Patents Examined by Teresa E Strzelecka
  • Patent number: 10287623
    Abstract: The present invention is directed to methods, compositions and systems for capturing and analyzing sequence information contained in targeted regions of a genome. Such targeted regions may include exomes, partial exomes, introns, combinations of exonic and intronic regions, genes, panels of genes, and any other subsets of a whole genome that may be of interest.
    Type: Grant
    Filed: June 6, 2016
    Date of Patent: May 14, 2019
    Assignee: 10X GENOMICS, INC.
    Inventors: Mirna Jarosz, Michael Schnall-Levin, Serge Saxonov, Benjamin Hindson, Xinying Zheng
  • Patent number: 10280392
    Abstract: Methods and devices for non-thermal PCR amplification of nucleic acid sequences. An electrical potential is applied to cause non-thermal separation of strands of a double-stranded nucleic acid or double-stranded nucleic acid/primer extension product.
    Type: Grant
    Filed: February 8, 2016
    Date of Patent: May 7, 2019
    Assignee: The Regents of the University of California
    Inventor: Hemantha Kumar Wickramasinghe
  • Patent number: 10266881
    Abstract: The present invention provides methods, compositions, kits, systems and apparatus that are useful for multiplex PCR of one or more nucleic acids present in a sample. In particular, various target-specific primers are provided that allow for the selective amplification of one or more target sequences. In one aspect, the invention relates to target-specific primers useful for the selective amplification of one or more target sequences associated with cancer or inherited disease. In some aspects, amplified target sequences obtained using the disclosed methods, kits, systems and apparatuses can be used in various downstream processes including nucleic acid sequencing and used to detect the presence of genetic variants.
    Type: Grant
    Filed: July 10, 2015
    Date of Patent: April 23, 2019
    Assignee: Life Technologies Corporation
    Inventors: John Leamon, Mark Andersen, Michael Thornton
  • Patent number: 10266896
    Abstract: Compositions and methods for the detection and treatment of T1D are provided.
    Type: Grant
    Filed: September 14, 2016
    Date of Patent: April 23, 2019
    Assignee: The Children's Hospital of Philadelphia
    Inventors: Hakon Hakonarson, Struan F. A. Grant, Jonathan P. Bradfield, Constantin Polychronakos
  • Patent number: 10246706
    Abstract: Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3? end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.
    Type: Grant
    Filed: April 9, 2018
    Date of Patent: April 2, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Shengxi Guan, Thomas C. Evans, Jr., Nicole Nichols, Yanxia Bei
  • Patent number: 10246744
    Abstract: Provided are compositions, methods and systems for determining the sequence of a template nucleic acid using a polymerase-based, sequencing-by-binding procedure. An examination step involves monitoring the interaction between a polymerase and template nucleic acid in the presence of one or more nucleotides. Identity of the next correct nucleotide in the sequence is determined without incorporation of any nucleotide into the structure of the primer by formation of a phosphodiester bond. An optional incorporation step can be used after the examination step to extend the primer by one or more nucleotides, thereby incrementing the template nucleotides that can be examined in a subsequent examination step. The sequencing-by-binding procedure does not require the use of labeled nucleotides or polymerases, but optionally can employ these reagents.
    Type: Grant
    Filed: October 4, 2017
    Date of Patent: April 2, 2019
    Assignee: OMNIOME, INC.
    Inventors: Kandaswamy Vijayan, Corey M. Dambacher, Eugene Tu, Mark A. Bernard, Joseph Rokicki, Kerry Wilson
  • Patent number: 10240148
    Abstract: Compositions and methods for performing a template-switching reaction are provided that may include reducing or eliminating concatemerization of the template-switching oligonucleotide (TSO). In some embodiments, the composition may comprise: a reverse transcriptase; a TSO that includes a recognition sequence for a site-specific double strand nucleic acid cleaving enzyme, wherein the TSO has at its 3? end at least one nucleotide capable of hybridizing to at least one or more non-templated nucleotides added to a templated cDNA strand by the reverse transcriptase; and a site-specific double strand nucleic acid cleaving enzyme that cleaves the TSO at the recognition sequence.
    Type: Grant
    Filed: August 18, 2016
    Date of Patent: March 26, 2019
    Assignee: New England Biolabs, Inc.
    Inventors: Shengxi Guan, Thomas C. Evans, Jr., Nicole Nichols, Yanxia Bei
  • Patent number: 10227624
    Abstract: The present invention provides reagents, kits, and methods for single-cell whole genome amplification using Phi 29 DNA polymerase.
    Type: Grant
    Filed: July 15, 2015
    Date of Patent: March 12, 2019
    Assignee: Fluidigm Corporation
    Inventors: Peilin Chen, Jing Wang, Andrew May
  • Patent number: 10214713
    Abstract: The current is directed to a device comprising, a reaction chamber where a reaction takes place, one or more feeding chambers which contain feeding solution comprising chemicals required for the reaction, and one or more porous membranes separating the reaction chamber from the one or more feeding chambers, and wherein the one or more porous membranes are in substantially vertical position. The current invention is also directed to an apparatus comprising a plurality of devices, wherein each device comprises of a reaction chamber where a reaction takes place, one or more feeding chambers which contain feeding solution comprising chemicals required for the reaction, and one or more porous membranes which separate the reaction chamber from feeding chambers, wherein the one or more porous membranes are in substantially vertical position. These devices and apparatuses can be used for high throughput synthesis of biomolecules and chemicals and biological screening assays.
    Type: Grant
    Filed: July 17, 2014
    Date of Patent: February 26, 2019
    Assignee: UNIVERSITY OF FLORIDA RESEARCH FOUNDATION, INCORPORATED
    Inventors: Zhonghui Hugh Fan, Kirsten Marie Jackson
  • Patent number: 10214760
    Abstract: Disclosed are methods for amplifying a nucleic acid target region using an amplification oligomer comprising a target-binding segment and a heterologous displacer tag situated 5? to the target-binding segment. Initiation of an amplification reaction from the tagged amplification oligomer produces an amplicon comprising the displacer tag, such that once the complement of the displacer tag has been incorporated into a second amplicon, a displacer oligonucleotide having a sequence substantially corresponding to the displacer tag sequence is used to participate in subsequent rounds of amplification for displacement of an extension product primed from a site within the second amplicon 5? to the displacer priming site. Also disclosed are related kits and reaction mixtures comprising the displacer-tagged amplification oligomer and corresponding displacer oligonucleotide.
    Type: Grant
    Filed: October 30, 2015
    Date of Patent: February 26, 2019
    Assignee: GEN-PROBE INCORPORATED
    Inventors: Norman C. Nelson, Margarita Batranina-Kaminsky
  • Patent number: 10214770
    Abstract: Compositions and methods are described for standardizing the DNA amplification efficiencies of a highly heterogeneous set of oligonucleotide primers as may typically be used to amplify a heterogeneous set of DNA templates that contains rearranged lymphoid cell DNA encoding T cell receptors (TCR) or immunoglobulins (IG). The presently disclosed embodiments are useful to overcome undesirable bias in the utilization of a subset of amplification primers, which leads to imprecision in multiplexed high throughput sequencing of amplification products to quantify unique TCR or Ig encoding genomes in a sample. Provided is a composition comprising a diverse plurality of template oligonucleotides in substantially equimolar amounts, for use as a calibration standard for amplification primer sets. Also provided are methods for identifying and correcting biased primer efficiency during amplification.
    Type: Grant
    Filed: May 10, 2016
    Date of Patent: February 26, 2019
    Assignee: ADAPTIVE BIOTECHNOLOGIES CORP.
    Inventors: Harlan Saul Robins, Christopher Scott Carlson, Robert J. Livingston, Ryan O. Emerson, Anna M. Sherwood
  • Patent number: 10203294
    Abstract: System and method of concentrating (or aligning) analytes at a droplet-bulk solution interface as a means of enhancing a detection sensitivity of the analytes at electrodes in a fluidic channel. A number of differing types of intermolecular forces and chemicals or materials can be employed to accomplish the concentrating (and/or aligning). For example, a measurement analogous to a conventional electrical impedance spectroscopy (EIS) measurement can be made by bringing an analyte (e.g., a molecule to be detected) to the edge of a droplet, and in so doing, positioning the analyte close to an electrode surface to aid in detection.
    Type: Grant
    Filed: May 14, 2015
    Date of Patent: February 12, 2019
    Assignee: The Regents of The University of California
    Inventors: Abraham P Lee, Melinda G. Simon
  • Patent number: 10202640
    Abstract: Methods and oligonucleotide reagents for analyzing individual T cells are disclosed. In particular, the present disclosure provides methods for analyzing individual T cells using high-throughput multiplex amplification and deep sequencing of nucleic acids encoding T cell receptors (TCRs) and various other T cell phenotypic markers. The present disclosure further provides methods of reconstituting TCRs from individual T cells for functional studies, ligand discovery, or screening therapeutics.
    Type: Grant
    Filed: April 30, 2015
    Date of Patent: February 12, 2019
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Mark M. Davis, Jacob Glanville, Arnold Han
  • Patent number: 10190153
    Abstract: The present invention provides a rapid and highly effective method for the preparation of biological samples for detection of both DNA and RNA target molecules. The method comprises treatment of the sample with a clay mineral followed by lysis of the sample with an alkaline solution. The method is particularly suited for preparing complex biological samples, such as blood or plasma, for the simultaneous detection of DNA and RNA targets. Samples prepared by the method of the invention may be directly used as targets in PCR amplification. The method of the invention may conveniently be coupled with further steps and devices to perform molecular analyses for diagnostic and other applications.
    Type: Grant
    Filed: May 7, 2014
    Date of Patent: January 29, 2019
    Assignee: MICRONICS, INC.
    Inventor: Heather K. Bouzek
  • Patent number: 10184148
    Abstract: Compositions, kits, methods and systems for single molecule nucleotide sequencing comprising producing polymerase reactions having lithium that control the median pulse width for incorporated nucleotides are disclosed. The levels of lithium are used to control pulse width while allowing other sequencing parameters to remain within a desirable range.
    Type: Grant
    Filed: April 5, 2017
    Date of Patent: January 22, 2019
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Andrei Fedorov, John Lyle, Keith Bjornson, Jeremiah Hanes
  • Patent number: 10174352
    Abstract: The present invention provides methods for amplifying a nucleic acid from a sample containing a mixture of nucleic acids utilizing a solid support. Methods are provided utilizing user-defined primer oligonucleotides for directional amplification that assists in further manipulation of the target nucleic acid, such as sequencing. Methods are also provided utilizing blocker and displacer oligonucleotides for generating amplified target nucleic acids of defined length. One of these methods provides a first oligonucleotide and a second oligonucleotide affixed to a solid support or separate solid supports. The first oligonucleotide is blocked to prevent extension from the 3?-terminus and has a sequence complementary to a first portion of a target nucleic acid. The second oligonucleotide has a sequence that is identical to a second portion of the target nucleic acid. In this method, a sample is applied to the solid support and the target nucleic acid within the sample binds said first oligonucleotide.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: January 8, 2019
    Inventors: Lyle J. Arnold, Norman C. Nelson
  • Patent number: 10166522
    Abstract: System, including methods, apparatus, compositions, and kits, for the mixing of small volumes of fluid by coalescence of multiple emulsions.
    Type: Grant
    Filed: November 11, 2015
    Date of Patent: January 1, 2019
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Benjamin J. Hindson, Billy W. Colston, Jr., Kevin D. Ness, Donald A. Masquelier
  • Patent number: 10161005
    Abstract: Provided is a new method for telomerase amplification—washing-free anchored-extension and telomeric-binding amplification (WATA). The method comprises: utilizing an anchored telomerase primer to conduct telomere TTAGGGG sequence (“G sequence”) extension; hybridizing with a template probe having a universal PCR primer sequence and six units of telomere CCCTAA sequence (“C sequence”) on the extended G sequence; removing the uncombined template probe via an enzyme digestion reaction; and the template probe combined with the G sequence conducts PCR reaction, the amplification product being a peculiar DNA fragment of a fixed length.
    Type: Grant
    Filed: December 7, 2015
    Date of Patent: December 25, 2018
    Assignee: ZHEJIANG JFK BIOLOGICAL TECHNOLOGY CO. LTD.
    Inventors: Ran Chen, Xiaozheng Jin
  • Patent number: 10125396
    Abstract: Provided in the present invention are an affinity mediated amplification method of telomeric C-ssDNA with a template probe and a detection kit using this method for performing alternative lengthening detection of telomeres.
    Type: Grant
    Filed: December 7, 2015
    Date of Patent: November 13, 2018
    Assignee: Zhejiang JFK Biological Technology Co. Ltd.
    Inventors: Ran Chen, Xiaozheng Jin
  • Patent number: 10119166
    Abstract: Disclosed are methods for determining one or more nucleotides at one or more nucleotide positions of a polynucleotide sample, the polynucleotide sample comprising heterogeneous polynucleotides having different nucleotides at the nucleotide positions. The disclosed methods may be utilized to control for sequencing bias during sequencing of the polynucleotide sample. Suitable samples may include patient samples for use in diagnosing, prognosing, and treating the patient.
    Type: Grant
    Filed: February 12, 2014
    Date of Patent: November 6, 2018
    Assignee: MDxHealth, SA
    Inventor: Wim Van Criekinge