Patents Examined by Joseph G Dauner
  • Nucleic acid sequence and capture by formation of an abasic site-derived cross-link
    Patent number: 11034996
    Abstract: Disclosed herein is a method of covalently crosslinking DNA strands. In certain aspects, the method comprises incubating a hybridized, double-stranded DNA polynucleotide (dsDNA), comprising a probe strand that comprises an abasic (Ap) residue and an at least partially complementary target strand that comprises a 2?-deoxyadenosine (dA) residue, wherein incubation occurs under conditions that allow for a covalent crosslinking reaction to occur between the Ap residue in the probe strand and the dA residue in the target strand.
    Type: Grant
    Filed: February 28, 2019
    Date of Patent: June 15, 2021
    Assignee: The Curators of the University of Missouri
    Inventors: Kent Gates, Li-Qun Gu, Maryam Imani Nejad, Ruicheng Shi, Xinyue Zhang
  • Additive for accelerating hybridization
    Patent number: 11021739
    Abstract: The present invention describes an additive for accelerating hybridization comprising: a) an aqueous solution of sodium dextran sulphate, b) a salt, c) a buffer system, d) a strong mineral base possibly mixed with at least one polar aprotic solvent, or at least one polar aprotic solvent. The additive described herein enables a reduction in the time required to perform the investigations with molecular probes on histological and cytological samples; the possibility of applying it to the protocol already in use in the routine practices of various laboratories in order to reduce the working time of histological and cytological samples for investigations with molecular probes, with no organisational impacts on the operators' work, enabling a more rapid diagnostic response for the patient and offering the possibility of using the additive described herein without formamide.
    Type: Grant
    Filed: February 3, 2016
    Date of Patent: June 1, 2021
    Assignee: ALMA MATER STUDIORUM UNEVERSETA DI BOLOGNA
    Inventors: Enrico Di Oto, Valentina Monti, Sofia Asioli
  • Transcriptome in vivo analysis (TIVA) and transcriptome in situ analysis (TISA)
    Patent number: 11021502
    Abstract: Compositions and methods of capturing one or more nucleic acid molecules of a cell or subcellular compartment are described. In certain aspects, the compositions comprise a caged molecule comprising one or more photolinkers and an antisense oligonucleotide, which when uncaged hybridizes to a target nucleic acid molecule.
    Type: Grant
    Filed: August 4, 2015
    Date of Patent: June 1, 2021
    Assignee: The Trustees of the University of Pennsylvania
    Inventors: James Eberwine, Ivan J. Dmochowski, Sean B. Yeldell, Julianne C. Griepenburg, Teresa L. Rapp, Jennifer M. Singh, Jai-Yoon Sul, Jaehee Lee
  • Methods of diagnosing and prognosing lung cancer
    Patent number: 11009508
    Abstract: The present invention provides methods of detecting cancer using biomarkers.
    Type: Grant
    Filed: January 23, 2019
    Date of Patent: May 18, 2021
    Assignees: Dana-Farber Cancer Institute, Inc., The General Hospital Corporation, Board of Regents of the University of Texas System
    Inventors: Kwok-Kin Wong, Bruce E. Johnson, Pasi A. Janne, Hongbin Ji, Nabeel Bardeesy, Norman E. Sharpless, Diego H. Castrillon
  • Diagnostic markers for platelet function and methods of use
    Patent number: 11008619
    Abstract: Disclosed herein are biomarkers of platelet function and methods for assessing platelet function in response to antiplatelet therapy and for determining a prognosis, diagnosis, or risk identification in a patient by detecting at least one biomarker of platelet function in the patient as well as determining amounts thereof. The biomarkers may be used to identify a patient as a candidate for treatment with an antiplatelet agent and to monitor and adjust antiplatelet therapy in a patient.
    Type: Grant
    Filed: May 16, 2019
    Date of Patent: May 18, 2021
    Assignee: Duke University
    Inventors: Geoffrey S. Ginsburg, Joseph E. Lucas, Thomas L. Ortel, Richard C. Becker, Deepak Voora, Jen-Tsan Chi
  • Correcting for deamination-induced sequence errors
    Patent number: 11008616
    Abstract: Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease. However, the value of such information can be compromised by errors introduced by or before the sequencing process including preparing nucleic acids for sequencing. Blunting single-stranded overhangs on nucleic acids in a sample can introduce deamination-induced sequencing errors. The disclosure provides methods of identifying and correcting for such deamination-induced sequencing errors and distinguishing them from real sequence variations.
    Type: Grant
    Filed: May 4, 2020
    Date of Patent: May 18, 2021
    Assignee: GUARDANT HEALTH, INC.
    Inventors: Marcin Sikora, Andrew Kennedy, Ariel Jaimovich, Darya Chudova, Stephen Fairclough
  • Compositions and methods for analyzing modified nucleotides
    Patent number: 11001876
    Abstract: Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map 5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map 5hmC in a DNA.
    Type: Grant
    Filed: February 27, 2019
    Date of Patent: May 11, 2021
    Assignee: New England Biolabs, Inc.
    Inventors: Romualdas Vaisvila, Theodore B. Davis, Shengxi Guan, Zhiyi Sun, Laurence Ettwiller, Lana Saleh
  • Use of C3AR1 as a biomarker in methods of treating inflammatory response syndromes
    Patent number: 10975437
    Abstract: Disclosed are methods for treating or inhibiting the development of infection-negative systemic inflammatory response syndrome (inSIRS) or infection-positive systemic inflammatory response syndrome (ipSIRS) based on the use of complement component 3a receptor 1 (C3AR1) as a biomarker for differentiating between inSIRS and ipSIRS.
    Type: Grant
    Filed: November 8, 2018
    Date of Patent: April 13, 2021
    Assignee: ImmuneXpress Pty Ltd
    Inventors: Richard Bruce Brandon, Leo Charles McHugh
  • Devices for detecting target biological molecules from cells and viruses
    Patent number: 10968474
    Abstract: Described herein are fluid-manipulation-based devices and methods of use. Fluid manipulations according to devices and methods as described herein can be configured to perform assays on biological samples. Devices and methods as described herein can manipulate and analyze nanoliter volumes of fluid, microliter volumes of fluid, milliliter volumes of fluid, or greater. Embodiments of the present disclosure can enable random biological assays and rapid, simultaneous analysis of multiple biological samples.
    Type: Grant
    Filed: March 27, 2019
    Date of Patent: April 6, 2021
    Assignee: University of Florida Research Foundation Inc.
    Inventor: Yunwei Charles Cao
  • Nanoporous gold and silver nanoparticles and substrates for molecular and biomolecular sensing
    Patent number: 10961564
    Abstract: A methodology for assays and diagnostics utilizes a nanoporous or corrugated metal-containing surface, fiber or particle which enhances or suppresses the optical detectability of a label. The resulting optical, electromagnetic, or imaging signal signals the presence of a pathogen or analyte of interest. Preferred embodiments pertain to label-free, in situ monitoring of individual DNA hybridization in microfluidics using molecular sentinel probes immobilized on nanoporous gold disks. By immobilizing molecular sentinel probes on nanoporous gold disks, single-molecule sensitivity is demonstrated via surface-enhanced Raman scattering which provides robust signals. The described methodology is generally applicable to most amplification independent assays and molecular diagnostics.
    Type: Grant
    Filed: May 22, 2015
    Date of Patent: March 30, 2021
    Assignee: UNIVERSITY OF HOUSTON SYSTEM
    Inventors: Wei-Chuan Shih, Richard Willson
  • Ligation-based detection of genetic variants
    Patent number: 10954566
    Abstract: The present invention provides assays systems and methods for detection of genetic variants in a sample, including copy number variation and single nucleotide polymorphisms. The invention preferably employs the technique of tandem ligation—, e.g., the ligation of two or more fixed sequence oligonucleotides and one or more bridging oligonucleotides complementary to a region between the fixed sequence oligonucleotides—combined with detection of levels of particular genomic regions using array hybridization.
    Type: Grant
    Filed: January 23, 2019
    Date of Patent: March 23, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Arnold Oliphant, Andrew Sparks, John Stuelpnagel, Ken Song
  • Molecular tag attachment and transfer
    Patent number: 10927405
    Abstract: Described herein are methods, compositions and kits for identifying modifications that could lead to false positive detections in nucleic acid sequencing. In some embodiments, the methods, compositions and kits provided herein are useful for reducing potential of false positive detection of variants caused by errors during sample preparation or sequencing.
    Type: Grant
    Filed: January 11, 2019
    Date of Patent: February 23, 2021
    Assignee: NUGEN TECHNOLOGIES, INC.
    Inventors: Douglas A. Amorese, Stephanie C. Huelga, Bin Li
  • High throughput discovery of new genes from complex mixtures of environmental microbes
    Patent number: 10920218
    Abstract: Compositions and methods for isolating new variants of known gene sequences are provided. The methods find use in identifying variants, particularly homologs, in complex mixtures. Compositions comprise hybridization baits that hybridize to gene families of interest, particularly agricultural interest, in order to selectively enrich the polynucleotides of interest from complex mixtures. Bait sequences may be specific for a number of genes from distinct gene families of interest and may be designed to cover each gene of interest by at least 2-fold. Thus methods disclosed herein are drawn to an oligonucleotide hybridization gene capture approach for identification of new genes of interest from environmental samples.
    Type: Grant
    Filed: January 4, 2018
    Date of Patent: February 16, 2021
    Assignee: AgBiome, Inc.
    Inventors: Vadim Beilinson, Janice Jones, Jessica Parks, Rebecca E. Thayer, Daniel J. Tomso, Scott Joseph Uknes, Sandy Volrath, Eric Russell Ward
  • Different levels in blood cell samples of EMT-markers for the diagnosis of cancer, in particular of colorectal (CRC) and pancreatic (PC) cancer
    Patent number: 10907210
    Abstract: The present invention concerns a method for determining if a subject is affected by a colorectal or pancreatic cancer or for determining the stage and/or the progression of a colorectal cancer. By measuring the presence of a panel of m RNAs encoding for transcription factors/genes involved in epithelial to mesenchymal transition in a blood sample, wherein different mRNA levels of a set of genes comprising TWIST1, SLUG, ZEB2, ZEB1 and CDH1, are indicative of colorectal cancer or pancreatic cancer diagnosis, and/or of colorectal cancer stage at diagnosis, and/or of CRC metastatic progression after surgery. The invention concerns also the use of kits to work the method.
    Type: Grant
    Filed: December 16, 2014
    Date of Patent: February 2, 2021
    Assignee: HUMANITAS MIRASOLE S.P.A.
    Inventors: Luigi Laghi, Giuseppe Celesti
  • Assay systems for genetic analysis
    Patent number: 10907198
    Abstract: The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.
    Type: Grant
    Filed: October 12, 2018
    Date of Patent: February 2, 2021
    Assignee: Ariosa Diagnostics, Inc.
    Inventors: Andrew Sparks, Arnold Oliphant, Jacob Zahn, Ken Song, John Stuelpnagel
  • Lysis buffers for extracting nucleic acids
    Patent number: 10894957
    Abstract: The present teachings relate to the extraction of nucleic acid from solid materials. Provided are useful compositions, methods and kits for obtaining nucleic acids from a solid biological sample or an adhesive material having a biological material adherent or embedded within the adhesive substrate. The extracted nucleic acid can be used in downstream applications such as genotyping, detection, quantification, and identification of the source of the biological material.
    Type: Grant
    Filed: June 21, 2018
    Date of Patent: January 19, 2021
    Assignee: Life Technologies Corporation
    Inventors: James Stray, Jason Yingjie Liu, Maxim Brevnov, Jaiprakash Shewale, Allison Holt
  • Compositions, methods, and kits for isolating nucleic acids
    Patent number: 10894976
    Abstract: Disclosed here is a composition for isolating nucleic acids from a biological sample, comprising a chaotropic compound and a solvent, wherein the solvent comprises a nitrile compound, tetrahydrofuran, or a combination thereof. Also disclosed is a method for binding nucleic acids to a matrix, comprising: contacting the nucleic acids from a biological sample with the matrix in the presence of a chaotropic compound and a solvent, wherein the solvent comprises a nitrile compound, tetrahydrofuran, or a combination thereof, thereby binding the nucleic acids to the matrix. Further disclosed is a kit for isolating nucleic acids from a biological sample comprising a binding buffer, wherein the binding buffer comprises a chaotropic compound and a solvent, wherein the solvent comprises a nitrile compound, tetrahydrofuran, or a combination thereof.
    Type: Grant
    Filed: February 15, 2018
    Date of Patent: January 19, 2021
    Assignee: Natera, Inc.
    Inventors: James Stray, Jason Tong, Xiaoke Wang
  • Method for identifying the quantitative cellular composition in a biological sample
    Patent number: 10894984
    Abstract: The present invention provides an epigenetic haemogram, also referred to as an epigenetic blood cell count that identifies the quantitative, comprehensive picture of cellular composition in a biological sample, wherein advantageously a normalization standard is used. The normalization standard is a nucleic acid molecule comprising at least one marker-region being specific for each of the blood cells to be detected, and at least one control-region being cell-unspecific, wherein said regions are present in the same number of copies on said molecule and/or a natural blood cell sample of known composition. Furthermore, the present invention relates to a kit and the use of a kit for performing the epigenetic assessment of comprehensive, quantitative cellular composition of a biological sample. The biological sample is derived from e.g.
    Type: Grant
    Filed: March 30, 2018
    Date of Patent: January 19, 2021
    Assignee: Epiontis GmbH
    Inventors: Sven Olek, Ulrich Hoffmüller
  • Genome methylation analysis
    Patent number: 10889852
    Abstract: Provided herein are methods for identifying sites and regions within a gene or genome that are amenable to analysis of methylation. The methods disclosed herein allow the efficient identification on a genome-wide scale of target restriction sites and fragments that provide targets for subsequent analysis.
    Type: Grant
    Filed: October 20, 2015
    Date of Patent: January 12, 2021
    Assignee: Commonwealth Scientific and Industrial Research Organisation
    Inventors: Peter Molloy, Susan Margaret Mitchell, Konsta Duesing
  • Thyroid tumors identified
    Patent number: 10889865
    Abstract: The invention relates to methods and kits for detecting thyroid cancer by detecting differences in the expression of genes that are differentially expressed in thyroid cancer cells.
    Type: Grant
    Filed: February 23, 2017
    Date of Patent: January 12, 2021
    Assignee: Cornell University
    Inventors: Thomas J. Fahey, III, Nimmi Kapoor, Theresa Scognamiglio