Patents Examined by Young J. Kim
  • Patent number: 11603561
    Abstract: A method for direct quantification of nucleic acids in real time qPCR. The invention discloses a method for specific quantification of nucleic acids in real time qPCR. The disclosed invention can be achieved in three ways; 1) using a modified primer for qPCR quantification; 2) using strand displacement based probes for qPCR quantification; 3) using label-free endonuclease probe for qPCR quantification. The mechanism of quantification is based on the fact that, DNA, RNA or modified oligonucleotide based light-up dye-aptamer system, where dye is not fluorescent in free state but its fluorescence increases multi-fold when it binds to its specific aptamer.
    Type: Grant
    Filed: November 30, 2018
    Date of Patent: March 14, 2023
    Inventors: Guhan Jayaraman, Sudeshna Sengupta, Shivansh Goyal
  • Patent number: 11597973
    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: July 31, 2020
    Date of Patent: March 7, 2023
    Inventor: Paul Ling-Fung Tang
  • Patent number: 11590495
    Abstract: A method may include maintaining a sample comprising an ionic species and an optical indicator at an elevated temperature above 25° C. on a semi-conductive microfluidic die during an incubation period, intermittently interrogating the sample with an interrogating light during the incubation period and sensing a response of the sample to the interrogating light, wherein the sample is interrogated with the interrogating light only during those times at which the sample is being sensed.
    Type: Grant
    Filed: July 28, 2017
    Date of Patent: February 28, 2023
    Assignee: Hewlett-Packard Development Company, L.P.
    Inventors: Hilary Ely, Matthew David Smith, Jeremy Sells, George H. Corrigan, Michael W. Cumbie, Chantelle Domingue
  • Patent number: 11584964
    Abstract: DNA is sequenced by (a) independently sequencing first and second strands of a dsDNA to obtain corresponding first and second sequences; and (b) combining the first and second sequences to generate a consensus sequence of the dsDNA. By independently sequencing first and second strands the error probability of the consensus sequence approximates a multiplication of those of the first and second sequences.
    Type: Grant
    Filed: November 18, 2020
    Date of Patent: February 21, 2023
    Assignee: Board of Regents, The University of Texas System
    Inventors: Zbyszek Otwinowski, Dominika Borek
  • Patent number: 11578361
    Abstract: A gene detection method, a gene detection kit, and a gene detection device, including the following steps: providing a plurality of separation cavities on a kit, using a plunger to separate adjacent separation cavities, and respectively providing a lysate solution, a washing solution and a reaction solution in the separation cavities; when detecting a sample, pushing each plunger to align a plunger hole of the plunger with the separation cavity, thereby making the separation cavities interconnected; then, controlling magnetic beads in the kit to drive the sample to be tested to pass through the separation cavities in sequence by an electromagnetic control method, carrying out a lysing, a washing and a reaction in sequence; and finally, performing a optical detection on a gene in the reaction solution from outside.
    Type: Grant
    Filed: June 6, 2018
    Date of Patent: February 14, 2023
    Inventors: Qian Song, Wenfei Xu, Xin Wang, Xiangzhao Zheng
  • Patent number: 11542545
    Abstract: Disclosed herein are methods and devices for rapid assessment of whether a microorganism present in a sample is susceptible or resistant to a treatment.
    Type: Grant
    Filed: November 5, 2015
    Date of Patent: January 3, 2023
    Assignees: California Institute of Technology, Talis Biomedical Corporation
    Inventors: Rustem F. Ismagilov, Eugenia Khorosheva, Travis S. Schlappi, Matthew S. Curtis, Nathan G. Schoepp, Hedia Maamar, Feng Shen, Erik B. Jue
  • Patent number: 11535903
    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: January 31, 2019
    Date of Patent: December 27, 2022
    Assignee: Juno Therapeutics, Inc.
    Inventors: Ruth Berry, Edwin Webb
  • Patent number: 11530455
    Abstract: Methods for human identification using polymorphisms in the Penta E short tandem repeat locus are significant in preventing allelic drop out. An exemplary method encompasses (a) contacting a first primer to a nucleic acid sample to be analyzed, (b) contacting a second primer to the nucleic acid sample, and (c) subjecting the nucleic acid sample, the first primer, and the second primer to an amplification reaction, and thereby forming an amplification product. The first primer, the second primer, or both the first and second primers can be labeled with a non-nucleic-acid label. Additionally, or alternatively, the amplification product can include an adenosine at position 14 from the 5? end of SEQ ID NO:1, a thymidine at position 21 from the 5? end of SEQ ID NO:2, or both an adenine at position 14 and a thymidine at position 21 from the 5? end of SEQ ID NO:3.
    Type: Grant
    Filed: November 16, 2020
    Date of Patent: December 20, 2022
    Inventor: Chang Zhong
  • Patent number: 11530441
    Abstract: The methods, compositions, and kits of the disclosure provide a novel approach for a whole genome, unbiased DNA analysis method that can be performed on limited amounts of DNA. can be used to analyze DNA to determine its modification status. Aspects of the disclosure relate to a method for amplifying bisulfite-treated deoxyribonucleic acid (DNA) molecules comprising: (a) ligating an adaptor to the DNA molecules, wherein the adaptor comprises a RNA polymerase promoter comprising bisulfite-protected cytosines; (b) treating the ligated DNA molecules with bisulfite; (c) hybridizing the bisulfite-treated DNA molecules with a primer; (d) extending the hybridized primer to make double stranded DNA; and (e) in vitro transcribing the double-stranded DNA to make RNA.
    Type: Grant
    Filed: July 26, 2019
    Date of Patent: December 20, 2022
    Assignee: The University of Chicago
    Inventors: Chuan He, Ji Nie, Xiao-Long Cui
  • Patent number: 11529626
    Abstract: The present invention relates to a low-cost, thermally reversible valve for paper-fluidic diagnostic devices. In particular, this invention demonstrates a tunable valve mechanism fabricated by wax-ink printing and localized heating via thin-film resistors to sequentially release liquids through a cellulose or nitrocellulose membrane. The wax-ink valve can obstruct fluid flow for a sustained time and are thermally actuated to release a controlled amount of liquid past the valve. This integrated paper-fluidic diagnostic assay device requires minimal user involvement, can be easily manufactured and tuned to meet various fluid delivery timing and incubation needs.
    Type: Grant
    Filed: April 19, 2021
    Date of Patent: December 20, 2022
    Assignee: Purdue Research Foundation
    Inventors: Jacqueline C. Linnes, Megan Zaiyi Chiu, Rui Shen
  • Patent number: 11525158
    Abstract: The present invention is concerned with linear double stranded DNA, which is coupled to a single support or a tag at the 3? end of its non-coding strand and methods for producing said linear double stranded DNA. The present invention further relates to the use of said linear double stranded DNA in an RNA in vitro transcription reaction and also to a method for producing RNA in vitro. The present invention also relates to a bioreactor for RNA in vitro transcription.
    Type: Grant
    Filed: December 21, 2018
    Date of Patent: December 13, 2022
    Assignee: CureVac SE
    Inventors: Benyamin Yazdan Panah, Tilmann Roos, Veronika Wagner, Carola Pongratz
  • Patent number: 11519030
    Abstract: The invention relates to a process and a device for analysing single molecules, particularly to the parallel analysis of a plurality of single molecules. It is suitable for detecting interactions, e.g. binding between single molecules and/or reactions, e.g. elongation or degradation of single molecules. Particularly, the process of the invention relates to the sequencing of single nucleic acid molecules. The single molecule to be analysed is present in free form, i.e. dissolved or suspended in a liquid medium, within a reaction space formed around the sample spot. According to the present invention, an electrical field is applied across the reaction space, whereby a concentration of single molecules, at the sample spots is effected.
    Type: Grant
    Filed: June 28, 2016
    Date of Patent: December 6, 2022
    Assignee: Gnothis Holding AG
    Inventor: Rudolf Rigler
  • Patent number: 11505823
    Abstract: A microfluidic system is intended for the analysis of a biological sample containing biological species. The system includes an optical detection device having a source configured to emit an optical signal and at least one sensor having a capture surface defining an optical signal reading zone. The system also includes a microfluidic device having a support in which an amplification chamber, in which an amplification reaction can be carried out, is made, and having an input channel opening into the amplification chamber. The amplification chamber includes at least one first zone located in the sensor reading zone and at least one protuberance forming a recess intended to receive a compound for internal control of the amplification reaction and arranged to be located outside the sensor reading zone or configured to be opaque to said optical signal.
    Type: Grant
    Filed: July 16, 2020
    Date of Patent: November 22, 2022
    Assignee: Commissariat a l'Energie Atomique et aux Energies Alternatives
    Inventors: Thomas Bordy, Anne-Gaelle Bourdat, Remi Toutain
  • Patent number: 11505820
    Abstract: The present disclosure provides methods and systems for sequencing nucleic acid molecules in a manner that enables higher sequencing accuracy. Methods and systems provided herein may enable sequences that may have low-accuracy reads, such as homopolymer sequences or other repeating sequences, to be determined at a higher accuracy and efficiency.
    Type: Grant
    Filed: July 23, 2020
    Date of Patent: November 22, 2022
    Inventors: Eliane Trepagnier, Mark Pratt, Theo Nikiforov, Gilad Almogy
  • Patent number: 11492663
    Abstract: The present invention regards a variety of methods and compositions for whole genome amplification and whole transcriptome amplification. In a particular aspect of the present invention, there is a method of amplifying a genome comprising a library generation step followed by a library amplification step. In specific embodiments, the library generating step utilizes specific primer mixtures and a DNA polymerase, wherein the specific primer mixtures are designed to eliminate ability to self-hybridize and/or hybridize to other primers within a mixture but efficiently and frequently prime nucleic acid templates.
    Type: Grant
    Filed: February 15, 2019
    Date of Patent: November 8, 2022
    Assignee: Takara Bio USA, Inc.
    Inventors: Emmanuel Kamberov, Tong Sun, Eric Bruening, Jonathon H. Pinter, Irina Sleptsova, Takao Kurihara, Vladimir L. Makarov
  • Patent number: 11485967
    Abstract: Provided herein are methods and systems for cell-free DNA extraction from liquid biological samples. The methods can be employed for determination of fetal DNA fraction and non-invasive prenatal screening of fetal aneuploidies and analyses of other types of cell-free DNA.
    Type: Grant
    Filed: October 25, 2016
    Date of Patent: November 1, 2022
    Assignee: Quest Diagnostics Investments Incorporated
    Inventors: Ben Anderson, Charles Strom, David Tsao, Yan Liu, Weimin Sun
  • Patent number: 11473141
    Abstract: The present invention relates to probes and primers beneficial for conducting amplification assays, such as those including loop-mediated isothermal amplification reactions. Also described herein are methods for detecting targets using such probes and/or primers.
    Type: Grant
    Filed: June 16, 2020
    Date of Patent: October 18, 2022
    Assignee: National Technology & Engineering Solutions of Sandia, LLC
    Inventors: Robert Meagher, Chung-Yan Koh, Yooli Kim Light, Cameron Scott Ball
  • Patent number: 11473131
    Abstract: The presently disclosed subject matter provides high-throughput methods for performing genomic DNA methylation assessments. The presently disclosed subject matter further provides methods for diagnosing a subject with a disease and/or disorder, and for determining the prognosis of a subject that has a disease and/or disorder. In certain embodiments, the present disclosure provides a diagnostic method that includes obtaining a biological sample from the subject; determining the methylation status of one or more genomic DNA loci in one or more cells of the biological sample; and diagnosing a disease and/or disorder in the subject, wherein the methylation status of the one or more genomic DNA loci indicates the presence of the disease and/or disorder in the subject.
    Type: Grant
    Filed: August 21, 2015
    Date of Patent: October 18, 2022
    Inventors: Martin Carroll, Stephen Master, Gerald Wertheim, Marlise Luskin
  • Patent number: 11466315
    Abstract: Disclosed is a method of amplifying a nucleic acid sequence, wherein the method comprises subjecting a reaction mixture to at least one amplification cycle, wherein the reaction mixture comprises a double-stranded nucleic acid and at least two primers capable of annealing to complementary strands of the double-stranded nucleic acid and amplifying at least one short tandem repeat (STR) using a Family A DNA polymerase in a Fast PCR protocol having a two-step amplification cycle in 25 seconds or less. Also disclosed are real-time PCR methods using the two-step protocol and kits for STR profiling using the Fast PCR protocol.
    Type: Grant
    Filed: December 13, 2019
    Date of Patent: October 11, 2022
    Assignee: Life Technologies Corporation
    Inventors: Dennis Wang, Lori Hennessy
  • Patent number: 11466313
    Abstract: This disclosure provides, among other things, a reagent system for nucleic acid analysis. In some embodiments, the system may comprise a plurality of oligonucleotide sets each set comprising at least (a) a competitor oligonucleotide that hybridizes to a target sequence and varies in concentration from mixture to mixture and (b) a detector oligonucleotide that also hybridizes to the target sequence and contains a barcode that indicates the concentration of the competitor oligonucleotide in the oligonucleotide set. The reagent system may be used to analyze a nucleic acid sample.
    Type: Grant
    Filed: April 12, 2019
    Date of Patent: October 11, 2022
    Inventors: Julia Salzman, Peter L. Wang, Caroline Horn