gunderson, Jingwei Bai, Matthew William Kellinger, John M. Beierle, Jonathan Mark Boutell, Roberto Rigatti, Maria Candelaria Rogert Bacigalupo, Boyan Boyanov, Klaus Maisinger
  • Patent number: 10612082
    Abstract: A method for amplification of nucleic acids in which substantially use is made of the fact that a pre-defined nucleic acid chain (target sequence) can be multiplied/amplified in the presence of a target sequence-specific activator oligonucleotide. The target sequence-specific activator oligonucleotide causes the separation of re-synthesized complementary primer extension products by strand displacement, so that a new primer oligonucleotide can attach to the respective template strand. The thus formed complex of a primer oligonucleotide and a template strand can initiate a new primer extension reaction. The thus formed primer extension products in turn function as templates, so that an exponential amplification reaction results.
    Type: Grant
    Filed: August 21, 2017
    Date of Patent: April 7, 2020
    Assignee: AGCT GmbH
    Inventors: Dmitry Cherkasov, Norbert Basler, Claus Becker, Hans-Joerg Hess, Andreas Mueller-Hermann
  • Patent number: 10596566
    Abstract: A testing device that integrates nucleic acid isolation, isothermal amplification and detection wherein a sample and reagents are transported through a capture/binding membrane by capillary forces and the positioning of a slidebar that supports said binding membrane. Flow control and fluid actuation are effected by the position of said slidebar which makes a fluidic connection through the capture membrane situated between a reservoir of liquid on the device and an absorbing pad, and where a sequence of operations for sample loading, washing, optionally amplification, and optical detection of analytes can be done conveniently and rapidly at the point of care. With minimal operator interaction, this device can lyse, isolate, amplify, and detect nucleic acids from clinical specimens and environmental samples.
    Type: Grant
    Filed: April 17, 2017
    Date of Patent: March 24, 2020
    Assignee: Mauk et al.
    Inventors: Michael G. Mauk, Dharma Teja Varapula, Sirisha Phanithra Gutta
  • Patent number: 10598577
    Abstract: A method includes providing a biological sample, providing a sample collection device, wherein the sample collection device includes a sample binding surface including a photodegradable polymer configured to bind the biological sample, contacting the biological sample with the sample binding surface of the sample collection device, and irradiating the sample binding surface and the bound biological sample using light emitted from a light source to initiate degradation of the photodegradable polymer of the sample binding surface to cause release of the biological sample.
    Type: Grant
    Filed: June 30, 2017
    Date of Patent: March 24, 2020
    Assignee: General Electric Company
    Inventors: Arunkumar Natarajan, John Richard Nelson, Patrick McCoy Spooner, Ralf Lenigk, Wei Gao, Kwok Pong Chan, Lakshmi Sireesha Kaanumalle, Abraham Joy, Nicholas Nun
  • Patent number: 10597651
    Abstract: The present disclosure relates to nucleic acid extraction and purification methods and devices to accomplish the same. The present disclosure proposes a novel approach to this problem wherein cell isolation and nucleic acid purification can be integrated in a single “step,” by using the same solid phase for both cell adsorption and nucleic acid purification. This is achieved by binding the cells to a solid support as a first step. The same solid support is then used under conditions that lyse the bound cells, and then subsequently enable the nucleic acid to bind to the support. Methods of the present disclosure relate to the isolation of nucleic acid, and especially to a method for isolating DNA from cells, biological or environmental samples using antibiotics, which bind nucleic acids.
    Type: Grant
    Filed: April 29, 2015
    Date of Patent: March 24, 2020
    Assignee: Accudx Corporation
    Inventor: Raveendran Pottathil
  • Patent number: 10597737
    Abstract: Methods and kits for detecting a genetic variation in a polynucleotide analyte in a sample. A fluorophore is attached to a first primer, a quencher is attached to a second primer, and the first primer and the second primer are specific for the polynucleotide analyte. At least one of the primers is configured to hybridize to a region of the polynucleotide analyte encoding the genetic variation. The primers are configured to amplify the polynucleotide analyte having the genetic variation and a corresponding polynucleotide analyte lacking the generic variation. There is a detectable difference between a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the polynucleotide analyte with the genetic variation, and a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the corresponding polynucleotide analyte lacking the genetic variation.
    Type: Grant
    Filed: August 22, 2018
    Date of Patent: March 24, 2020
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Aditya Rajagopal, Mark D. Goldberg, Erika F. Garcia, Xiomara L. Madero, Thomas A. Tombrello, Axel Scherer
  • Patent number: 10597716
    Abstract: A method for sequencing a nucleic acid strand, comprising the steps of: providing a solution containing truncated strands having lengths different from one another terminating with a respective dideoxynucleotide from among ddATP, ddTTP, ddGTP, and ddCTP; functionalizing first masses by a donor molecule and second masses by an acceptor molecule such as to generate a light emission when they come into mutual contact; coupling a first mass to a first end of each truncated strand; coupling the second masses to a respective terminal dideoxynucleotide of each strand; applying an AC electrical field having variable frequencies that are such as to generate, on each second mass, a net movement directed towards the first mass; acquiring a plurality of light radiations for each frequency value; and associating each light radiation acquired to a respective dideoxynucleotide and, thus, to a respective nucleotide base.
    Type: Grant
    Filed: December 29, 2016
    Date of Patent: March 24, 2020
    Assignee: STMICROELECTRONICS S.R.L.
    Inventors: Alessandro Paolo Bramanti, Marco Angelo Bianchessi
  • Patent number: 10590476
    Abstract: The present disclosure relates to methods for determining the amount or concentration of a nucleic acid of interest in an unprocessed sample by analyzing a processed sample and a reference sample with digital polymerase chain reaction (dPCR).
    Type: Grant
    Filed: September 21, 2017
    Date of Patent: March 17, 2020
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Alan Furlan, Michael Zeder
  • Patent number: 10584376
    Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time comprising one or more primer oligonucleotides comprising a 5? nicking enzyme recognition site and a 3?-terminal region comprising a 2?-modified nucleotide. These methods are compatible with amplification of target oligonucleotides in a test sample, including biological samples, using a nicking amplification reaction.
    Type: Grant
    Filed: August 30, 2018
    Date of Patent: March 10, 2020
    Assignee: ENVIROLOGIX INC.
    Inventors: Daniel Shaffer, Stephen A. Judice
  • Patent number: 10577601
    Abstract: The invention provides methods for preparing DNA sequencing libraries by assembling short read sequencing data into longer contiguous sequences for genome assembly, full length cDNA sequencing, metagenomics, and the analysis of repetitive sequences of assembled genomes.
    Type: Grant
    Filed: May 12, 2017
    Date of Patent: March 3, 2020
    Assignee: University of Washington
    Inventors: Jay Shendure, Joseph Hiatt, Rupali Patwardhan, Emily Turner
  • Patent number: 10570465
    Abstract: This disclosure provides a method for improving the efficiency and timing of detecting whether sepsis-related microorganisms are present in a fluid sample. The method comprises the steps of: collecting the fluid sample from a patient; fractioning the fluid sample to isolate a quantity of microorganism cells; extracting a portion of the microorganism cells from the fluid sample; lysing a portion of the microorganism cells extracted from the fluid sample to extract microorganism DNA; amplifying the microorganism DNA from the microorganism cells from a predetermined set of DNA primers to determine whether sepsis-related microorganisms are present within the fluid sample.
    Type: Grant
    Filed: March 22, 2019
    Date of Patent: February 25, 2020
    Inventor: Brett Eric Etchebarne
  • Patent number: 10570441
    Abstract: The present invention provides compositions and methods for assaying the activity of nicking enzyme and polymerase in a reaction involving the use of a nucleic acid substrate molecule that detects nicking enzyme and polymerase extension activities by the release of a detectable reporter (e.g., a fluorophore).
    Type: Grant
    Filed: January 25, 2016
    Date of Patent: February 25, 2020
    Assignee: ENVIROLOGIX INC.
    Inventor: Stephen A. Judice