Patents Examined by David C. Thomas
  • Patent number: 11319588
    Abstract: This application discloses methods of producing a DNA strand for sequencing, as well as genetic constructs, libraries, and arrays using DNA strands produced according to these methods. The application also discloses methods of sequencing using the DNA strands, genetic constructs, libraries, and arrays produced. In certain aspects, DNA being sequenced includes a target sequence and at least one adaptor sequence.
    Type: Grant
    Filed: March 8, 2019
    Date of Patent: May 3, 2022
    Assignee: MGI Tech Co., Ltd.
    Inventors: Rongqin Ke, Snezana Drmanac, Radoje Drmanac, Guangyang Cai, Matthew Callow
  • Patent number: 11319580
    Abstract: Disclosed is a method for high-throughput detection of genome-wide modifications in a nucleic acid genome obtained from a cell or tissue caused by the activity of a designer nuclease comprising the following steps: a) Extraction of the genomic DNA from cells that were exposed to a designer nuclease under conditions which allow the designer nuclease to introduce a DNA double-strand break (DSB) in the genomic DNA of the cell, b) fragmentation of the nucleic acid to obtain random fragments, c) performing an end repair in order to obtain blunt ends, d) ligation with a linker comprising a sequence complementary to a so called “linker primer”, e) performing a first nucleic acid amplification reaction with a “linker primer” and a so called “ON-target primer”, whereby one primer is located upstream and one primer is located downstream of the on-target site, wherein at least one decoy primer is present in the reaction mixture, f) performing a second nucleic acid amplification reaction whereby so called “nested prim
    Type: Grant
    Filed: September 19, 2019
    Date of Patent: May 3, 2022
    Assignees: Albert-Ludwigs-Universitaet Freiburg, Deutsches Krebsforschungszentrum Stiftung des oeffentlichen Rechts
    Inventors: Toni Cathomen, Giandomenico Turchiano, Georges Blattner, Gianni Monaco, Melanie Boerries, Geoffroy Andrieux
  • Patent number: 11319579
    Abstract: The present invention provides a method for easily and exponentially amplifying circular DNA, particularly long chain circular DNA, in a cell-free system. Specifically, the present invention provides a method for amplifying circular DNA in which circular DNA having a replication origin sequence (origin of chromosome (oriC)) is mixed with a reaction solution containing the following enzyme groups to form a reaction mixture, which is then reacted under an isothermal condition, the enzyme groups being: (1) a first enzyme group that catalyzes replication of circular DNA; (2) a second enzyme group that catalyzes an Okazaki fragment maturation and synthesizes two sister circular DNAs constituting a catenane and (3) a third enzyme group that catalyzes a separation of two sister circular DNAs.
    Type: Grant
    Filed: April 1, 2019
    Date of Patent: May 3, 2022
    Assignee: OriCiro Genomics, Inc.
    Inventors: Masayuki Su'etsugu, Hiroko Kobayashi
  • Patent number: 11299767
    Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.
    Type: Grant
    Filed: June 30, 2021
    Date of Patent: April 12, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Je-Hyuk Lee, Richard C. Terry, Evan R. Daugharthy
  • Patent number: 11299774
    Abstract: A method for spatially tagging nucleic acids of a biological specimen, including steps of (a) providing a solid support comprising different nucleic acid probes that are randomly located on the solid support, wherein the different nucleic acid probes each includes a barcode sequence that differs from the barcode sequence of other randomly located probes on the solid support; (b) performing a nucleic acid detection reaction on the solid support to locate the barcode sequences on the solid support; (c) contacting a biological specimen with the solid support that has the randomly located probes; (d) hybridizing the randomly located probes to target nucleic acids from portions of the biological specimen; and (e) modifying the randomly located probes that are hybridized to the target nucleic acids, thereby producing modified probes that include the barcode sequences and a target specific modification, thereby spatially tagging the nucleic acids of the biological specimen.
    Type: Grant
    Filed: September 20, 2021
    Date of Patent: April 12, 2022
    Assignees: Spatial Transcriptomics AB, Illumina Inc
    Inventors: Jonas Frisen, Patrik Stahl, Joakim Lundeberg, Gordon M. Cann, Leila Bazargan, Alex Aravanis
  • Patent number: 11299780
    Abstract: Provided are methods of producing nucleic acid libraries. In certain aspects, the methods include combining target nucleic acids (e.g., 5? phosphorylated nucleic acids) and an oligonucleotide pool. Oligonucleotides of the oligonucleotide pool may include complementarity regions of varying length and nucleotide sequence, and a complementarity region identification sequence. In such aspects, the combining is under conditions in which oligonucleotides of the oligonucleotide pool hybridize to nucleic acids of the target nucleic acids (e.g., 5? phosphorylated nucleic acids) having overhang regions that are complementary in sequence and have corresponding lengths with respect to the complementarity regions of the oligonucleotides. Compositions and kits that find use, e.g., in practicing the methods of the present disclosure are also provided.
    Type: Grant
    Filed: July 13, 2017
    Date of Patent: April 12, 2022
    Assignee: The Regents of the University of California
    Inventor: Richard E. Green
  • Patent number: 11293051
    Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.
    Type: Grant
    Filed: April 23, 2021
    Date of Patent: April 5, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Jehyuk Lee, Daniel Levner, Michael Super
  • Patent number: 11293052
    Abstract: Methods of making a three-dimensional matrix of nucleic acids within a cell is provided.
    Type: Grant
    Filed: April 23, 2021
    Date of Patent: April 5, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Jehyuk Lee, Daniel Levner, Michael Super
  • Patent number: 11286523
    Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.
    Type: Grant
    Filed: January 28, 2020
    Date of Patent: March 29, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Xiaoliang Sunney Xie, Katsuyuki Shiroguchi, Peter A. Sims, Tony Z. Jia
  • Patent number: 11279982
    Abstract: Provided herein is technology relating to detecting molecular markers relevant to cancer and particularly, but not exclusively, to methods and compositions for quantifying and/or detecting EGFR mRNA and/or EGFRvIII mRNA in biological samples.
    Type: Grant
    Filed: January 2, 2020
    Date of Patent: March 22, 2022
    Assignee: ABBOTT MOLECULAR INC.
    Inventors: Jeffrey D. Wuitschick, Kevin S. Nelson, Shihai Huang, Rupinder Kular, Carolyn Mullen, James Rhoads
  • Patent number: 11274338
    Abstract: Provided are processes for the use of a single dried blood sample for the preparation of test samples including targets of differing structures. The processes allow the same dried blood sample to be used for preparation of a first test sample including a non-nucleic acid target, and the same dried blood sample to be subsequently processed for preparation of a test sample that includes a nucleic acid target whereby the processes preserve the ability of the nucleic acid to be detected in subsequent detection assays following prior isolation of non-nucleic acid targets.
    Type: Grant
    Filed: October 15, 2018
    Date of Patent: March 15, 2022
    Assignee: PerkinElmer Health Sciences, Inc.
    Inventors: Stephanie Dallaire, Jordan Haddock, Cristina Gutierrez-Mateo, Anna M. Potier, Joseph D. Trometer
  • Patent number: 11273442
    Abstract: Described herein are devices, systems, fluidic devices, kits, and methods for detection of target nucleic acids associated with diseases, cancers, genetic disorders, a genotype, a phenotype, or ancestral origin. The devices, systems, fluidic devices, kits, and methods may comprise reagents of a guide nucleic acid targeting a target nucleic acid, a programmable nuclease, and a single stranded detector nucleic acid with a detection moiety. The target nucleic acid of interest may be indicative of a disease, and the disease may be communicable diseases, or of a cancer or genetic disorder. The target nucleic acid of interest may be indicative of a genotype, a phenotype, or ancestral origin.
    Type: Grant
    Filed: September 29, 2020
    Date of Patent: March 15, 2022
    Assignee: MAMMOTH BIOSCIENCES, INC.
    Inventors: Janice Sha Chen, Ashley Tehranchi, Andrew Besancon Lane, James Paul Broughton, Lucas Benjamin Harrington, Maria-Nefeli Tsaloglou, Xin Miao, Clare Louise Fasching, Jasmeet Singh, Pedro Patrick Draper Galarza
  • Patent number: 11274086
    Abstract: Provided herein is technology relating to amplification of nucleic acids and particularly, but not exclusively, to compositions and methods for doing improving the polymerase chain reaction and providing reagents for polymerase chain reaction with improved stability.
    Type: Grant
    Filed: December 20, 2019
    Date of Patent: March 15, 2022
    Assignee: Abbott Molecular Inc.
    Inventors: Tomasz Krupinski, Jeffrey D. Wuitschick, Shihai Huang
  • Patent number: 11274351
    Abstract: Compositions, reactions mixtures, kits, and systems for detecting bacterial contamination are provided, as well as methods of using the same.
    Type: Grant
    Filed: July 2, 2019
    Date of Patent: March 15, 2022
    Assignee: DCH MOLECULAR DIAGNOSTICS, INC.
    Inventors: James Jian Quan Wang, Xiangmin Cui, Wayne Jer Hsieh, HiuNam Chan
  • Patent number: 11268085
    Abstract: The invention provides novel methods and kits for isolating nucleic acids from biological samples, including cell-free DNA and/or cell-free DNA and nucleic acids including at least RNA from microvesicles, and for extracting nucleic acids from the microvesicles and/or from the biological samples.
    Type: Grant
    Filed: October 7, 2019
    Date of Patent: March 8, 2022
    Assignee: Exosome Diagnostics, Inc.
    Inventors: Johan Karl Olov Skog, Daniel Enderle, Aparna Ramachandran, Haoheng Yan, Emily Berghoff, Tai-Fen Wei, Mikkel Noerholm
  • Patent number: 11267738
    Abstract: A method is described for recovering resources from a microbe supporting environment such as a water treatment system, comprising the steps of using microbial DNA sequencing to analyze the microbiome of the microbe supporting environment and identifying adjustments to the microbial content of the microbiome that will be useful in extracting resources from the microbe supporting environment such as a water treatment system, wherein the resources extracted can include, for example, methane released by microbes, nitrogen, phosphorus, or other contaminants generated by microbes, and/or clean water obtained by removing contaminants in a water treatment system.
    Type: Grant
    Filed: May 7, 2018
    Date of Patent: March 8, 2022
    Assignee: MICROBE DETECTIVES LLC
    Inventor: Trevor Wayne Ghylin
  • Patent number: 11261492
    Abstract: The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e.g. a fetus by analyzing a cellular sample from the subject.
    Type: Grant
    Filed: October 7, 2019
    Date of Patent: March 1, 2022
    Assignees: The General Hospital Corporation, Verinata Health, Inc., GPB Scientific, LLC
    Inventors: Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs
  • Patent number: 11261491
    Abstract: Provided herein are, inter alia, nucleic acids, methods, and kits for detecting unmethylated DNA in body fluid sample of a subject. The disclosure includes compositions, methods, and kits for detecting unmethylation at a CpG site in an insulin gene promoter of a subject.
    Type: Grant
    Filed: July 8, 2019
    Date of Patent: March 1, 2022
    Assignee: City of Hope
    Inventors: Kevin Ferreri, Mohamed I. Husseiny Elsayed
  • Patent number: 11254976
    Abstract: A method including (a) providing an amplification reagent including an array of sites, and a solution having different target nucleic acids; and (b) reacting the amplification reagent to produce amplification sites each having a clonal population of amplicons from a target nucleic acid from the solution. The reacting can include simultaneously transporting the nucleic acids to the sites at an average transport rate, and amplifying the nucleic acids that transport to the sites at an average amplification rate, wherein the average amplification rate exceeds the average transport rate. The reacting can include producing a first amplicon from a nucleic acid that transports to each of the sites, and producing subsequent amplicons from the nucleic acid or from the first amplicon, wherein the average rate at which the subsequent amplicons are generated exceeds the average rate at which the first amplicon is generated.
    Type: Grant
    Filed: August 19, 2019
    Date of Patent: February 22, 2022
    Assignee: Illumina, Inc.
    Inventors: Min-Jui Richard Shen, Jonathan Mark Boutell, Kathryn M. Stephens, Mostafa Ronaghi, Kevin L. Gunderson, Bala Murali Venkatesan, M. Shane Bowen, Kandaswamy Vijayan
  • Patent number: 11254973
    Abstract: A method for quantifying labels on a substrate is performed by an electronic device with one or more processors and memory. The method includes obtaining digital data corresponding to a multi-dimensional measurement over the substrate; identifying a first set of sub-portions of the digital data; and, for a respective sub-portion of the first set of sub-portions of the digital data: increasing a quantity of labels, and subtracting a reference signal distribution from the respective sub-portion to obtain subtracted sub-portion data. The method also includes obtaining subtracted digital data. The subtracted digital data includes the subtracted sub-portion data for the respective sub-portion. The method further includes identifying a second set of one or more sub-portions of the subtracted digital data; and, for a respective sub-portion of the second set of one or more sub-portions of the subtracted digital data, increasing a quantity of labels.
    Type: Grant
    Filed: September 1, 2017
    Date of Patent: February 22, 2022
    Assignee: Invitae Corporation
    Inventors: Hywel Bowden Jones, Andrea Lynn McEvoy