Patents Examined by Young J. Kim
  • Patent number: 12264371
    Abstract: Provided are methods of detecting replication competent virus, e.g., replication competent retrovirus such as gammaretrovirus or lentivirus, in a sample containing a cell transduced with a viral vector particle encoding a recombinant and/or heterologous molecule, e.g., heterologous gene product. The methods may include assessing transcription of one or more target genes, such as viral genes, that are expressed in a retrovirus but not expressed in the viral vector particle. Replication competent retrovirus may be determined to be present if the levels of RNA of the one or more target genes is higher than a reference value, which can be measured directly or indirectly, including from a positive control sample containing RNA from the respective target gene at a known level and/or at or above the limit of detection of the assay.
    Type: Grant
    Filed: November 22, 2022
    Date of Patent: April 1, 2025
    Assignee: Juno Therapeutics, Inc.
    Inventors: Ruth Berry, Edwin Webb
  • Patent number: 12264365
    Abstract: Disclosed herein are primers and probes related to the detection of SARS-CoV-2 via nucleic acid amplification testing (NAAT), for example to amplify and determine the presence of SARS-CoV-2 in test samples and/or to diagnose Covid-19. Specifically, the present disclosure describes primers and probes that bind to the N gene, ORF1ab, or E gene of SARS-CoV-2 coronavirus for detection via loop mediated isothermal amplification (LAMP) and molecular beacon hybridization.
    Type: Grant
    Filed: June 25, 2020
    Date of Patent: April 1, 2025
    Assignee: Talis Biomedical Corporation
    Inventors: Nadya Andini, Kathy Chiu, Xuewen Jiang, Hédia Maamar
  • Patent number: 12252742
    Abstract: The present disclosure provides methods for processing a nucleic acid sample. For example, a method of the present disclosure may simultaneously process two populations of nucleic acid (NA) templates for two different sequencing modalities: (i) a first population comprising circularized NA templates having a size smaller than a size threshold (e.g., smaller than 2 kilobase (kb)), and (ii) a second population comprising uncircularized NA templates having a size greater than or equal to the size threshold.
    Type: Grant
    Filed: March 26, 2024
    Date of Patent: March 18, 2025
    Assignee: AXBIO INC.
    Inventors: Hui Tian, Igor Constantin Ivanov, Vladimir Ivanovich Bashkirov
  • Patent number: 12252738
    Abstract: Described herein is a complex comprising multiple nucleic acid molecules that are hybridized together, each comprising, from 5? to 3?, a first complementary sequence, a spacer sequence and a second complementary sequence, and either/or a 5? end sequence that is 5? of the first complementary sequence and terminates in a 5? phosphate and a 3? end sequence that is 3? of the second complementary sequence and terminates in a 3? hydroxyl. In this complex: the first complementary sequence of one molecule is directly or indirectly hybridized with the second complementary sequence of another molecule in the complex and the spacer sequence and the 3? and/or 5? end sequences are single-stranded. Methods of making and using the complex are also provided.
    Type: Grant
    Filed: March 29, 2022
    Date of Patent: March 18, 2025
    Assignee: PIXELGEN TECHNOLOGIES AB
    Inventors: Simon Fredriksson, Filip Karlsson
  • Patent number: 12247250
    Abstract: The present invention relates to the rapid and electricity-free, point-of-care, multiplexed detection and quantification of at least one or more nucleic acid sequences from nucleic acids corresponding to a plurality of pathogens or biomarkers using a micropatterned lateral flow device. Rapid and molecular-level sensitive differential diagnosis of a disease condition may be enabled without the need for a delayed laboratory test so that timely treatment can be administered.
    Type: Grant
    Filed: July 28, 2020
    Date of Patent: March 11, 2025
    Assignees: GODX, INC, THE UNITED STATES OF AMERICA, AS REPRESENTED BY THE SECRETARY, DEPARTMENT OF HEALTH & HUMAN SERVICES
    Inventors: Chang Hee Kim, Wendy A. Henderson, Sarah K. Abey, Nicolaas H. Fourie, Eric G. Ferguson
  • Patent number: 12241057
    Abstract: Methods and apparatus of some aspects of the invention relate to the synthesis of high fidelity polynucleotides. In particular, aspects of the invention relate to concurrent enzymatic removal of amplification sequences and ligation of processed oligonucleotides into nucleic acid assemblies. According to some embodiments, the invention provides a method for producing a target nucleic acid having a predefined sequence. In some embodiments, the method comprises the step of providing a plurality of oligonucleotides, wherein each oligonucleotides comprises (i) an internal sequence identical to a different portion of a sequence of a target nucleic acid, (ii) a 5? sequence flanking the 5? end of the internal sequence and a 3? flanking sequence flanking the 3? end of the internal sequence, each of the flanking sequence comprising a primer recognition site for a primer pair and a restriction enzyme recognition site.
    Type: Grant
    Filed: June 28, 2021
    Date of Patent: March 4, 2025
    Assignee: Gen9, Inc.
    Inventors: Michael E. Hudson, Li-Yun A. Kung, Daniel Schindler, Stephen Archer, Ishtiaq Saaem
  • Patent number: 12234512
    Abstract: In some aspects, the present disclosure provides methods for identifying sequence variants in a nucleic acid sample. In some embodiments, a method comprises identifying sequence differences between sequencing reads and a reference sequence, and calling a sequence difference that occurs in at least two different circular polynucleotides, such as two circular polynucleotides having different junctions, as the sequence variant. In some aspects, the present disclosure provides compositions and systems useful in the described methods.
    Type: Grant
    Filed: February 3, 2023
    Date of Patent: February 25, 2025
    Assignee: AccuraGen Holdings Limited
    Inventors: Shengrong Lin, Zhaohui Sun, Grace Qizhi Zhao, Paul Ling-Fung Tang
  • Patent number: 12234503
    Abstract: The present application provides certain advantageous ways of conducting multiplexed imaging.
    Type: Grant
    Filed: February 19, 2020
    Date of Patent: February 25, 2025
    Assignee: Ultivue, Inc.
    Inventors: Stephanie Rae Hennek, Mael Manesse, Abdul Mohammed, Xi Chen, Michael Jules Natan
  • Patent number: 12234504
    Abstract: The subject invention provides a novel fluorescence-based, T5 exonuclease-amplified DNA cleavage assay for gyrase poisoning inhibitor discovery. According to the assay, multiple gyrase molecules can simultaneously bind to a plasmid DNA molecule to form multiple gyrase-DNA cleavage complexes on the same plasmid. These gyrase-DNA cleavage complexes, greatly stabilized by a gyrase poisoning inhibitor, and can be trapped by a detergent such as sarkosyl. Digestion of gyrase by proteinase K results in the production of small DNA fragments, which can be digested by T5 exonuclease. This fluorescence-based DNA cleavage HTS assay is also suitable for screening large compound libraries to identify inhibitors against DNA topoisomerases, including human DNA topoisomerase II?.
    Type: Grant
    Filed: October 1, 2024
    Date of Patent: February 25, 2025
    Assignee: The Florida International University Board of Trustees
    Inventors: Fenfei Leng, Matthew Dias
  • Patent number: 12227801
    Abstract: The present disclosure provides a method and systems for processing or analyzing a nucleic acid molecule. A method for processing or analyzing a double-stranded nucleic molecule may comprise providing the double-stranded nucleic acid molecule and a double-stranded adapter. The double-stranded adapter may comprise a nicking site within a sense strand or an anti-sense strand of the double-stranded adapter. The double-stranded adapter may then be coupled to the double-stranded nucleic acid molecule, and the double-stranded nucleic acid molecule coupled to the double-stranded adapter may be circularized to generate a circularized double-stranded nucleic acid molecule.
    Type: Grant
    Filed: February 3, 2023
    Date of Patent: February 18, 2025
    Assignee: AXBIO INC.
    Inventors: Suhua Deng, Vladimir Ivanovich Bashkirov, Hui Tian, Igor Constantin Ivanov
  • Patent number: 12227792
    Abstract: Improved multiple displacement amplification (MDA) reagents and methods are provided.
    Type: Grant
    Filed: October 18, 2023
    Date of Patent: February 18, 2025
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Ronald Lebofsky, Jeremy Agresti, George Karlin-Neumann
  • Patent number: 12220705
    Abstract: Systems and methods are disclosed for rapid PCR testing. Example embodiments may include a PCR testing module that includes a housing having a PCR machine disposed therein; a sample input station on the housing, wherein the sample input station is configured to receive a sample collection device (SCD) comprising a biological specimen sample provided by the patient; an SCD processing mechanism configured to transfer a lysed microportion of the biological specimen sample into a PCR sample tube attached to the SCD; at least one mechanism configured to separate the PCR sample tube from the SCD and transfer the PCR sample tube to the PCR machine; and a controller configured to (i) use the PCR machine to conduct a PCR test on contents of the PCR sample tube, and (ii) generate results of the PCR test.
    Type: Grant
    Filed: March 24, 2022
    Date of Patent: February 11, 2025
    Assignee: Amazon Technologies, Inc.
    Inventors: Jasmin B. Farshi, Pan Zhang, Jonathan Barry Hirst, Babak Ziaie, Bela Incze, Babar M. Koraishy
  • Patent number: 12220698
    Abstract: Provided are a microfluidic chip, and an apparatus and a method for detecting biomolecules by using the microfluidic chip. According to an example embodiment, the microfluidic chip includes: a first storage configured to accommodate a sample, the sample including target materials; a plurality of second storages connected to the first storage, the plurality of second storages including reactants for the target materials; and a plurality of well arrays connected to the plurality of second storages, respectively, and configured to accommodate a solution of the sample, in which the reactants for the target materials are dissolved.
    Type: Grant
    Filed: June 9, 2021
    Date of Patent: February 11, 2025
    Assignee: SAMSUNG ELECTRONICS CO., LTD.
    Inventors: Moon Seong Park, Kak Namkoong, Won Jong Jung
  • Patent number: 12214347
    Abstract: Devices and methods are provided for identifying individual monomeric units in sequential order as they are released or cleaved from a polymer strand via an enzyme, which acts on the polymer, and the monomeric units translocate through a transmembrane channel. Methods are also provided for identifying molecules as they translocate through a transmembrane channel.
    Type: Grant
    Filed: August 30, 2023
    Date of Patent: February 4, 2025
    Assignee: ELECTRONIC BIOSCIENCES, INC.
    Inventors: Anna E. P. Schibel, Eric N. Ervin, Sean German
  • Patent number: 12209281
    Abstract: The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Though massively parallel sequencing instruments are in principle well-suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. One example of this approach, called “Safe-SeqS” for (Safe-Sequencing System) includes (i) assignment of a unique identifier (UID) to each template molecule; (ii) amplification of each uniquely tagged template molecule to create UID-families; and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are truly mutant (“super-mutants”) if ?95% of them contain the identical mutation.
    Type: Grant
    Filed: June 10, 2022
    Date of Patent: January 28, 2025
    Assignee: The Johns Hopkins University
    Inventors: Bert Vogelstein, Kenneth W. Kinzler, Nickolas Papadopoulos, Isaac A. Kinde
  • Patent number: 12186757
    Abstract: Provided herein are devices for monitoring nucleic acid amplification, nucleic acid amplification monitors, methods of quantifying nucleic acid amplification, methods of identifying an unknown nucleic acid molecule, and systems for monitoring nucleic acid amplification. The disclosed devices, methods, and systems comprise at least one nuclemeter, comprising at least one sample chamber and at least one reaction-diffusion conduit in fluid communication with the chamber.
    Type: Grant
    Filed: July 1, 2015
    Date of Patent: January 7, 2025
    Assignee: THE TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA
    Inventors: Changchun Liu, Haim H. Bau
  • Patent number: 12188077
    Abstract: The invention provides a method for optimizing isHCR for multiplexed labeling, which combines binder-biomolecule interactions with hybridization Chain Reaction (HCR).
    Type: Grant
    Filed: October 11, 2022
    Date of Patent: January 7, 2025
    Assignee: GenAns Biotechnology Co., Ltd
    Inventors: Rui Lin, Minmin Luo
  • Patent number: 12174192
    Abstract: This disclosure relates to methods for detecting a level of expression of one or more genes (or proteins) in a subject having or suspected of having cancer, and optionally treating the subject with an adenosine pathway antagonist, for example an adenosine A2A receptor (ADORA2A) antagonist, to treat the cancer.
    Type: Grant
    Filed: July 12, 2019
    Date of Patent: December 24, 2024
    Assignee: Corvus Pharmaceuticals, Inc.
    Inventors: Stephen Willingham, Andrew Hotson, Richard A. Miller
  • Patent number: 12173362
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Grant
    Filed: November 5, 2021
    Date of Patent: December 24, 2024
    Assignee: Exact Sciences Corporation
    Inventors: Hatim T. Allawi, William G. Weisburg, Graham P. Lidgard, Michael W. Kaiser, Abram M. Vaccaro, Gracie Shea
  • Patent number: 12173373
    Abstract: The invention provides a selecting method for domestic rabbits with a agouti/Belgian hair color based on homozygous genotype selection. The purification method is applicable to purification of various domestic rabbits with the agouti/Belgian hair color. The method includes the following steps: firstly, selecting the domestic rabbits with a hair color phenotype which is the agouti/Belgian hair color; then detecting an ASIP gene, a MC1R gene and a TYR gene at the same time by utilizing a first primer set, a second primer set and a third primer set; screening the domestic rabbits with genotypes of AA (corresponding to the ASIP gene), EE (corresponding to the MC1R gene) and CC (corresponding to the TYR gene). The domestic rabbits with the genotype of AAEECC, which are obtained by the screening method of the invention, are agouti/Belgian hair color homozygotes and the recessive white gene is eliminated.
    Type: Grant
    Filed: April 26, 2021
    Date of Patent: December 24, 2024
    Assignees: SHANDONG AGRICULTURAL UNIVERSITY, QINGDAO KANGDA RABBIT INDUSTRY DEVELOPMENT CO., LTD.
    Inventors: Xinzhong Fan, Yongxu Liu, Xibo Qiao, Chunhui Hui, Hong Zhao, Mingyong Li, Bo Wang, Aiguo Yang, Jiaqing Hu