Patents Examined by Frank W Lu
  • Patent number: 11946096
    Abstract: The present invention relates to methods of imaging template hybridisation for estimating cluster numbers prior to solid phase amplification and sequencing. More particularly, an initial round of imaging is carried out at the single molecule template hybridisation stage which allows a general estimation of cluster numbers prior to clusters being formed. Amplification of the signal allows single molecule imaging to be carried out using standard sequencing imaging apparatus.
    Type: Grant
    Filed: June 14, 2021
    Date of Patent: April 2, 2024
    Inventors: Isabelle Marie Julia Rasolonjatovo, Jonathan Mark Boutell, Vincent Peter Smith, Roberto Rigatti
  • Patent number: 11939622
    Abstract: Disclosed herein include systems, methods, kits, and compositions for labeling nuclear target-associated DNA in a cell. Some embodiments provide digestion compositions comprising a DNA digestion enzyme and a binding reagent capable of specifically binding to the nuclear target. Some embodiments provide conjugates comprising a transposome and a binding reagent capable of specifically binding to a nuclear target. The transposome can comprise a transposase (e.g., Tn5 transposase), a first adaptor having a first 5? overhang, and a second adaptor having a second 5? overhang. The methods can comprise contacting a permeabilized cell comprising a nuclear target associated with dsDNA, such as genomic DNA (gDNA), with the compositions provided herein to generate a plurality of nuclear target-associated dsDNA fragments (e.g., nuclear target-associated gDNA fragments) each comprising the one or two single-stranded overhangs.
    Type: Grant
    Filed: July 21, 2020
    Date of Patent: March 26, 2024
    Assignee: Becton, Dickinson and Company
    Inventor: Hye-Won Song
  • Patent number: 11906523
    Abstract: Disclosed herein are embodiments of a signaling conjugate, embodiments of a method of using the signaling conjugates, and embodiments of a kit comprising the signaling conjugate. The disclosed signaling conjugate comprises a latent reactive moiety and a chromogenic moiety that may further comprise a linker suitable for coupling the latent reactive moiety to the chromogenic moiety. The signaling conjugate may be used to detect one or more targets in a biological sample and are capable of being covalently deposited directly on or proximally to the target. Particular disclosed embodiments of the method of using the signaling conjugate comprise multiplexing methods.
    Type: Grant
    Filed: April 23, 2020
    Date of Patent: February 20, 2024
    Inventors: Nelson Alexander, William Day, Jerome W. Kosmeder, II, Mark Lefever, Larry Morrison, Anne M. Pedata, Stacey Stanislaw
  • Patent number: 11901041
    Abstract: In certain aspects, methods of the invention involve performing modification state specific enzymatic reaction of nucleic acid in a sample, determining a value associated with efficiency of the modification state specific enzymatic reaction based on a control, determining an amount of target nucleic acid in the sample, and normalizing the amount of target nucleic acid based on the efficiency value. Based on the normalized amount of target nucleic acid, the method further includes determining whether the normalized amount of target nucleic acid is indicative of a condition.
    Type: Grant
    Filed: October 3, 2014
    Date of Patent: February 13, 2024
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Michael Samuels, Jeffrey Olson, Darren R. Link
  • Patent number: 11891632
    Abstract: A DNA polymerase in which a mutation is induced at a specific amino acid position to increase gene mutation specificity, a nucleic acid sequence encoding the polymerase, a vector comprising the nucleic acid sequence, and a host cell transformed with the vector are disclosed. Provided are a method for in vitro detecting one or more gene mutations or SNPs in one or more templates by using a DNA polymerase having increased gene mutation specificity, a composition for detecting a gene mutation or SNP comprising the DNA polymerase, and a PCR kit comprising said composition. Furthermore, provided are a PCR buffer composition for increasing the activity of a DNA polymerase having increased gene mutation specificity and a PCR kit for detecting a gene mutation or SNP comprising the PCR buffer composition and/or the DNA polymerase having increased gene mutation specificity.
    Type: Grant
    Filed: May 31, 2018
    Date of Patent: February 6, 2024
    Assignee: GENECAST CO., LTD
    Inventors: Byung Chul Lee, Il Hyun Park, Huy Ho Lee
  • Patent number: 11884963
    Abstract: Provided are methods of depleting a target nucleic acid from an initial collection of nucleic acids. Aspects of the methods include contacting the initial collection with a nucleic acid guided nuclease specific for the target nucleic acid in a manner sufficient to deplete the target nucleic acid from the initial collection. Depending on a given application, depletion of a target nucleic acid may vary, e.g., where depleting may include cleaving a target nucleic acid in, or selectively separating a target nucleic acid from, the initial collection of nucleic acids. Also provided are compositions and kits for practicing embodiments of the methods.
    Type: Grant
    Filed: April 20, 2021
    Date of Patent: January 30, 2024
    Assignee: Takara Bio USA, Inc.
    Inventors: Andrew Alan Farmer, Craig Betts, Nathalie Bolduc
  • Patent number: 11873483
    Abstract: The disclosure provides methods and compositions useful for labeling of target molecules with origin-specific nucleic acid identifiers (for example, barcodes), which can be used subsequently to identify, quantify, or otherwise characterize a feature or activity of target molecules originating from a particular discreet volume. Such target molecules can include polypeptides expressed by cells, in which nucleic acid molecules encoding the polypeptides are labeled with the same, or matched, origin-specific nucleic acid identifiers.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: January 16, 2024
    Inventors: Robert Nicol, Andrew David Griffiths, Baptiste Saudemont, Timothy V. Kirk
  • Patent number: 11845983
    Abstract: Compositions, methods, and systems are provided for sample preparation techniques and sequencing of macromolecular constituents derived from a cell (i.e., a cell bead) in a multiplexed reaction. Using the compositions, systems, and methods disclosed herein, the association of the macromolecular constituents with the biological particle from which they are derived and the association of the cell bead with the cell bead sample from which they are derived is maintained.
    Type: Grant
    Filed: January 8, 2020
    Date of Patent: December 19, 2023
    Assignee: 10X GENOMICS, INC.
    Inventors: Zahra Kamila Belhocine, Andrew D. Price
  • Patent number: 11821109
    Abstract: The invention describes a method for the synthesis of compounds comprising the steps of: (a) compartmentalising two or more sets of primary compounds into microcapsules; such that a proportion of the microcapsules contains two or more compounds; and (b) forming secondary compounds in the microcapsules by chemical reactions between primary compounds from different sets; wherein one or both of steps (a) and (b) is performed under microfluidic control; preferably electronic microfluidic control The invention further allows for the identification of compounds which bind to a target component of a biochemical system or modulate the activity of the target, and which is co-compartmentalised into the microcapsules.
    Type: Grant
    Filed: March 15, 2018
    Date of Patent: November 21, 2023
    Assignees: President and Fellows of Harvard College, United Kingdom Research and Innovation
    Inventors: Andrew David Griffiths, David A. Weitz, Darren Roy Link, Keunho Ahn, Jerome Bibette
  • Patent number: 11807896
    Abstract: Disclosed herein are compositions, systems, kits and methods related to preserving physical linkage information of isolated DNA subject to DNA damage, and identifying a nucleic acid preservative. Physical linkage information and DNA integrity may be preserved by methods relating to reassembly of chromatin onto isolated DNA molecules so as to protect the nucleic acids, preserve physical linkage information, or size select molecules of interest. Nucleic acid compositions produced by methods disclosed herein are preserved so as to be analyzed, for example, by high throughput sequencing methods.
    Type: Grant
    Filed: March 25, 2016
    Date of Patent: November 7, 2023
    Assignee: Dovetail Genomics, LLC
    Inventors: Brandon J. Rice, David Haussler
  • Patent number: 11802303
    Abstract: Systems and methods for multiplexed cell sorting are provided herein. The disclosed cell sorting system is referred to as DNA gated sorting (DGS). An exemplary system provides a set of orthogonal sorting probes and release probes for sorting cells of one or more different cell types from a biological specimen.
    Type: Grant
    Filed: February 7, 2019
    Date of Patent: October 31, 2023
    Assignee: Georgia Tech Research Corporation
    Inventors: Gabriel A. Kwong, Shreyas N. Dahotre
  • Patent number: 11788124
    Abstract: The present invention relates to detection of nucleic acids and provides a composition comprising a Signal Generating Complex, wherein the composition comprises: (A) a pair of target probes (TPs), wherein a first TP of the pair of TPs comprises a nucleic acid sequence comprising two segments; (B) a pair of base PPAs comprising the first and second base PPAs, wherein the first base PPA comprises a nucleic acid sequence comprising three segments; (C) a set of extension PPAs comprising the first and second extension PPAs, wherein the first extension PPA comprises a nucleic acid sequence comprising two segments; (D) a plurality of pre-amplifiers (PAs), wherein the PAs comprise a nucleic acid sequence comprising three segments; (E) a plurality of amplifiers (AMPs), wherein the AMPs comprise a nucleic acid sequence comprising two segments; and (F) a plurality of label probes (LPs), wherein the LPs comprise a nucleic acid sequence comprising two segments.
    Type: Grant
    Filed: April 8, 2019
    Date of Patent: October 17, 2023
    Inventors: Yuling Luo, Xiao-Jun Ma, Steve Chen, Nan Su, Emerald Doolittle, Bingqing Zhang, Xiaoming Wang, Xingyong Wu, Xiao Yan Pimentel, Helen Jarnagin
  • Patent number: 11781177
    Abstract: Compositions comprising covalently modified and mutated biotin-binding proteins, particularly biotin-binding proteins having a negative charge at physiological pH, are provided. Methods of producing such proteins are also provided, as are methods of immobilizing, sequencing, and making nucleic acids employing such proteins.
    Type: Grant
    Filed: April 6, 2020
    Date of Patent: October 10, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Satwik Kamtekar, Lubomir Sebo, Leewin Chern, Thomas Linsky, Jeremiah Hanes, Erik Miller, Ying Yang, Stephen Yue
  • Patent number: 11781173
    Abstract: An RNA tagging system for visualization of single mRNA molecules based on a MSB-MCP system, as well as methods of use.
    Type: Grant
    Filed: April 19, 2018
    Date of Patent: October 10, 2023
    Assignee: Albert Einstein College of Medicine
    Inventors: Robert H. Singer, Evelina Tutucci, Maria Vera Ugalde
  • Patent number: 11767549
    Abstract: An integrated sample purification system includes a housing, a sample container rack, a filter holder, and a cylindrical magnet. The sample container rack and the filter device holder are disposed in the housing. The sample container rack is configured to hold one or more sample containers, the filter device holder is configured to hold one or more filter devices. The cylindrical magnet is adjacent to and external to the sample container rack, and is rotated about a central, longitudinal axis of the magnet by an electric motor disposed in the housing to lyse cells. Molecules of interest in the lysed cells are purified using filters that bind specifically to the molecules of interest. The system is readily amenable to automation and rapid purification and analysis of molecules of interest, such as nucleic acids and proteins.
    Type: Grant
    Filed: December 30, 2020
    Date of Patent: September 26, 2023
    Inventors: Christopher G. Cooney, Rebecca Holmberg, Phillip Belgrader, Peter Qiang Qu
  • Patent number: 11753676
    Abstract: This invention relates to imaging, such as by expansion microscopy, labelling, and analyzing biological samples, such as cells and tissues, as well as reagents and kits for doing so.
    Type: Grant
    Filed: October 10, 2018
    Date of Patent: September 12, 2023
    Inventor: Mahender Babu Dewal
  • Patent number: 11732291
    Abstract: The invention provides an improved stem-loop target capture oligomer and methods of use. Such a target capture oligomer has a target-binding segment forming a loop flanked by stem segments forming a stem. The stem segments are of unequal length. Such probes show little or no binding to immobilized probes in the absence of a target nucleic acid but offer good target sensitivity. The probes are particularly useful in multiplex methods of detection in which multiple target capture oligomers are present for detecting of multiple target nucleic acids (for example, detecting multiple polymorphic forms of a target gene).
    Type: Grant
    Filed: April 15, 2020
    Date of Patent: August 22, 2023
    Inventors: James Carlson, Reinhold Pollner, Steven T. Brentano
  • Patent number: 11725235
    Abstract: The invention relates to new methods of attaching one or more polynucleotide binding proteins to a target polynucleotide. The invention also related to new methods of characterising target polynucleotides.
    Type: Grant
    Filed: August 14, 2019
    Date of Patent: August 15, 2023
    Assignee: Oxford Nanopore Technologies PLC
    Inventors: Andrew John Heron, Clive Gavin Brown, Rebecca Victoria Bowen, James White, Daniel John Turner, Joseph Hargreaves Lloyd, Christopher Peter Youd
  • Patent number: 11705217
    Abstract: Methods and systems for single molecule sequencing using concatemers of copies of sense and antisense strands. Concatemers are provided, for example, by carrying out rolling circle amplification on a circular molecule having sense and antisense regions to produce repeated copies of the sense and antisense regions connected by linking regions. The circular molecules can be produced by ligating hairpin adapters to each end of a double-stranded nucleic acid having a sense and antisense strand. The ligations can be carried out, for example using blunt end ligation. In some cases, a single molecule consensus sequence for a single template molecule is obtained. A single read from each template molecule can be obtained by comparing the sequence information of the sense and antisense regions.
    Type: Grant
    Filed: January 19, 2018
    Date of Patent: July 18, 2023
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Kevin Travers, Geoff Otto, Stephen Turner, Cheryl Heiner, Congcong Ma
  • Patent number: 11674171
    Abstract: Provided herein are reagents and kits for detection of multiple target sequences in a single-tube, single-color assay, and methods of use thereof. In particular, multiplex assays are provided for the detection of Mycobacterium tuberculosis complex target sequences (e.g., katG, rpoB, inhA promotor, pncA, etc.).
    Type: Grant
    Filed: August 10, 2020
    Date of Patent: June 13, 2023
    Assignee: Brandeis University
    Inventors: Lawrence J. Wangh, Kenneth E. Pierce, John E. Rice