Patents Examined by Stephanie K. Mummert
  • Patent number: 10316362
    Abstract: The invention provides methods for simultaneously amplifying multiple nucleic acid regions of interest in one reaction volume as well as methods for selecting a library of primers for use in such amplification methods. The invention also provides library of primers with desirable characteristics, such as minimal formation of amplified primer dimers or other non-target amplicons.
    Type: Grant
    Filed: October 20, 2015
    Date of Patent: June 11, 2019
    Assignee: Natera, Inc.
    Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
  • Patent number: 10316358
    Abstract: One embodiment of the present invention provides for a method for amplifying a template of nucleic acid target sequence contained in a sample. The method includes contacting the sample with an amplification reaction mixture containing a primer complementary to the template of nucleic acid target sequence. A temperature of the reaction is oscillated between an upper temperature and a lower temperature wherein the change in temperature is no greater than about 20° C. during a plurality of temperature cycles. The template of nucleic acid target sequence is amplified.
    Type: Grant
    Filed: August 25, 2016
    Date of Patent: June 11, 2019
    Assignee: Mesa Biotech, Inc.
    Inventors: Hong Cai, Nathan J. Cobb
  • Patent number: 10316350
    Abstract: The present invention provides a method capable of realizing pretreatment process of genetic screening according to a POCT mode. The method includes: making a sample, extraction liquid for extracting nucleic-acid contained in the sample, silica particles, and a filtering material contact with each other; making the filtering material carry composite material of the nucleic-acid and the silica particles thereon; and then delivering the filtering material to a nucleic-acid-amplifying process by means of reaction solution for amplifying nucleic-acid, wherein particle diameters of the silica particles and concentration of the silica particles in the reaction solution for amplifying nucleic-acid are set up within a predetermined range.
    Type: Grant
    Filed: September 2, 2015
    Date of Patent: June 11, 2019
    Assignee: MIZUHO MEDY CO., LTD.
    Inventors: Kazutomi Yamakawa, Takashi Nagano
  • Patent number: 10316365
    Abstract: The present invention relates, in general, to gene expression profiles, and in particular, to a peripheral blood gene expression profile of an environmental exposure, ionizing radiation. The invention further relates to methods of screening patients for radiation exposure based on gene expression profiling and to kits suitable for use in such methods.
    Type: Grant
    Filed: November 27, 2013
    Date of Patent: June 11, 2019
    Assignee: Duke University
    Inventors: John Chute, Joseph Nevins, Holly Dressman, Nelson Chao
  • Patent number: 10316366
    Abstract: This invention provides methods and materials for measuring telomere abundance from chromosomes in a sample having telomeres within a pre-determined length range, e.g., short telomeres up to a certain length. The methods can involve a first step of performing a time-limited extension reaction calibrated to produce extension products from a double-stranded chromosomal DNA template of no more than a defined length, and a second step of amplifying, from the extension products, sequences bounded by a sub-telomeric sequence and the anchor sequence, to produce a length-limited telomere sequence product. The abundance of telomeric sequences in this product can be measured, and the measures can be correlated to a variety of indices.
    Type: Grant
    Filed: May 22, 2014
    Date of Patent: June 11, 2019
    Assignee: TELOMERE DIAGNOSTICS, INC.
    Inventors: Calvin Harley, Jue Lin, Yajing Hu
  • Patent number: 10301688
    Abstract: Provided herein are reagents for improving PCR accuracy.
    Type: Grant
    Filed: January 23, 2014
    Date of Patent: May 28, 2019
    Assignee: BRANDEIS UNIVERSITY
    Inventors: John Rice, Lawrence Wangh, Arthur H. Reis, Jr., Kenneth Pierce, Cristina Hartshorn, J. Acquiles Sanchez, Stephen Van Hooser, Skye Fishbein
  • Patent number: 10301686
    Abstract: The present invention relates to a method for specifically detecting Mycobacterium tuberculosis and nontuberculous mycobacteria by simultaneously amplifying and analyzing target genes using various primers and probes, and a kit using same. The method of the present invention is capable of selectively detecting Mycobacterium tuberculosis and nontuberculous mycobacteria with very high efficiency through a multiplex real-time polymerase chain reaction (PCR) using probes and primers specific to target genes (particularly, IS6110, 16S rRNA and ?-actin). Also, the kit of the present invention is capable of conveniently and efficiently detecting the target genes in a sample through a multiplex real-time PCR. Therefore, the method and the kit of the present invention are capable of selectively detecting with ease whether or not there is an infection with Mycobacterium tuberculosis or nontuberculous mycobacteria in a sample, and can be more accurately applied to the treatment of diseases on the basis thereof.
    Type: Grant
    Filed: March 19, 2014
    Date of Patent: May 28, 2019
    Assignee: HYUNIL-BIO CO.
    Inventor: Jeong Uk Kim
  • Patent number: 10287627
    Abstract: The invention provides compositions and methods for rapid assembly of one or more assembled polynucleotides from a plurality of component polynucleotides, as well as methods of designing polynucleotide primer and linker sets useful in the assembly methods of the invention.
    Type: Grant
    Filed: February 9, 2015
    Date of Patent: May 14, 2019
    Assignee: The Regents of the University of Colorado, a body corporate
    Inventors: Ryan T. Gill, Ramsey Zeitoun, Andrew Garst
  • Patent number: 10280451
    Abstract: Methods, compositions, and kits are provided for quantification of genome editing.
    Type: Grant
    Filed: January 8, 2016
    Date of Patent: May 7, 2019
    Assignees: Bio-Rad Laboratories, Inc., J. David Gladstone Institutes
    Inventors: Jennifer Berman, Samantha Cooper, George Karlin-Neumann, Yuichiro Miyaoka, Bruce Conklin, Josh Shinoff
  • Patent number: 10266901
    Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
    Type: Grant
    Filed: January 4, 2016
    Date of Patent: April 23, 2019
    Assignee: ADAPTIVE BIOTECHNOLOGIES CORP.
    Inventors: Malek Faham, Thomas Willis
  • Patent number: 10266880
    Abstract: The present invention relates to the technical field of molecular biology, provides a method for measuring short RNA using amplified DNA fragment length polymorphism, and comprises the following steps: first using at least two synthesized miRNAs as the internal measurement standard, said synthesized miRNAs containing no natural homologous sequence in comparison with the short RNA to be measured, and mixing the synthesized miRNAs using different molecule numbers so as to form a dynamic miRNA standard molecular gradient; mixing the same quantity of the dynamic miRNA standard with the short RNA to be measured, and performing RNA reverse transcription, cDNA tailing, PCR synchronous amplification, and fluorescent quantitative analysis on the length polymorphism fragment of the PCR product DNA so as to measure the relative ratio of the fluorescence intensity of the DNA fragment produced by the amplification of the short RNA to be measured to the dynamic miRNA standard fluorescence intensity gradient.
    Type: Grant
    Filed: September 15, 2015
    Date of Patent: April 23, 2019
    Inventors: Kai Xu, Fang Tang, Yaoyi Zhang, Zihao Feng, Yu Yang, Xiujin Wu, Feifei Zhang
  • Patent number: 10262755
    Abstract: The invention provides methods, systems, and computer readable medium for detecting ploidy of chromosome segments or entire chromosomes, for detecting single nucleotide variants and for detecting both ploidy of chromosome segments and single nucleotide variants. In some aspects, the invention provides methods, systems, and computer readable medium for detecting cancer or a chromosomal abnormality in a gestating fetus.
    Type: Grant
    Filed: October 14, 2015
    Date of Patent: April 16, 2019
    Assignee: NATERA, INC.
    Inventors: Joshua Babiarz, Tudor Pompiliu Constantin, Lane A. Eubank, George Gemelos, Matthew Micah Hill, Huseyin Eser Kirkizlar, Matthew Rabinowitz, Onur Sakarya, Styrmir Sigurjonsson, Bernhard Zimmermann
  • Patent number: 10253378
    Abstract: The present invention relates to utilization of an artificially synthesized nucleic acid, and more particularly, to a quantitative analysis method capable of quantitatively adjusting gene-based microbial community analysis results by preparing a microorganism 16S rDNA gene, which has a single nucleotide polymorphism (SNP) at a particular location so as to be differentiated from a gene of a target microorganism on the nucleotide sequence, and then using the microorganism 16S rDNA gene as an internal standard material which is quantifiable through nucleotide sequencing.
    Type: Grant
    Filed: November 18, 2014
    Date of Patent: April 9, 2019
    Assignee: Korea Research Institute of Standards and Science
    Inventors: Inchul Yang, Hannah Yu, Hyo-jin Yang, Sook-Kyung Kim, Sang-Ryoul Park
  • Patent number: 10253369
    Abstract: Provided are methods of determining whether a subject having ER+ breast cancer is expected to benefit from treatment with combination endocrine therapy and mTOR inhibitor therapy. Also provided are methods of treating a subject having ER+ breast cancer.
    Type: Grant
    Filed: May 28, 2015
    Date of Patent: April 9, 2019
    Assignee: BIOTHERANOSTICS, INC.
    Inventors: Catherine Schnabel, Yi Zhang, Mark G. Erlander
  • Patent number: 10246746
    Abstract: A method of sequencing a target nucleic acid polymer by (a) modifying a target nucleic acid polymer to produce a modified nucleic acid polymer; (b) producing fragments of the modified nucleic acid polymer, wherein the fragments are attached to locations on a solid support surface (c) determining nucleotide sequences from the fragments at the locations; and (d) producing a representation of the nucleotide sequence for the target nucleic acid polymer based on the nucleotide sequences from the fragments and the relative distances between the locations on the solid support surface.
    Type: Grant
    Filed: December 16, 2014
    Date of Patent: April 2, 2019
    Assignee: Illumina, Inc.
    Inventors: Jeffrey S. Fisher, Frank J. Steemers, Sasan Amini, Kevin L. Gunderson
  • Patent number: 10246752
    Abstract: There is a need for improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer. Provided herein are methods for using DNA sequencing to identify personalized biomarkers in patients with autoimmune disease and other conditions. Identified biomarkers can be used to determine the disease state for a subject with an autoimmune disease or other condition.
    Type: Grant
    Filed: November 22, 2017
    Date of Patent: April 2, 2019
    Assignee: Adaptive Biotechnologies Corp.
    Inventors: Malek Faham, Thomas Willis
  • Patent number: 10233440
    Abstract: Methods and reagents are provided for the rapid extraction of nucleic acids from a fixed paraffin embedded sample (e.g., a FFPET sample). In some embodiments, the methods comprise incubating one or more sections of said tissue sample in a lysis solution comprising a buffer sufficient to maintain the pH of said solution at a pH ranging from about pH 4 to about pH 9; a chaotropic agent; a chelating agent; and a detergent; where the incubating is at a temperature ranging from about 50 C to about 100 C; and recovering the nucleic acid from said lysis solution.
    Type: Grant
    Filed: September 26, 2013
    Date of Patent: March 19, 2019
    Assignee: CEPHEID
    Inventors: Edwin Wei-Lung Lai, Reuel Van Atta, Kenneth E. Ho
  • Patent number: 10226770
    Abstract: A thermal cycler for a microfluidic device includes a controller operable to provide a series of electrical signals, a heat sink, and a heating element in thermal communication with the heat sink and operable to receive the series of electrical signals from the controller. The thermal cycler also includes a thermal chuck in thermal communication with the heating element. The thermal chuck comprises a heating surface operable to make thermal contact with the microfluidic device. The heating surface is characterized by a temperature ramp rate between 2.5 degrees Celsius per second and 5.5 degrees Celsius per second and a temperature difference between a first portion of the heating surface supporting a first portion of the microfluidic device and a second portion of the heating surface supporting a second portion of the microfluidic device is less than 0.25° C.
    Type: Grant
    Filed: September 24, 2015
    Date of Patent: March 12, 2019
    Assignee: Fluidigm Corporation
    Inventors: Jake Kimball, Brandon Ripley, Gang Sun, Dominique Toppani, Myo Thu Maung
  • Patent number: 10214759
    Abstract: The present invention pertains to an in vitro method in which the frequency of the targeted nucleotide sequence containing the DNA fragment of interest is increased stepwise, by several rounds of 1) dilution of a sample containing the DNA fragment of interest into several replicates (separation), 2) randomly amplifying DNA in the replicates (concentration), 3) detecting the DNA fragment of interest in at least one of the diluted and amplified replicates (selection) and repeating steps 1) through 3) until the DNA fragment of interest can be sequenced by standard sequencing techniques.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: February 26, 2019
    Assignee: Samplix ApS
    Inventors: Thomas Kvist, Marie Just Mikkelsen
  • Patent number: 10208336
    Abstract: A method of sample analysis is provided. In certain embodiments, the method may comprise: (a) filtering a liquid sample containing rolling circle amplification (RCA) products using a porous capillary membrane, thereby producing an array of the RCA products on the membrane; wherein the sample contains at least a first population of RCA products and a second population of RCA products, wherein the first and second populations of labeled RCA products are distinguishably labeled; and (b) determining the amount of the first labeled population of RCA products and the amount of the second labeled population of RCA products in an area of the membrane.
    Type: Grant
    Filed: May 2, 2016
    Date of Patent: February 19, 2019
    Assignee: Vanadis Diagnostics
    Inventors: Ove Öhman, Fredrik Persson, Mathias Howell