Patents Examined by Juliet C. Switzer
  • Patent number: 11898196
    Abstract: The invention includes methods and apparatus for separating mutations, especially rare and unknown mutations, using heteroduplex binding proteins. Nucleic acids may optionally be nicked at or near the mutation in order to promote heteroduplex binding protein recognition and binding. In particular, using the disclosed methods, it is possible to separate heteroduplexed nucleic acid strand pair from homoduplexed nucleic acid strand pairs having similar sequences and being at a much higher concentration. Once the heteroduplexed nucleic acids are isolated and recovered, it is straightforward to analyze the sequences of the heteroduplexed nucleic acids, e.g., using sequencing or hybrid assays.
    Type: Grant
    Filed: August 18, 2021
    Date of Patent: February 13, 2024
    Assignee: Quantum-Si Incorporated
    Inventors: Andrea Marziali, Milenko Despotovic, Matthew Wiggin, Joel Pel
  • Patent number: 11873532
    Abstract: The present invention relates to methods, systems and kits for the diagnosis, prognosis and the determination of progression of cancer in a subject. The invention also provides biomarkers that define subgroups of prostate cancer, clinically useful classifiers for distinguishing prostate cancer subtypes, bioinformatic methods for determining clinically useful classifiers, and methods of use of each of the foregoing. The methods, systems and kits can provide expression-based analysis of biomarkers for purposes of subtyping prostate cancer in a subject. Further disclosed herein, in certain instances, are probe sets for use in subtyping prostate cancer in a subject. Classifiers for subtyping a prostate cancer are provided. Methods of treating cancer based on molecular subtyping are also provided.
    Type: Grant
    Filed: March 9, 2018
    Date of Patent: January 16, 2024
    Assignees: Decipher Biosciences, Inc., 2. The Regents of the University of Michigan
    Inventors: Elai Davicioni, Nicholas Erho, Shuang G. Zhao, S. Laura Chang, Felix Y. Feng
  • Patent number: 11866793
    Abstract: The present invention provides methods and kits for identifying Amaranthus palmeri plant material using genetic markers. The methods may be used to determine whether a sample contains Amaranthus palmeri plant material or to genotype an Amaranthus plant.
    Type: Grant
    Filed: March 26, 2021
    Date of Patent: January 9, 2024
    Assignee: REGENTS OF THE UNIVERSITY OF MINNESOTA
    Inventors: Anthony Brusa, Kevin Dorn
  • Patent number: 11859257
    Abstract: Provided herein are compositions, kits, and methods for detecting methicillin-resistant Staphylococcus aureus (MRSA) nucleic acids. In some embodiments, the compositions, kits, and methods can be used to detect one or more of type i, ii, iii, iv, v, vi, vii, viii, ix, xii, xiii, xiv, xv, or xxi SCCmec right extremity junction (MREJ) MRSA nucleic acids and one or more of mecA, mecC, and/or an additional S. aureus-specific gene.
    Type: Grant
    Filed: August 9, 2018
    Date of Patent: January 2, 2024
    Assignee: Gen-Probe Incorporated
    Inventors: Patrick Peterson, Paul Darby, Matthias Jost, Siobhan Miick, Matthew Brentnall, JoAnn Jackson
  • Patent number: 11788118
    Abstract: The present application relates to multiplex detection of nucleic acid molecules. In particular, the present application provides a method for detecting target nucleic acid sequences, said method can simultaneously detect the presence of multiple target nucleic acid sequences in a sample. In addition, the present application further provides a probe set, and a kit comprising one or more said probe sets, said probe set and said kit can be used to carry out the method of the invention.
    Type: Grant
    Filed: August 2, 2021
    Date of Patent: October 17, 2023
    Assignee: XIAMEN ZEESAN BIOTECH CO., LTD.
    Inventors: Qingge Li, Dongmei Chen, Qiuying Huang, Ye Xu, Yiqun Liao
  • Patent number: 11781188
    Abstract: The present disclosure is directed to methods of detecting cell-free DNA (cfDNA) in biological samples and using it to quantify organ damage and identify pathogens. In some aspects, the biological samples are from patients who have undergone solid-organ transplantation. The disclosure is also directed to methods of detecting and analyzing methylation patterns in cell-free DNA from organ transplant patients to identify the presence of pathogens as well as quantify contributing tissue proportions as a measurement of the host response.
    Type: Grant
    Filed: April 5, 2018
    Date of Patent: October 10, 2023
    Assignee: CORNELL UNIVERSITY
    Inventors: Iwijn De Vlaminck, John Richard Lee, Philip Smith Burnham, Alexandre Pellan Cheng, Manikkam Suthanthrian, Darshana Dadhania
  • Patent number: 11680294
    Abstract: The present invention relates to a method, in particular an in vitro method, for identifying non-classical monocytes, comprising analyzing the methylation status of at least one CpG position in the mammalian genomic region comprising an amplicon, wherein a demethylation or lack of methylation of said region is indicative for a non-classical monocyte, when compared to a classical monocyte or a non-monocyte cell. The analyses according to the invention can identify non-classical monocytes on an epigenetic level and distinguish them from all other cells in complex samples, such as, for example, other blood or immune cells. The present invention furthermore provides an improved method for quantifying non-classical monocytes, in particular in complex samples. The method can be performed without a step of purifying and/or enriching cells, preferably in whole blood and/or non-trypsinized tissue.
    Type: Grant
    Filed: October 26, 2018
    Date of Patent: June 20, 2023
    Assignee: Precision for Medicine GmbH
    Inventor: Sven Olek
  • Patent number: 11680298
    Abstract: There is provided a method of identifying risk of cancer in a human subject, the method comprising: determining in a biological sample of the subject, whether a copy number amplification of at least one continuous genomic region specific to human chromosome 1q21 is present, wherein the presence of a copy number amplification of the region specific to human chromosome 1q21 represents an elevated risk of cancer in the subject and the at least one continuous genomic region is selected from the group consisting of: a human TUFT 1 gene or a gene from the human S100 family. It is also provided a method of treating cancer in a subject determined to have a copy number amplification of a region specific to human chromosome 1q21, the method comprising administering a therapeutic agent capable of suppressing IRAK1, IRAK4 or a S100 family member, such as Pacritinib. There are also provided a method of treating cancer, related polynucleotides, kits, therapeutic agents and use of the therapeutic agents.
    Type: Grant
    Filed: September 7, 2017
    Date of Patent: June 20, 2023
    Assignees: Agency for Science, Technology and Research, Tan Tock Seng Hospital Pte. Ltd.
    Inventors: Qiang Yu, Jian Yuan Goh, Min Feng, Ern Yu Tan
  • Patent number: 11661632
    Abstract: Methods and compositions are provided for diagnosing lung cancer in a mammalian subject by use of 10 or more selected genes, e.g., a gene expression profile, from the blood of the subject which is characteristic of disease. The gene expression profile includes 10 or more genes of Table I or Table II herein.
    Type: Grant
    Filed: June 21, 2017
    Date of Patent: May 30, 2023
    Assignee: The Wistar Institute of Anatomy and Biology
    Inventors: Michael Showe, Louise C. Showe, Andrei V. Kossenkov
  • Patent number: 11643695
    Abstract: The invention provides a Siniperca chuatsi IL-6 gene and a detection method for a disease-resistant SNP marker. A cDNA sequence of S. chuatsi IL-6 gene is cloned, as shown in SEQ ID NO: 1. A IL-6 gene gDNA sequence containing an intron of the S. chuatsi IL-6 gene is cloned, as shown in SEQ ID NO: 2. A primer for amplifying a disease-resistant SNP locus is designed according to IL-6 gDNA sequence, and S. chuatsi IL-6 gene is amplified to obtain an amplification product which is sequenced, and the SNPs loci relevant to virus disease-resistance are found out and the SNP locus is determined according to DNA peak profile. The IL-6 cDNA full-length sequence and IL-6 gDNA full-length sequence are cloned firstly. The SNP locus relevant to virus disease resistance of S. chuatsi IL-6 gene is detected, thereby providing a new method for breeding of S. chuatsi.
    Type: Grant
    Filed: March 3, 2021
    Date of Patent: May 9, 2023
    Assignee: SOOCHOW UNIVERSITY
    Inventors: Hezhong Huang, Yao Lu, Ruiming Jin, Ze Li
  • Patent number: 11608535
    Abstract: The present invention relates to methods of detecting an infection in a subject based on the relative abundance of target molecules indicative of the expression of at least the gene pair DUSP1 and IFI27. In particular, the invention relates to a method of distinguishing between a bacterial infection or a non-bacterial infection in a subject, especially between bacterial and non-bacterial lower respiratory system infections using the gene pair. Further, the invention provides the medical use of therapeutic agents in the treatment of a bacterial or non-bacterial infection in a subject identified as having such an infection through use of a method of the invention, and monitoring the therapeutic effectiveness.
    Type: Grant
    Filed: April 11, 2019
    Date of Patent: March 21, 2023
    Inventor: Michael Griffiths
  • Patent number: 11603568
    Abstract: Although tumor-associated macrophages have been extensively studied in the control of response to radiotherapy, the molecular mechanisms involved in the ionizing radiation-mediated activation of macrophages remain elusive. Here the present inventors show that ionizing radiation induces the expression of interferon-regulatory factor 5 (IRF5) promoting thus macrophage activation toward a pro-inflammatory phenotype. They reveal that the activation of the Ataxia telangiectasia mutated (ATM) kinase is required for ionizing radiation-elicited macrophage activation, but also for macrophage reprogramming after treatments with ?-interferon, lipopolysaccharide or chemotherapeutic agent (such as cis-platin), underscoring the fact that the kinase ATM plays a central role during macrophage phenotypic switching toward a proinflammatory phenotype. They further demonstrate that NADPH oxidase 2 (NOX2)-dependent ROS production is upstream to ATM activation and is essential during this process.
    Type: Grant
    Filed: September 19, 2017
    Date of Patent: March 14, 2023
    Assignee: Institut Gustave Roussy
    Inventors: Jean-Luc Perfettini, Eric Deutsch, Awatef Allouch
  • Patent number: 11603563
    Abstract: Provided is a method of predicting differentiation potential of undifferentiated iPS cells into cartilage cells. Provided is a genetic marker for predicting differentiation potential of undifferentiated iPS cells into cartilage cells. A method of predicting differentiation potential of undifferentiated iPS cells into cartilage cells based on gene expression data of the undifferentiated iPS cells. A method of predicting differentiation potential of undifferentiated iPS cells into cartilage cells by predicting differentiation potential of the iPS cells into neural crest cells (NC cells) based on gene expression data of the undifferentiated iPS cells.
    Type: Grant
    Filed: June 8, 2018
    Date of Patent: March 14, 2023
    Assignees: Shimadzu Corporation, Kyoto University
    Inventors: Makoto Watanabe, Taka-Aki Sato, Junya Toguchida
  • Patent number: 11603566
    Abstract: The current disclosure relates to therapeutic treatments and diagnostic methods for esophageal cancer based on the expression level of biomarker miRNAs.
    Type: Grant
    Filed: August 4, 2017
    Date of Patent: March 14, 2023
    Assignee: Cancer Diagnostics Research Innovation
    Inventors: Ajay Goel, Jinsei Miyoshi
  • Patent number: 11578368
    Abstract: The present invention provides a method of assessing type 2 diabetes susceptibility and/or predicting treatment responsiveness in a human subject, the method comprising determining the identity of at least one allele at each of three or more positions of single nucleotide polymorphism (SNP) selected from the group consisting of: SLC16A11-rs75493593; HNF1A-rs483353044; TCF7L2-rs7903146; CDKN2A/B-rs10811661; CDKAL1-rs7756992; SLC30A8-rs3802177; IGF2BP2-rs4402960; FTO-rs9936385; PPARG-rs1801282; HHEX/IDE-rs1111875; ADCYS-rs11717195; JAZF1-rs849135; WSF1-rs4458523; INS-IGF2-rs149483638; KCNQ1-rs2237897; and KCNJ11-rs5219, and/or an SNP in linkage disequilibrium with any one of said SNPs at r2>0.8. Also provided are a genotyping tool and a type 2 diabetes risk assessment system for use in the method of the invention.
    Type: Grant
    Filed: April 28, 2020
    Date of Patent: February 14, 2023
    Assignee: Patia Biopharma, S.A. De C.V.
    Inventors: Laureano Simón Buela, Mirella G. Zulueta
  • Patent number: 11566291
    Abstract: The present disclosure provides for and relates to the identification of novel biomarkers for diagnosis and prognosis of prostate cancer or the biochemical reoccurrence of prostate cancer. The biomarkers of the invention show altered methylation levels of certain CpG loci relative to normal prostate tissue, as set forth.
    Type: Grant
    Filed: March 13, 2014
    Date of Patent: January 31, 2023
    Assignees: HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY, THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY
    Inventors: Richard M. Myers, James D. Brooks, Marie K. Kirby
  • Patent number: 11525160
    Abstract: Systems and methods for detecting at least two genomic alleles associated with corneal dystrophy in a sample from a human subject are disclosed in which cells (e.g., epithelial) of the subject are adhered to a tip of a substrate. The tip of the substrate is agitated in a lysis solution that lyses cells adhered to the substrate. The substrate is removed from the lysis solution upon completion of this agitation. The resulting lysis solution is incubated and then genomic DNA from the lysis solution is isolated to form a gDNA solution. From this, identity of at least two nucleotides present in the human TGF?I gene is determined using at least two oligonucleotide primer pairs and the gDNA solution. These at least two nucleotides are located at respective independent positions of the TGF?I gene corresponding to respective independent single nucleotide polymorphisms (SNPs) associated with corneal dystrophy.
    Type: Grant
    Filed: May 13, 2016
    Date of Patent: December 13, 2022
    Assignee: Avellino Lab USA, Inc.
    Inventors: Connie Chao-Shern, Sun-Young Cho, Gene Lee
  • Patent number: 11492664
    Abstract: The present invention relates to methods of nucleic acid analyte detection by PCR. In particular, methods and kits for the detection of a plurality of nucleic acid analytes and the generation of kinetic signatures are provided. Further provided are methods and kits of nested PCR and PCR using limiting primers.
    Type: Grant
    Filed: August 1, 2018
    Date of Patent: November 8, 2022
    Assignee: California Institute of Technology
    Inventors: Aditya Rajagopal, Emil P. Kartalov
  • Patent number: 11447830
    Abstract: Methods for identifying and treating cancers that are DNA repair, such as homologous recombination (HR) repair, defective or sensitive to PARP inhibitors or platinum-based therapy. In some aspects, DNA repair, such as HR repair, defective cancers are treated with a PARP inhibitor therapy or cisplatin. Methods for sensitizing cancers to a PARP inhibitor therapy are also provided.
    Type: Grant
    Filed: March 5, 2018
    Date of Patent: September 20, 2022
    Assignee: Board of Regents, The University of Texas System
    Inventors: Shiaw-Yih Lin, Daniel McGrail, Gordon Mills
  • Patent number: 11421280
    Abstract: The present invention describes biomarkers that have been discovered to correlate with varied individual responses (e.g., efficacy, adverse effect, and other end points) to enzastaurin, in treating diseases such as, DLBCL, GBM, and other cancer types. The newly discovered biomarkers and others in linkage disequilibrium with them can be used in companion diagnostic tests which can help to predict drug responses and apply drugs only to those who will be benefited, or exclude those who might not be beneficial, by the treatment.
    Type: Grant
    Filed: August 31, 2017
    Date of Patent: August 23, 2022
    Assignee: Denovo Biopharma, LLC
    Inventors: Wen Luo, Hong Sun