Patents Examined by Cynthia B. Wilder
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Patent number: 11656233Abstract: 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: GrantFiled: March 29, 2018Date of Patent: May 23, 2023Assignee: The Board of Trastees of the Leland Stanford Junior UniversityInventors: Carolyn Bertozzi, Stephen J. Galli, Kaori Mukai, Peter Robinson, Cheng-ting Tsai, Mindy Tsai
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Patent number: 11649494Abstract: 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: GrantFiled: December 18, 2019Date of Patent: May 16, 2023Assignee: Keygene N.V.Inventors: Michael Josephus Theresia Van Eijk, Adrianus Johannes Van Tunen
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Patent number: 11643682Abstract: 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: GrantFiled: August 31, 2022Date of Patent: May 9, 2023Assignee: ST. JUDE CHILDREN'S RESEARCH HOSPITAL, INC.Inventors: Charles Gawad, John Easton, Veronica Gonzalez-Pena
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Patent number: 11643694Abstract: 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: GrantFiled: March 7, 2022Date of Patent: May 9, 2023Assignee: GUARDANT HEALTH, INC.Inventors: Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
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Patent number: 11634782Abstract: This disclosure relates to methods of determining quantification conditions for a microorganism and methods of quantifying microorganism concentration in a sample.Type: GrantFiled: August 23, 2019Date of Patent: April 25, 2023Assignee: HYGIENA, LLCInventor: Tyler Stephens
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Patent number: 11608518Abstract: 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: GrantFiled: March 21, 2022Date of Patent: March 21, 2023Assignee: Cambridge Epigenetix LimitedInventors: 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
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Patent number: 11603565Abstract: 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: GrantFiled: June 14, 2019Date of Patent: March 14, 2023Assignees: 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
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Patent number: 11603553Abstract: 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: GrantFiled: March 19, 2020Date of Patent: March 14, 2023Assignee: GRAIL, LLCInventors: Eugeni Namsaraev, Maneesh Jain
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Patent number: 11597974Abstract: 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: GrantFiled: June 6, 2022Date of Patent: March 7, 2023Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
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Patent number: 11591650Abstract: 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: GrantFiled: March 30, 2020Date of Patent: February 28, 2023Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGYInventors: Alexander A. Shishkin, Mitchell Guttman, Christine F. Surka, Eric Lander
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Patent number: 11560590Abstract: Disclosed herein, inter alia, are substrates, kits, and efficient methods of preparing and sequencing two or more regions of a double-stranded polynucleotide.Type: GrantFiled: June 14, 2022Date of Patent: January 24, 2023Assignee: SINGULAR GENOMICS SYSTEMS, INC.Inventors: Daan Witters, Eli N. Glezer, Allen Lipson
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Patent number: 11555217Abstract: 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: GrantFiled: July 16, 2020Date of Patent: January 17, 2023Assignee: UNIVERSITY OF MIAMIInventors: Sylvia Daunert, Sapna K. Deo, Erin Kobetz, David Broyles, Anita Manfredi
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Patent number: 11541394Abstract: 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: GrantFiled: November 19, 2019Date of Patent: January 3, 2023Assignees: Nippon Sheet Glass Company, Limited, Go!Foton, Inc.Inventors: Takashi Fukuzawa, Naofumi Nishizawa, Hisao Nagata
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Patent number: 11535891Abstract: 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: GrantFiled: May 1, 2020Date of Patent: December 27, 2022Assignee: The Regents of the University of CaliforniaInventors: Richard Green, Balaji Sundararaman
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Patent number: 11529380Abstract: 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: GrantFiled: December 22, 2017Date of Patent: December 20, 2022Assignee: MURDOCH CHILDREN'S RESEARCH INSTITUTE ParkvilleInventors: Peter Vuillermin, Anne-Louise Ponsonby, Mimi Tang
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Patent number: 11530436Abstract: The present disclosure provides a method for assembly of genomic DNA using multiplex end-tagging amplification of genomic fragments.Type: GrantFiled: May 23, 2018Date of Patent: December 20, 2022Assignee: President and Fellows of Harvard CollegeInventors: Xiaoliang Sunney Xie, Dong Xing, Chi-Han Chang, Longzhi Tan
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Patent number: 11519039Abstract: 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: GrantFiled: June 10, 2022Date of Patent: December 6, 2022Assignee: Guardant Health, Inc.Inventors: Stefanie Ann Ward Mortimer, AmirAli Talasaz, Darya Chudova, Helmy Eltoukhy
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Patent number: 11519033Abstract: 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: GrantFiled: March 7, 2022Date of Patent: December 6, 2022Assignee: 10x Genomics, Inc.Inventors: Michael Schnall-Levin, Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Patrik Stahl, Jonas Frisen, Maja Marklund, Enric Llorens Bobadilla
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Patent number: 11519032Abstract: 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: GrantFiled: June 6, 2022Date of Patent: December 6, 2022Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Paul Giresi, Jason D. Buenrostro, Howard Y. Chang, William J. Greenleaf
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Patent number: 11505824Abstract: 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: GrantFiled: November 7, 2019Date of Patent: November 22, 2022Assignee: Siemens Healthcare GmbHInventor: Yiwei Huang