Patents Examined by Ethan Whisenant
  • Patent number: 9856471
    Abstract: Disclosed are methods for synthesizing and/or assembling at least one polynucleotide product having a predefined sequence from a plurality of different oligonucleotides. In exemplary embodiments, the methods involve synthesis and/or amplification of different oligonucleotides immobilized on a solid support, release of synthesized/amplified oligonucleotides in solution to form droplets, recognition and removal of error-containing oligonucleotides, moving or combining two droplets to allow hybridization and/or ligation between two different oligonucleotides, and further chain extension reaction following hybridization and/or ligation to hierarchically generate desired length of polynucleotide products.
    Type: Grant
    Filed: June 27, 2014
    Date of Patent: January 2, 2018
    Assignee: Gen9, Inc.
    Inventors: Joseph Jacobson, George Church, Larry Li-Yang Chu
  • Patent number: 9856516
    Abstract: The present disclosure relates to improved methods for the isolation of genomic material and detection of disease related single nucleotide polymorphisms. In some aspects, these methods increase the total recovery of genomic DNA from buccal cell samples by improving cell lysis conditions. In other aspects, these methods allow for the reuse of patient buccal swab samples, reducing the likelihood of having to collect additional patient samples for re-testing. Finally, in some aspects, these methods increase the sensitivity of SNP detection using an improved real-time PCR assay protocol.
    Type: Grant
    Filed: June 30, 2015
    Date of Patent: January 2, 2018
    Inventor: Connie Chao-Shern
  • Patent number: 9371564
    Abstract: Methods are provided for the isolation of biological macromolecules including peptides, proteins, and nucleic acids from mature plant fibers such as cotton fibers and from textiles. The biological macromolecules can be used to characterize the plant fiber (source, origin, genomic composition of producing plant etc.).
    Type: Grant
    Filed: August 6, 2009
    Date of Patent: June 21, 2016
    Assignee: Bayer Bioscience N.V.
    Inventors: Antonio Arioli, Steven Engelen
  • Patent number: 9334533
    Abstract: The present invention relates to a method and a kit for detecting nucleic acid sequence variation using melting curve analysis, especially relates to a method and a kit for detecting nucleic acid sequence variation by melting curve analysis using self-quenched probe. Said method provides the characteristics of the self-quenched probe employed, as well as the corresponding nucleic acid amplification conditions, so that the probe can bind to the amplified target sequence, and variations of the target sequence can be detected by melting curve analysis. The present invention also encompasses a kit assembled according to the method described.
    Type: Grant
    Filed: February 17, 2014
    Date of Patent: May 10, 2016
    Inventors: Qingge Li, Qiuying Huang
  • Patent number: 9284604
    Abstract: Methods and compositions for identifying a cellular nascent RNA transcript are provided.
    Type: Grant
    Filed: May 22, 2013
    Date of Patent: March 15, 2016
    Assignee: The Regents of the University of California
    Inventors: Jonathan Weissman, Lee Stirling Churchman
  • Patent number: 9127302
    Abstract: The invention relates generally to the field of identification of DNA sequences, genes or chromosomes. Methods and composition to obtain Unique Sequence DNA probes are provided. Composition comprises of any double stranded DNA containing Unique Sequences from which the repetitive sequences are eliminated according to the method described in this invention. The invention also relates to the preservation of cells that have been identified after immunomagnetic selection and fluorescent labeling in order to further interrogate the cells of interest. Furthermore the invention relates to genetic analysis of cells that have been identified after immunomagnetic selection and fluorescent labeling.
    Type: Grant
    Filed: September 20, 2006
    Date of Patent: September 8, 2015
    Assignee: Janssen Diagnostics, LLC
    Inventors: John A Verrant, Arjan G. J. Tibbe, Brad Foulk, Joost F. Swennenhuis, Leon W. M. M. Terstappen, Mark Carle Connelly, Michael T. Kagan
  • Patent number: 9051611
    Abstract: Methods, systems and compositions where a target nucleic acid includes a registration sequence disposed therein for identification of the number or relative position of determined sequence from the template sequence. Particularly preferred aspects include a registration sequence in a circular template nucleic acid sequence which is, in turn, used in sequence by incorporation processes that rely upon template dependent, polymerase mediated primer extension in the identification of the sequence of the template.
    Type: Grant
    Filed: August 14, 2013
    Date of Patent: June 9, 2015
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Fred Christians, Stephen Turner
  • Patent number: 8940484
    Abstract: The invention provides allelic ladder mixtures and individual alleles suitable for use in such mixtures. The allelic ladder mixtures give improved identification and distinguishing capabilities, particularly suitable in forensic investigations.
    Type: Grant
    Filed: February 7, 2013
    Date of Patent: January 27, 2015
    Assignee: Qiagen GmbH
    Inventors: Rebecca A. L. Barber, Michael D. Barber, Peter E. Johnson, Sharon M. Gillbard, Marc D. Haywood, Carolyn D. Smith, Jennifer A. Arnold, Trudy Burke, Andrew J. Urquhart, Peter P. Gill
  • Patent number: 8932809
    Abstract: The invention generally relates to methods and kits for isolating nucleic acids from an organism. In certain embodiments, methods of the invention involve contacting a plurality of lytic enzymes to an organism, thereby lysing a cell wall of the organism to release the nucleic acid, and introducing at least one agent to separate the nucleic acid from the lysed cells, thereby isolating the nucleic acid.
    Type: Grant
    Filed: January 19, 2010
    Date of Patent: January 13, 2015
    Assignee: OpGen, Inc.
    Inventor: John Kevin Henkhaus
  • Patent number: 8906612
    Abstract: The invention provides a novel class of scaffold-based labeled polymerase enzyme substrates. The polymerase enzyme substrates have a multivalent core or scaffold to which is attached fluorescent dye moieties and nucleoside phosphate moities. The polymerase enzyme substrates have multiple fluorescent dye moities and/or multiple nucleoside phosphate moieties. Preferred multivalent cores comprise trifunctional six membered aromatic moities. The invention also provides for sequencing methods and kits with scaffold-based labeled polymerase enzyme substrates.
    Type: Grant
    Filed: August 25, 2011
    Date of Patent: December 9, 2014
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Lubomir Sebo, Stephen Yue, Wei-Chuan Sun, Louis Brogley, Andrei Fedorov
  • Patent number: 8889355
    Abstract: Ligation-enhanced nucleic acid detection assay embodiments for detection of RNA or DNA are described. The assay embodiments rely on ligation of chimeric oligonucleotide probes to generate a template for amplification and detection. The assay embodiments are substantially independent of the fidelity of a polymerase for copying compromised nucleic acid. Very little background amplification is observed and as few as 1000 copies of target nucleic acid can be detected. Method embodiments are particularly adept for detection of RNA from compromised samples such as formalin-fixed and paraffin-embedded samples. Heavily degraded and cross-linked nucleic acids of compromised samples, in which classic quantitative real time PCR assays typically fail to adequately amplify signal, can be reliably detected and quantified.
    Type: Grant
    Filed: April 26, 2013
    Date of Patent: November 18, 2014
    Assignee: Applied Biosystems, LLC
    Inventors: R. Scott Kuersten, Brittan Pasloske
  • Patent number: 8883412
    Abstract: A size standard, kit includes a size standard, method of defining a size standard and method of analysis using a size standard. The size standard is intended to include size standard elements which have a size greater than and/or less than and/or different from the components of a sample which are to be sized. This means that the same characteristic unit, such as a dye, can be used to label the component and the size standard. A further characteristic unit, from amongst a limited number of such characteristic units is liberated from use only on size standards for use on components. The method is therefore particularly useful in multiplex amplification of STRs.
    Type: Grant
    Filed: June 29, 2009
    Date of Patent: November 11, 2014
    Assignee: Qiagen GmbH
    Inventors: Valerie Carol Tucker, Pieris Koumi, Andrew John Hopwood, Keith Elliot
  • Patent number: 8877436
    Abstract: The present invention comprises a method that provides fast and reliable results for detecting the presence of a target nucleic acid molecule in a sample.
    Type: Grant
    Filed: October 26, 2009
    Date of Patent: November 4, 2014
    Assignee: Qiagen Gaithersburg, Inc.
    Inventors: Paul Eder, Eric Payne, Irina Nazarenko, Suganthi Ramachandran, Arvind Virmani, Laura Bell
  • Patent number: 8859201
    Abstract: A sequencing method is presented in which a biomolecule is hybridized with a specially chosen pool of different probes of known sequence which can be electrically distinguished. The different probe types are tagged such that they can be distinguished from each other in a Hybridization Assisted Nanopore Sequencing (HANS) detection system, and their relative positions on the biomolecule can be determined as the biomolecule passes through a pore or channel. The methods eliminate, resolve, or greatly reduce ambiguities encountered in previous sequencing methods.
    Type: Grant
    Filed: November 9, 2011
    Date of Patent: October 14, 2014
    Assignee: NABsys, Inc.
    Inventor: Peter H. Goldstein
  • Patent number: 8785120
    Abstract: The invention generally provides a method for the sample preparation for a subsequent preparation, processing or analysis method of a sample containing an at least one species of nucleic acid and/or one species of protein, whereby the method comprises the following steps: A) providing a sample which contains at least one species of a nucleic acid and/or of a protein, B) contacting the sample with a fluid or solid composition to produce a fluid sample preparation, whereby the composition contains at least a nitrogenous compound, which is selected from the group consisting of a) polyamines, b) amino acids, and oligo- and polypeptides, c) nitrogenous heterocyclic compounds, including homo-oder heteropolymeres, which comprise these nitrogenous compounds, d) amines of the type R1R2NR3, whereby R1, R2 and R3 are chosen independently from one another from the group consisting of H, C1-C5-alkyl groups and aryl groups, whereby R1, R2 and R3 are not H simultaneously, e) carbonxylic acid amides, f) inorganic ammonium sa
    Type: Grant
    Filed: August 24, 2010
    Date of Patent: July 22, 2014
    Assignee: Qiagen GmbH
    Inventors: Christian Korfhage, Friederike Wilmer, Dirk Loffert, Ralf Himmelreich, Claudia Fritz, Kathleen Rieske
  • Patent number: 8507198
    Abstract: The invention relates to methods for isolating and/or identifying nucleic acids. The invention also provides kits for isolating and/or identifying nucleic acids.
    Type: Grant
    Filed: May 22, 2009
    Date of Patent: August 13, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Douglas A. Bost, Lawrence Greenfield
  • Patent number: 8465921
    Abstract: Conjugates between a minor groove binding molecule, such as the trimer of 1,2-dihydro-(3H)-pyrrolo[3,2-e]indole-7-carboxylate (CDPI3), and an oligonucleotide form unusually stable hybrids with complementary target sequences, in which the tethered CDPI3 group resides in the minor groove of the duplex. These conjugates can be used as probes and primers. Due to their unusually high binding affinity, conjugates as short as 8-mers can be used as amplification primers with high specificity and efficiency. MGB conjugation also increases the discriminatory power of short oligonucleotides, providing enhanced detection of nucleotide sequence mismatches by short oligonucleotides.
    Type: Grant
    Filed: August 31, 2010
    Date of Patent: June 18, 2013
    Assignee: Elitech Holding B.V.
    Inventors: Joel Hedgpeth, Irina A. Afonina, Igor V. Kutyavin, Eugeny A. Lukhtanov, Evgeniy S. Belousov, Rich B. Meyer, Jr.
  • Patent number: 8323206
    Abstract: A mouthpiece with an eject mechanism is disclosed. The mouthpiece includes an eject mechanism adapted to conform to a testing device, such as a breath analysis device. The eject mechanism allows for hygienic removal of a used mouthpiece from the testing device. A guiding surface allows for alignment of the mouthpiece with the testing device.
    Type: Grant
    Filed: March 27, 2008
    Date of Patent: December 4, 2012
    Assignee: Lifeloc Technologies
    Inventor: Alan C. Castrodale
  • Patent number: 8298140
    Abstract: Features indicative of hypoglycaemia in EEG signals are detected by: —dividing EEG signals into a sequence of time segments, —for each time segment determining whether a pattern of EEG signals is present which is indicative of hypoglycaemia and, where a pattern of EEG signals indicative of hypoglycaemia is determined to be present in a time segment, recording this as an event, —integrating the number of events recorded during a selected number of preceding time segments which together constitute a selected time period, optionally in a time weighted manner, and—determining that the EEG signals are indicative that hypoglycaemia is present based on said integration when the said integrated number of events exceeds a preset threshold number and/or when there exists a threshold level of matching between a curve of said integration over time and a previously established ideal model of said curve indicative of hypoglycaemia.
    Type: Grant
    Filed: June 7, 2007
    Date of Patent: October 30, 2012
    Assignee: Hypo-Safe A/S
    Inventors: Henning Beck-Nielsen, Rasmus Elsborg Madsen
  • Patent number: 8148071
    Abstract: The present invention relates to compositions and methods for isolating and purifying nucleic acid. In particular, the present invention relates to methods of isolating nucleic acid from cells for use in further analysis.
    Type: Grant
    Filed: September 30, 2009
    Date of Patent: April 3, 2012
    Assignee: Northwestern University
    Inventors: David M. Kelso, Sujit Jangam, Douglas Yamada, Sally McFall