Patents Examined by Aaron A Priest
  • Non-invasive prenatal diagnosis of fetal genetic condition using cellular DNA and cell free DNA
    Patent number: 9982295
    Abstract: Disclosed are methods for determining at least one sequence of interest of a fetus of a pregnant mother. In various embodiments, the method can determine one or more sequences of interest in a test sample that comprises a mixture of fetal cellular DNA and mother-and-fetus cfDNA. In some embodiments, methods are provided for determining whether the fetus has a genetic disease. In some embodiments, methods are provided for determining whether the fetus is homozygous in a disease causing allele when the mother is heterozygous of the same allele. In some embodiments, methods are provided for determining whether the fetus has a copy number variation (CNV) or a non-CNV genetic sequence anomaly.
    Type: Grant
    Filed: July 17, 2015
    Date of Patent: May 29, 2018
    Assignee: Illumina, Inc.
    Inventors: AmirAli Hajhossein Talasaz, Gordon M. Cann
  • Synthetic nucleic acid spike-ins
    Patent number: 9976181
    Abstract: This disclosure provides methods for determining relative abundance of one or more non-host species in a sample from a host. Also provided are methods involving addition of known concentrations of synthetic nucleic acids to a sample and performing sequencing assays to identify non-host species such as pathogens. Also provided are methods of tracking samples, tracking reagents, and tracking diversity loss in sequencing assays.
    Type: Grant
    Filed: March 24, 2017
    Date of Patent: May 22, 2018
    Assignee: KARIUS, INC.
    Inventors: Fred C. Christians, Igor D. Vilfan, Michael Kertesz, Timothy A. Blauwkamp, Shivkumar Venkatasubrahmanyam, Michael Rosen, Rene Sit
  • Base sequence analysis apparatus
    Patent number: 9976960
    Abstract: There is provided a base sequence analysis method including: a nucleic acid amplification procedure of obtaining an amplification product by a nucleic acid amplification reaction, a turbidity measurement procedure of measuring turbidity of a reaction solution of the nucleic acid amplification reaction; and a melting curve analysis procedure of performing melting curve analysis of a probe nucleic acid chain and the amplification product at a reaction site of the nucleic acid amplification reaction. This base sequence analysis method makes it possible to consecutively perform a nucleic acid amplification reaction and melting curve analysis at the same reaction site.
    Type: Grant
    Filed: July 7, 2015
    Date of Patent: May 22, 2018
    Assignee: SONY CORPORATION
    Inventors: Tomohiko Nakamura, Junji Kajihara
  • Diagnostic methods and markers for bacterial vaginosis
    Patent number: 9970064
    Abstract: A method of diagnosing bacterial vaginosis in a woman, which involves determining an amount of each of more than one BV-associated bacterium in a vaginal sample obtained from the female and assessing a BV status of the female based on the amount of each of the more than one BV-associated bacterium in the sample.
    Type: Grant
    Filed: May 9, 2017
    Date of Patent: May 15, 2018
    Assignee: Laboratory Corporation of America Holdings
    Inventors: Charles Paul Cartwright, Bryndon Denae Lembke, Kalpana Ramachandran
  • Methods and apparatus that increase sequencing-by-binding efficiency
    Patent number: 9951385
    Abstract: A method of nucleic acid detection including (a) contacting a primed template with a polymerase, nucleotide cognate of a first base type and nucleotide cognate of a second base type under ternary complex stabilizing conditions; (b) contacting the primed template nucleic acid with a polymerase, nucleotide cognate of the first base type and nucleotide cognate of a third base type under ternary complex stabilizing conditions; (c) examining products of (a) and (b) for signals produced by a ternary complex that includes the primed template nucleic acid, polymerase and next correct nucleotide, wherein signals for the product of (a) are ambiguous for the first and second base type, and signals for the product of (b) are ambiguous for the first and third base type; (d) disambiguating signals acquired in (c) to identify the next correct nucleotide.
    Type: Grant
    Filed: September 22, 2017
    Date of Patent: April 24, 2018
    Assignee: Omniome, Inc.
    Inventors: Kandaswamy Vijayan, Arnold Oliphant
  • Genotyping by next-generation sequencing
    Patent number: 9951384
    Abstract: Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing.
    Type: Grant
    Filed: May 28, 2015
    Date of Patent: April 24, 2018
    Assignee: DATA2BIO
    Inventors: Patrick S. Schnable, Sanzhen Liu, Wei Wu
  • Method for production of single-stranded macronucleotides
    Patent number: 9944966
    Abstract: The invention relates to a method for production of single-stranded macronucleotides by amplifying and ligating an extended monomeric single-stranded target nucleic acid sequence (targetss) into a repetitive cluster of double-stranded target nucleic acid sequences (targetds), and subsequently cloning the construct into a vector (aptagene vector). The aptagene vector is transformed into host cells for replication of the aptagene and isolated in order to optain single-stranded target sequences (targetss). The invention also relates to single-stranded nucleic acids, produced by a method of the invention.
    Type: Grant
    Filed: March 4, 2014
    Date of Patent: April 17, 2018
    Assignee: Technische Universität Kaiserslautern
    Inventors: Ralf Stadtmüller, Nils Tippkötter, Roland Ulber
  • Biomarker panel for diagnosis and prediction of graft rejection
    Patent number: 9938579
    Abstract: Methods are provided for monitoring a subject having a graft for an acute rejection (AR) response, e.g., to predict, to diagnose, and/or to characterize an AR response. In practicing the subject methods, the expression level of at least one gene in a sample from the subject, e.g., a blood or biopsy sample, is evaluated, e.g., at the nucleic acid and/or protein level, to monitor the subject. Also provided are compositions, systems, kits and computer program products that find use in practicing the subject methods.
    Type: Grant
    Filed: January 11, 2010
    Date of Patent: April 10, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventor: Minnie M. Sarwal
  • Rapid serotyping assay
    Patent number: 9932642
    Abstract: Processes for the serotype specific detection and identification of one or more Salmonella serotypes are provided. A family of specific primers and probes are provided that allow screening of biological or environmental samples for robust, rapid, and reproducible detection and identification of one or more Salmonella serotypes in the sample.
    Type: Grant
    Filed: July 20, 2015
    Date of Patent: April 3, 2018
    Assignee: The United States of America, as represented by the Secretary, Department of Health and Human Services
    Inventors: Patricia Fields, John R. McQuiston, Collette Fitzgerald Leaumont
  • On-slide staining by primer extension
    Patent number: 9909167
    Abstract: A method for analyzing planar sample is provided. In some cases the method comprises: (a) incubating the planar sample with a capture agent that is linked to an oligonucleotide, wherein the capture agent specifically binds to complementary sites in the planar sample; (b) reading a fluorescent signal caused by extension of a primer that is hybridized to the oligonucleotide, using fluorescence microscopy. Several implementations of the method, and multiplexed versions of the same, are also provided.
    Type: Grant
    Filed: December 4, 2014
    Date of Patent: March 6, 2018
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Nikolay Samusik, Garry P. Nolan, Yury Goltsev
  • Cartridge, cartridge reader and method for preventing reuse of the cartridge
    Patent number: 9908114
    Abstract: A disposable fluidic cartridge has a recess therein. A mechanically-actuated mechanism is disposed within the recess for effecting an operation of the fluidic cartridge. The cartridge further comprises a machine-readable identification code on a breakable label covering at least a portion of the recess such that the portion of the breakable label covering the recess may be broken upon insertion of a mechanical actuator into the recess to actuate the mechanically-actuated mechanism. This renders the identification code unreadable and prevents reuse of the cartridge.
    Type: Grant
    Filed: July 28, 2014
    Date of Patent: March 6, 2018
    Assignee: Atlas Genetics Limited
    Inventors: Jay Kendall Taylor, Ben Arlett
  • Method of synthesizing nucleic acid
    Patent number: 9909168
    Abstract: The present invention relates to an oligonucleotide having a novel structure and a method of synthesizing nucleic acid by using the same as a primer. This oligonucleotide is provided at the 5?-side of the primer with a nucleotide sequence substantially the same as a region synthesized with this primer as the origin of synthesis. The present invention realizes synthesis of nucleic acid based on an isothermal reaction with a simple constitution of reagents. Further, the present invention provides a method of synthesizing highly specific nucleic acid on the basis of this method of synthesizing nucleic acid.
    Type: Grant
    Filed: December 9, 2008
    Date of Patent: March 6, 2018
    Assignee: EIKEN KAGAKU KABUSHIKI KAISHA
    Inventors: Tsugunori Notomi, Tetsu Hase
  • Systems for processing multiple assays background
    Patent number: 9903003
    Abstract: Methods, devices, and systems for performing polymerase chain reaction (PCR) amplification and melt data acquisition according to a single slug approach in which a single slug in a microfluidic channel fills an entire thermal zone of the microfluidic channel, and the thermal zone used for both PCR temperature cycling and melt data acquisition. A detector may be configured to detect fluorescence from the thermal zone during the PCR temperature cycling for real-time PCR and/or during temperature ramping in the melt data acquisition. Slug position control may be achieved by detecting leading or trailing edges in a slug build target zone into which a slug passes after passing through the thermal zone. The single slug approach may break coupling between one or more events of the PCR amplification and melt data acquisition and enable events to be independently optimized.
    Type: Grant
    Filed: March 15, 2013
    Date of Patent: February 27, 2018
    Assignee: Canon U.S. Life Sciences, Inc.
    Inventors: Johnathan S. Coursey, Kenton C. Hasson, Brian Bean, Scott Corey
  • High-throughput single cell barcoding
    Patent number: 9902950
    Abstract: Methods and compositions for high-throughput, single cell analyzes are provided. The methods and compositions can be used for analysis of genomes and transcriptomes, as well as antibody discovery, HLA typing, haplotyping and drug discovery.
    Type: Grant
    Filed: October 11, 2011
    Date of Patent: February 27, 2018
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Francois Vigneault
  • High-throughput structure determination using nucleic acid calipers
    Patent number: 9897597
    Abstract: Provided herein are compositions and methods for determining the structure of individual targets using nucleic acid caliper by determining long-range distances within such targets.
    Type: Grant
    Filed: April 23, 2015
    Date of Patent: February 20, 2018
    Assignees: Children's Medical Center Corporation, Dana-Farber Cancer Institude, Inc.
    Inventors: William M. Shih, Wesley Philip Wong
  • Detection of target nucleic acid sequences using dual-labeled immobilized probes on solid phase
    Patent number: 9885081
    Abstract: The present invention relates to a novel method for detection of target nucleic acid sequences on a solid phase using dual-labeled immobilized probes and its resistance to a 5? to 3? exonuclease activity of a DNA polymerase. Because the label is remained on the solid substrate by resistance to nucleases due to labeling of a base component the internal nucleotide, the present invention requires no consideration of a suitability of position of the label for remaining on the solid substrate. The present invention ensures to minimize background signal by positioning labels at a site on probes suitable to maximize quenching efficiency of the dual label system, since it permits to freely determine the position of the internal label on probes.
    Type: Grant
    Filed: October 20, 2011
    Date of Patent: February 6, 2018
    Assignee: Seegene, Inc.
    Inventor: Jong Yoon Chun
  • Detection of target nucleic acid sequence by PTO cleavage and extension-dependent signaling oligonucleotide hybridization assay
    Patent number: 9868980
    Abstract: The present invention relates to the detection of a target nucleic acid sequence by a PCE-SH (PTO Cleavage and Extension-Dependent Signaling Oligonucleotide Hybridization) assay. The present invention does not use probes to be hybridized with target nucleic acid sequences for providing target signals. Interestingly, the present invention uses probes (signaling oligonucleotides) to be hybridized with the extended strand formed in a target-dependent manner in which the extended strand is synthesized using the CTO artificially selected as templates.
    Type: Grant
    Filed: July 3, 2012
    Date of Patent: January 16, 2018
    Assignee: SEEGENE, INC.
    Inventors: Jong Yoon Chun, Young Jo Lee
  • Endometrial phase or endometrial cancer biomarkers
    Patent number: 9863005
    Abstract: Methods for detecting endometrial diseases or an endometrium phase in a subject are described comprising measuring endometrial markers or polynucleotides encoding the markers in a sample from the subject. The invention also provides localization or imaging methods for endometrial diseases, and kits for carrying out the methods of the invention. The invention also contemplates therapeutic applications for endometrial diseases employing endometrial markers, polynucleotides encoding the markers, and/or binding agents for the markers.
    Type: Grant
    Filed: August 13, 2014
    Date of Patent: January 9, 2018
    Inventor: Paul Walfish
  • Removal of PCR inhibitors
    Patent number: 9856515
    Abstract: Provided herein is technology relating to processing and preparing samples and particularly, but not exclusively, to methods, systems, and kits for removing assay inhibitors, e.g., compounds that inhibit polymerase chain reaction, from samples comprising nucleic acids. In particular, the technology is directed toward treating crude sample preparations, such as supernatants from homogenized stool samples, with insoluble polyvinylpyrrolidone (PVP) to form PVP-assay inhibitor complexes, and filtration to separate the PVP-assay inhibitor complexes from the crude sample preparations to produce clarified samples that exhibit reduced assay inhibition.
    Type: Grant
    Filed: March 3, 2015
    Date of Patent: January 2, 2018
    Assignee: Exact Sciences Corporation
    Inventors: Janelle J. Bruinsma, Hemanth D. Shenoi, Michael J. Domanico, James P. Light, II
  • Method for electrochemically identifying target nucleotide sequences
    Patent number: 9856526
    Abstract: A method and assembly for electrochemically identifying target nucleotide sequences. The method includes supplying a biological sample that may contain a predetermined target nucleotide sequence; supplying activatable amplification materials comprising free nucleotides to form replicated target nucleotide sequences; supplying an oxido-reducible compound capable of being inserted during replication between the nucleotides forming the replicated target sequences; and activating the activatable amplification materials before applying an electric field to the sample in order to activate the oxido-reducible compound. The replicated target sequences cause inhibition of electrochemical activity of the inserted oxido-reducible compound, and the presence of the predetermined target nucleotide sequence is determined in instances where the electric current decreases.
    Type: Grant
    Filed: January 15, 2015
    Date of Patent: January 2, 2018
    Assignees: UNIVERSITE PARIS DIDEROT-PARIS 7, CENTRE NATIONAL DE LA RECHERCHE SCIENTIFIQUE (CNRS)
    Inventors: Benoît Limoges, Thibaut Defever, Damien Marchal