Patents Examined by Cynthia B. Wilder
  • Patent number: 11656233
    Abstract: Methods and reagents for multiplex detection of antibodies are disclosed. In particular, the invention relates to multiplex detection of antibodies using antigen-DNA and antibody-binding agent-DNA conjugates carrying DNA barcodes for identifying and quantitating disease-relevant antibody isotypes, such as those involved in allergic responses, autoimmune diseases, infections, and inflammation.
    Type: Grant
    Filed: March 29, 2018
    Date of Patent: May 23, 2023
    Assignee: The Board of Trastees of the Leland Stanford Junior University
    Inventors: Carolyn Bertozzi, Stephen J. Galli, Kaori Mukai, Peter Robinson, Cheng-ting Tsai, Mindy Tsai
  • Patent number: 11649494
    Abstract: Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.
    Type: Grant
    Filed: December 18, 2019
    Date of Patent: May 16, 2023
    Assignee: Keygene N.V.
    Inventors: Michael Josephus Theresia Van Eijk, Adrianus Johannes Van Tunen
  • Patent number: 11643682
    Abstract: Provided herein are compositions and methods for accurate and scalable Primary Template-Directed Amplification (PTA) nucleic acid amplification and sequencing methods, and their applications for research, diagnostics, and treatment.
    Type: Grant
    Filed: August 31, 2022
    Date of Patent: May 9, 2023
    Assignee: ST. JUDE CHILDREN'S RESEARCH HOSPITAL, INC.
    Inventors: Charles Gawad, John Easton, Veronica Gonzalez-Pena
  • Patent number: 11643694
    Abstract: Disclosed herein are methods for use in detection of single nucleotide variants (SNVs) or indels. The methods may comprise enriching cell-free DNA molecules for a panel of genomic regions and deep sequencing the enriched cfDNA to detect the SNVs or indels.
    Type: Grant
    Filed: March 7, 2022
    Date of Patent: May 9, 2023
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
  • Patent number: 11634782
    Abstract: This disclosure relates to methods of determining quantification conditions for a microorganism and methods of quantifying microorganism concentration in a sample.
    Type: Grant
    Filed: August 23, 2019
    Date of Patent: April 25, 2023
    Assignee: HYGIENA, LLC
    Inventor: Tyler Stephens
  • Patent number: 11608518
    Abstract: Provided herein are methods, systems, and compositions for determining a base in a polynucleotide. In various aspects, the methods, systems, and compositions presented herein are useful for performing 4-base, 5-base, or 6-base sequencing of polynucleotide molecules, for example, from liquid biopsy samples or wherein the base is a low frequency mutation.
    Type: Grant
    Filed: March 21, 2022
    Date of Patent: March 21, 2023
    Assignee: Cambridge Epigenetix Limited
    Inventors: Shankar Balasubramanian, Jens Fullgrabe, Walraj Singh Gosal, Joanna Dawn Holbrook, Sidong Liu, David Morley, Oliver Nentwich, Tobias Ost, Michael Steward, Albert Vilella, Nicolas James Walker, Shirong Yu, Helen Rachel Bignell, Rita Santo San-Bento
  • Patent number: 11603565
    Abstract: The invention is a method of identifying a cognate antigen for a T-cell receptor using neoantigens from a patient's tumor cells combined with the patient's T-cells and using cell sorting, genome sequencing, expressing TCR genes, presenting tumor neoantigens on MHC complex and uniquely barcoding the T-cells where TCR recognition occurs to tag all components of the TCR recognition complex.
    Type: Grant
    Filed: June 14, 2019
    Date of Patent: March 14, 2023
    Assignees: ROCHE SEQUENCING SOLUTIONS, INC., VENTANA MEDICAL SYSTEMS, INC.
    Inventors: Nelson R. Alexander, Aoune Barhoumi, Jan Berka, Rui Chen, Lisa L. Gallegos, Toumy Guettouche, Seoyoung Kim, Maeve E. O'Huallachain, Sedide Ozturk, Jigar Patel, Florian Rubelt, Stacey Stanislaw
  • Patent number: 11603553
    Abstract: Provided herein are methods for enriching a biological sample for a target nucleic acid, and analyzing the nucleic acid. In some cases, a biological sample is enriched for target nucleic acids associated with a cancer or tumor. In some cases, a biological sample is enriched for target nucleic acids, and the target nucleic acids vary in length. In some cases, one or more probes are used to enrich the biological sample for the target nucleic acid. In some cases, one or more probes hybridize to one or more ends of a target nucleic acid.
    Type: Grant
    Filed: March 19, 2020
    Date of Patent: March 14, 2023
    Assignee: GRAIL, LLC
    Inventors: Eugeni Namsaraev, Maneesh Jain
  • Patent number: 11597974
    Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.
    Type: Grant
    Filed: June 6, 2022
    Date of Patent: March 7, 2023
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
  • Patent number: 11591650
    Abstract: The disclosed invention is related to a universal strand-specific protocol for the sequencing preparation of all classes of RNA. The protocol allows for sequencing for dozens to more than thousands of samples simultaneously. Specifically, the disclosed invention is a method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification.
    Type: Grant
    Filed: March 30, 2020
    Date of Patent: February 28, 2023
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Alexander A. Shishkin, Mitchell Guttman, Christine F. Surka, Eric Lander
  • Patent number: 11560590
    Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.
    Type: Grant
    Filed: June 14, 2022
    Date of Patent: January 24, 2023
    Assignee: SINGULAR GENOMICS SYSTEMS, INC.
    Inventors: Daan Witters, Eli N. Glezer, Allen Lipson
  • Patent number: 11555217
    Abstract: Kits and methods for detecting pathogens without the need for laboratory equipment are disclosed. The kits and methods described herein allow for near-room temperature amplification of pathogen polynucleotides in a biological sample in a one-compartment reaction vessel. The kits and methods may be used to detect any target nucleic acid, such as DNA or RNA from a bacterial, fungal, or viral pathogen.
    Type: Grant
    Filed: July 16, 2020
    Date of Patent: January 17, 2023
    Assignee: UNIVERSITY OF MIAMI
    Inventors: Sylvia Daunert, Sapna K. Deo, Erin Kobetz, David Broyles, Anita Manfredi
  • Patent number: 11541394
    Abstract: A reaction processor is provided with a reaction processing vessel in which a channel is formed, a liquid feeding system, a temperature control system for providing a high temperature region and a low temperature region to the channel, and a fluorescence detector for detecting the sample passing through a fluorescence detection region of the channel, and a CPU for controlling the liquid feeding system based on a signal that is detected. A target stop position X[L]0(n+1) of the sample in the low temperature region in an (n+1)th cycle is corrected from a target stop position X[L]0(n) of the sample in the low temperature region in the nth cycle based on the result of stopping control on the sample in the nth cycle.
    Type: Grant
    Filed: November 19, 2019
    Date of Patent: January 3, 2023
    Assignees: Nippon Sheet Glass Company, Limited, Go!Foton, Inc.
    Inventors: Takashi Fukuzawa, Naofumi Nishizawa, Hisao Nagata
  • Patent number: 11535891
    Abstract: Aspects of the present disclosure include methods of making barcoded solid supports. In some embodiments, the methods include producing a concatemer by rolling circle amplification (RCA) of a circular nucleic acid template, where the circular nucleic acid template includes a barcode and a stem-loop forming region, and where the concatemer includes a plurality of linked units, each unit including the barcode and a stem-loop structure formed from the stem-loop forming region. Such methods further include disposing the concatemer on a solid support to produce a barcoded solid support including a plurality of the stem-loop structures extending from the surface of the solid support. The methods may further include treating the stem-loop structures with an agent that produces stem structures having ends compatible with target nucleic acids, and attaching the target nucleic acids to the stem structures. Barcoded solid supports and methods of using the barcoded solid supports are also provided.
    Type: Grant
    Filed: May 1, 2020
    Date of Patent: December 27, 2022
    Assignee: The Regents of the University of California
    Inventors: Richard Green, Balaji Sundararaman
  • Patent number: 11529380
    Abstract: The invention relates to allergic disease, to the development of allergic disease in infants, to determining the likelihood of development of allergic disease in infants and to minimizing the likelihood of development of allergic disease in infants.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: December 20, 2022
    Assignee: MURDOCH CHILDREN'S RESEARCH INSTITUTE Parkville
    Inventors: Peter Vuillermin, Anne-Louise Ponsonby, Mimi Tang
  • Patent number: 11530436
    Abstract: The present disclosure provides a method for assembly of genomic DNA using multiplex end-tagging amplification of genomic fragments.
    Type: Grant
    Filed: May 23, 2018
    Date of Patent: December 20, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Xiaoliang Sunney Xie, Dong Xing, Chi-Han Chang, Longzhi Tan
  • Patent number: 11519039
    Abstract: Disclosed herein are methods for use in detection of molecular residual disease. The methods may comprise deep sequencing a panel of genomic regions in cell-free DNA molecules and computer processing sequence reads to detect variants that are indicative of molecular residual disease.
    Type: Grant
    Filed: June 10, 2022
    Date of Patent: December 6, 2022
    Assignee: Guardant Health, Inc.
    Inventors: Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
  • Patent number: 11519033
    Abstract: The present disclosure relates to materials and methods for spatially analyzing nucleic acids that have been fragmented with a transposase enzyme, alone or in combination with other types of analytes.
    Type: Grant
    Filed: March 7, 2022
    Date of Patent: December 6, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: Michael Schnall-Levin, Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Patrik Stahl, Jonas Frisen, Maja Marklund, Enric Llorens Bobadilla
  • Patent number: 11519032
    Abstract: Provided herein is a method for analyzing polynucleotides such as genomic DNA. In certain embodiments, the method comprises: (a) treating chromatin isolated from a population of cells with an insertional enzyme complex to produce tagged fragments of genomic DNA; (b) sequencing a portion of the tagged fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the genome of the cells by mapping information obtained from the sequence reads to the region. A kit for performing the method is also provided.
    Type: Grant
    Filed: June 6, 2022
    Date of Patent: December 6, 2022
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
  • Patent number: 11505824
    Abstract: A method includes (i) providing an RNA polynucleotide; (ii) modifying the RNA polynucleotide by annealing and ligating a polynucleotide comprising a 3? terminal random multimer segment and having a stem-loop form; (iii) optionally performing a reverse transcription of the RNA polynucleotide; (iv) cleaving the stem-loop segment of the annealed polynucleotide to yield a 3? A overhang; (v) connecting an adaptor polynucleotide complex associated with an RNA translocase enzyme and at least one cholesterol tether segment to the polynucleotide obtained in step (iv); (vi) contacting the modified RNA polynucleotide obtained in step (v) with a transmembrane pore such that the RNA translocase controls the movement of the RNA polynucleotide through the transmembrane pore and the cholesterol tether anchors the RNA polynucleotide in the vicinity of the transmembrane pore; and (vii) taking one or more measurements during the movement of the RNA polynucleotide through the transmembrane pore Other features are also disclosed.
    Type: Grant
    Filed: November 7, 2019
    Date of Patent: November 22, 2022
    Assignee: Siemens Healthcare GmbH
    Inventor: Yiwei Huang