Patents Examined by Kaijiang Zhang
  • Patent number: 10894979
    Abstract: The invention pertains to construction of next-generation DNA sequencing (NGS) libraries for whole genome sequencing, targeted resequencing, sequencing-based screening assays, metagenomics, or any other application requiring sample preparation for NGS.
    Type: Grant
    Filed: September 21, 2018
    Date of Patent: January 19, 2021
    Assignee: INTEGRATED DNA TECHNOLOGIES, INC.
    Inventors: Zachary Zwirko, Yu Zheng, Mirna Jarosz, Caifu Chen, Joseph Walder
  • Patent number: 10894959
    Abstract: Disclosed herein are methods for the generation of highly accurate nucleic acid libraries encoding for predetermined variants of a nucleic acid sequence. The nucleic acid sequence may encode for all or part of a reference domain of a CAR. The degree of variation may be complete, resulting in a saturated variant library, or less than complete, resulting in a non-saturating library of variants. The variant nucleic acid libraries described herein may be designed for further processing by transcription or translation. The variant nucleic acid libraries described herein may be designed to generate variant RNA, DNA and/or protein populations. Further provided herein are method for identifying variant species with increased or decreased activities, with applications in regulating biological functions and the design of therapeutics for treatment or reduction of a disease, such as cancer.
    Type: Grant
    Filed: March 14, 2018
    Date of Patent: January 19, 2021
    Assignee: TWIST BIOSCIENCE CORPORATION
    Inventors: Anthony Cox, Siyuan Chen
  • Patent number: 10865410
    Abstract: Provided herein is technology relating to next-generation sequencing and particularly, but not exclusively, to methods and compositions for preparing a next-generation sequencing library comprising short overlapping DNA fragments and using the library to sequence one or more target nucleic acids.
    Type: Grant
    Filed: June 29, 2018
    Date of Patent: December 15, 2020
    Assignee: ABBOTT MOLECULAR INC.
    Inventor: Dae Hyun Kim
  • Patent number: 10858651
    Abstract: Methods are provided for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids, e.g., sequence analysis. The methods result in a subset of the initial population enriched for a target region, which is typically located within one or more target fragments. The methods are particularly useful for analyzing populations having a high degree of complexity, e.g., chromosomal-derived DNA, whole genomic DNA, or mRNA populations.
    Type: Grant
    Filed: August 28, 2019
    Date of Patent: December 8, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Yu-Chih Tsai, Igor Vilfan, Khai Luong
  • Patent number: 10851427
    Abstract: The present invention relates to methods, kits and systems for the prognosis of the disease outcome of breast cancer, said method comprising: (a) determining in a tumor sample from said patient the RNA expression levels of at least 2 of the following 9 genes: UBE2C, BIRC5, RACGAP1, DHCR7, STC2, AZGP1, RBBP8, IL6ST, and MGP (b) mathematically combining expression level values for the genes of the said set which values were determined in the tumor sample to yield a combined score, wherein said combined score is indicative of a prognosis of said patient; and kits and systems for performing said method.
    Type: Grant
    Filed: January 17, 2020
    Date of Patent: December 1, 2020
    Assignee: MYRIAD INTERNATIONAL GMBH
    Inventors: Mareike Dartmann, Inke Sabine Feder, Mathias Gehrmann, Guido Hennig, Karsten Weber, Christian Von Törne, Ralf Kronenwett, Christoph Petry
  • Patent number: 10844426
    Abstract: The present invention relates to a method of identifying a target genomic nucleic acid sequence including hybridizing a set of probes to the target genomic nucleic acid sequence, wherein the set of probes has a unique associated barcode sequence for identification of the target genomic nucleic acid sequence, wherein each probe of the set includes (1) a complementary sequence complementary to a first strand of the target genomic nucleic acid sequence and (2) the associated barcode sequence or a portion of the associated barcode sequence, sequencing the associated barcode sequence from probes hybridized to the target genomic nucleic acid sequence using a fluorescence-based sequencing method, and identifying the target genomic nucleic acid sequence by the sequenced barcode sequence.
    Type: Grant
    Filed: March 17, 2017
    Date of Patent: November 24, 2020
    Inventors: Evan R. Daugharthy, Son C. Nguyen, Chao-ting Wu, George M. Church
  • Patent number: 10837012
    Abstract: Methods are provided for assembly of a target polynucleotide sequence comprising at least a first double stranded polynucleotide (DSP) and at least second DSP, and optionally further DSPs. The method comprises an assembly reaction comprising steps including providing a first single stranded polynucleotide (SSP) comprising the polynucleotide sequence of one strand of the first DSP, and a second SSP comprising the polynucleotide sequence of one strand of the second DSP and converting the SSPs to double stranded form via a primer and polymerase-mediated extension reaction. The DSPs comprise polynucleotide sequences that are complementary to other polynucleotide sequences within the assembly reaction such that the ordering and directionality of each of the first and second, and further DSPs is determined by unique overhang pairing. Nucleic acid libraries and methods of making such libraries are also provided.
    Type: Grant
    Filed: September 15, 2016
    Date of Patent: November 17, 2020
    Assignee: LABGENIUS LTD
    Inventors: James Edward John Field, Harrison Frederick Rickerby
  • Patent number: 10822655
    Abstract: The invention relates to a method for detection of analyte interaction with a channel molecule held in a membrane, comprising the optical detection of a modification in the flux of a signal molecule as it passes through the channel molecule by the action of a membrane potential, wherein the modification in the flux is caused by at least partial blockage of the channel molecule by the analyte. The invention further relates to bilayer arrays, components, methods of manufacture and use.
    Type: Grant
    Filed: July 9, 2015
    Date of Patent: November 3, 2020
    Assignee: OXFORD UNIVERSITY INNOVATION LIMITED
    Inventors: Mark Wallace, Hagan Bayley, Shuo Huang, Oliver Kieran Castell, Mercedes Romero-Ruiz
  • Patent number: 10822605
    Abstract: A method of retrieving a subset of polynucleotide molecules from a mixture of polynucleotide molecules includes receiving a mixture of nucleotide sequences comprising one or more polynucleotide molecules, synthesizing one or more identifier (ID) regions onto the one or more polynucleotide molecules, and sequencing members of the population of polynucleotide molecules to associate the sequence of one or more of the molecules (the “Polynucleotide Sequence”) with the sequence of the attached ID region (the “ID Sequence”). The method also includes generating a bead-bound library of one or more beads comprising subsets of identical polynucleotide molecules. Each bead is identified by the ID Sequence of the associated Polynucleotide Sequence.
    Type: Grant
    Filed: May 2, 2014
    Date of Patent: November 3, 2020
    Assignee: GENSINTA, INC.
    Inventors: Austen Heinz, Anselm Levskaya, John T. Mulligan
  • Patent number: 10815536
    Abstract: The present invention provides novel methods, systems, tools, and kits for the simultaneous detection, identification and/or characterization of all viruses known or suspected to infect vertebrates. The methods, systems, tools, and kits described herein are based upon the virome capture sequencing platform (“VirCapSeq-VERT”), a novel platform developed by the inventors. The invention also provides methods and kits for designing and constructing of the virome capture sequencing platform.
    Type: Grant
    Filed: September 19, 2016
    Date of Patent: October 27, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Walter Ian Lipkin, Omar Jabado, Thomas Briese, Amit Kapoor, Jan Gogarten, Komal Jain, Nischay Mishra
  • Patent number: 10816543
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from one or more cells. Such polynucleotide processing may be useful for a variety of applications, including characterization of major histocompatibility complex (MHC) molecules. The compositions, methods, systems, and devices disclosed herein generally describe peptides and barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing MHC molecules from one or more cells.
    Type: Grant
    Filed: April 4, 2019
    Date of Patent: October 27, 2020
    Assignee: 10X GENOMICS, INC.
    Inventor: Katherine Pfeiffer
  • Patent number: 10801059
    Abstract: The invention generally relates to sequencing library preparation methods. In certain embodiments, two or more template nucleic acids are joined together by a linking molecule, such as a PEG derivative. Identical copies of a nucleic acid fragment or both strands of a duplex fragment may be linked together. The linked nucleic acids are amplified, creating linked amplicons. Emulsion PCR with linked primers creates linked template nucleic acids for seeding sequencing clusters and errors can be readily identified by their presence on only one of the linked fragments.
    Type: Grant
    Filed: March 28, 2017
    Date of Patent: October 13, 2020
    Assignee: Boreal Genomics, Inc.
    Inventors: Joel Pel, Andrea Marziali
  • Patent number: 10787706
    Abstract: Methods and systems are provided for massively parallel genetic analysis of single cells in emulsion droplets or reaction containers. Genetic loci of interest are targeted in a single cell using a set of probes, and a fusion complex is formed by molecular linkage and amplification techniques. Methods are provided for high-throughput, massively parallel analysis of the fusion complex in a single cell in a population of at least 10,000 cells. Also provided are methods for tracing genetic information back to a cell using barcode sequences.
    Type: Grant
    Filed: October 3, 2019
    Date of Patent: September 29, 2020
    Assignee: GigaGen, Inc.
    Inventors: David Scott Johnson, Everett Hurteau Meyer
  • Patent number: 10780412
    Abstract: The present disclosure provides methods, compositions, and kits for methods that can improve techniques nucleic acid analysis, and can allow for more reliable and accurate targeted, multiplexed, high throughput sequencing. The methods, compositions, and kits can be used for sequencing target loci of nucleic acid. The methods, compositions, and kits disclosed herein can be used for assisted de novo targeted sequencing. The methods, compositions, and kits disclosed herein can also be used for library labeling for de novo sequencing and phasing.
    Type: Grant
    Filed: April 9, 2018
    Date of Patent: September 22, 2020
    Assignee: THE SCRIPPS RESEARCH INSTITUTE
    Inventors: Steven Robert Head, Phillip T. Ordoukhanian, Daniel R. Salomon
  • Patent number: 10773232
    Abstract: De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
    Type: Grant
    Filed: August 8, 2019
    Date of Patent: September 15, 2020
    Assignee: Twist Bioscience Corporation
    Inventors: William Banyai, Bill James Peck, Andres Fernandez, Siyuan Chen, Pierre Indermuhle
  • Patent number: 10760125
    Abstract: A method for designing test or control sequences may include identifying, using a variant caller, loci with systematic errors present in a plurality of sequencing runs included in a training set of sequencing runs obtained using sequencing-by-synthesis; and selecting a representative set of loci, including selecting from the identified loci an approximately equal number of loci involving errors in A, T, C, and G homopolymers and selecting from the identified loci an approximately equal number of loci involving homopolymers having a length of two, three, and four.
    Type: Grant
    Filed: March 16, 2018
    Date of Patent: September 1, 2020
    Assignee: Life Technologies Corporation
    Inventor: Marcin Sikora
  • Patent number: 10753925
    Abstract: The present invention provides high throughput assays for identifying compounds that modulate a contractile function, as well as devices suitable for use in these assays.
    Type: Grant
    Filed: July 28, 2017
    Date of Patent: August 25, 2020
    Assignee: President and Fellows of Harvard College
    Inventors: Kevin Kit Parker, Adam W. Feinberg, Patrick W. Alford, Anna Grosberg, Mark Daniel Brigham, Josue A. Goss
  • Patent number: 10752946
    Abstract: High-fidelity, high-throughput nucleic acid sequencing enables healthcare practitioners and patients to gain insight into genetic variants and potential health risks. However, previous methods of nucleic acid sequencing often introduce sequencing errors (for example, mutations that arise during the preparation of a nucleic acid library, during amplification, or sequencing). Provided herein are methods and compositions for sequencing nucleic acids. Further provided are methods of identifying an error in a nucleic acid sequence.
    Type: Grant
    Filed: January 17, 2018
    Date of Patent: August 25, 2020
    Assignee: MYRIAD WOMEN'S HEALTH, INC.
    Inventors: Clement S. Chu, Noah C. Welker, Henry H. Lai
  • Patent number: 10738303
    Abstract: Sensitive, unbiased methods for genome-wide detection of potential CRISPR-Cas9 off-target cleavage sites from cell type-specific genomic DNA samples.
    Type: Grant
    Filed: December 22, 2017
    Date of Patent: August 11, 2020
    Assignee: The General Hospital Corporation
    Inventors: J. Keith Joung, Shengdar Tsai
  • Patent number: 10738352
    Abstract: The present invention relates to a method of analyzing a composition of nucleic acids derived from a single cell using a microplate including a plurality of reaction wells, the microplate having one bead arranged in one reaction well, the one bead having bound thereto a plurality of molecules of single-stranded oligonucleotides, the single-stranded oligonucleotides each having a nucleic acid capture sequence exposed at the 3? end and a barcode sequence on the 5? side of the nucleic acid capture sequence, the barcode sequence including a base sequence that differs from bead to bead.
    Type: Grant
    Filed: April 7, 2015
    Date of Patent: August 11, 2020
    Assignee: IDAC THERANOSTICS, INC.
    Inventors: Shin-ichi Hashimoto, Shuichi Kaneko, Kouji Matsushima