Involving Nucleic Acid Patents (Class 435/6.1)
  • Patent number: 10662479
    Abstract: Methods of treating a tumor in a subject and methods of determining a treatment regimen for a subject with a tumor are provided herein. In exemplary aspects, the methods comprise measuring the level of expression of immunoglobulin, FCGR2B, a gene listed in Table 4, or a combination thereof. In exemplary aspects, the subject is a subject from which a sample was obtained, wherein the level of immunoglobulin, FCGR2B, a gene listed in Table 4, or a combination thereof, has been measured from the sample. Related kits, computer readable-storage media, systems, and methods implemented by a processor in a computer are further provided.
    Type: Grant
    Filed: August 8, 2014
    Date of Patent: May 26, 2020
    Assignee: Onyx Therapeutics, Inc.
    Inventors: Brian Tuch, Jeremiah Degenhardt, Andrea Loehr, Kevin Kwei, Christopher J. Kirk
  • Patent number: 10662473
    Abstract: The present invention is directed to methods and compositions for acquiring nucleotide sequence information of target sequences. In particular, the present invention provides methods and compositions for improving the efficiency of sequencing reactions by using fewer labels to distinguish between nucleotides and by detecting nucleotides at multiple detection positions in a target sequence.
    Type: Grant
    Filed: August 3, 2018
    Date of Patent: May 26, 2020
    Assignee: Complete Genomics, Inc.
    Inventor: Radoje Drmanac
  • Patent number: 10663423
    Abstract: A system for detecting electrical properties of a molecular complex is disclosed. The system includes an electrode electrically coupled to a molecular complex that outputs an electrical signal affected by an electrical property of the molecular complex, wherein the effect of the electrical property of the molecular complex on the electrical signal is characterized by an expected bandwidth. The system further includes an integrating amplifier circuit configured to receive the electrical signal from the electrode. The integrating amplifier circuit is further configured to selectively amplify and integrate a portion of the electrical signal over time within a predetermined bandwidth, wherein the predetermined bandwidth is selected at least in part based on the expected bandwidth.
    Type: Grant
    Filed: November 7, 2018
    Date of Patent: May 26, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventor: Roger J. A. Chen
  • Patent number: 10658071
    Abstract: Ancestry deconvolution includes obtaining unphased genotype data of an individual; phasing, using one or more processors, the unphased genotype data to generate phased haplotype data; using a learning machine to classify portions of the phased haplotype data as corresponding to specific ancestries respectively and generate initial classification results; and correcting errors in the initial classification results to generate modified classification results.
    Type: Grant
    Filed: November 11, 2015
    Date of Patent: May 19, 2020
    Assignee: 23andMe, Inc.
    Inventors: Chuong Do, Eric Yves Jean-Marc Durand, John Michael Macpherson
  • Patent number: 10656157
    Abstract: The invention generally relates to methods for rare event detection using mass tags. In certain embodiments, the invention provides methods for detecting a target analyte in a sample that involve conducting an assay that specifically associates a mass tag with a target analyte in a sample, generating ions of the mass tag, and analyzing the generated ions of the mass tag, thereby detecting the target analyte from the sample.
    Type: Grant
    Filed: September 23, 2015
    Date of Patent: May 19, 2020
    Assignee: Purdue Research Foundation
    Inventors: Robert Graham Cooks, Zheng Ouyang
  • Patent number: 10655180
    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: March 14, 2019
    Date of Patent: May 19, 2020
    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: 10654841
    Abstract: This invention claims processes that comprise the appending of nucleotides having a 3?-ONH2 moiety to the 3?-ends of oligonucleotide primers using 3?-deoxynucleoside triphosphates of 2?-deoxynucleoside derivatives that have, instead of a 3?-OH moiety, a 3?-ONH2 moiety, where the nucleotides contain non-standard nucleobases.
    Type: Grant
    Filed: October 17, 2017
    Date of Patent: May 19, 2020
    Inventors: Steven A Benner, Nicole A Leal
  • Patent number: 10655162
    Abstract: The present disclosure, in some aspects, provides compositions, systems and methods for proximity-based detection of target biomolecules of interest.
    Type: Grant
    Filed: March 3, 2017
    Date of Patent: May 19, 2020
    Assignee: The Broad Institute, Inc.
    Inventors: Alon Goren, Robert Nicol, Harris Nusbaum
  • Patent number: 10648022
    Abstract: A composition includes a nanopore including first and second sides and an aperture, nucleotides each including an elongated tag, and a first polynucleotide that is complementary to a second polynucleotide. A polymerase can be disposed adjacent to the first side of the nanopore and configured to add nucleotides to the first polynucleotide based on a sequence of the second polynucleotide. A permanent tether can include a head region anchored to the polymerase, a tail region, and an elongated body disposed therebetween that occurs in the aperture of the nanopore. A first moiety can be disposed on the elongated body that binds to the elongated tag of a first nucleotide upon which the polymerase is acting. A reporter region can be disposed on the elongated body that indicates when the first nucleotide is complementary or is not complementary to a next nucleotide in the sequence of the second polynucleotide.
    Type: Grant
    Filed: June 2, 2016
    Date of Patent: May 12, 2020
    Assignee: Illumina, Inc.
    Inventors: Kevin L. Gunderson, Jeffrey G. Mandell
  • Patent number: 10648025
    Abstract: Provided herein is technology relating to the amplification-based detection of bisulfite-treated DNAs and particularly, but not exclusively, to methods and compositions for multiplex amplification of low-level sample DNA prior to further characterization of the sample DNA. The technology further provides methods for isolating DNA from blood or blood product samples, e.g., plasma samples.
    Type: Grant
    Filed: December 13, 2017
    Date of Patent: May 12, 2020
    Assignee: EXACT SCIENCES DEVELOPMENT COMPANY, LLC
    Inventors: Hatim T. Allawi, William G. Weisburg, Graham P. Lidgard, Michael W. Kaiser, Abram M. Vaccaro, Gracie Shea
  • Patent number: 10648021
    Abstract: Disclosed are methods and compositions for detection and amplification of nucleic acids, wherein two DNA strands hybridized to an RNA strand are ligated. In one aspect, the disclosed methods include removal of an energy source, such as ATP, upon charging a ligase to form an enzyme-AMP intermediate, and then adding substrate, which results in one complete round of RNA-templated DNA ligation. In another aspect, the ligation reaction is accomplished by use of a mixture of at least two different ligase enzymes. The disclosed methods and compositions for RNA-templated DNA ligation may be particularly useful for detection of RNA sequence variants, for example RNA splice variants, and for quantitative expression analysis.
    Type: Grant
    Filed: October 30, 2017
    Date of Patent: May 12, 2020
    Assignee: AFFYMETRIX, INC.
    Inventors: Eugeni A. Namsaraev, Xin Miao, John E. Blume
  • Patent number: 10640833
    Abstract: The invention generally relates to a method for detecting a target nucleic acid in a sample. This invention is useful for detecting bacterial or viral agents in a sample, and is able to detect nucleic acids from a broad variety of, e.g., bacteria, rather than only one or a few different bacteria at a time.
    Type: Grant
    Filed: June 26, 2015
    Date of Patent: May 5, 2020
    Assignee: University of Florida Research Foundation, Inc.
    Inventors: Kenneth H. Rand, Herbert J. Houck
  • Patent number: 10640764
    Abstract: There is disclosed a process for in vitro synthesis and assembly of long, gene-length polynucleotides based upon assembly of multiple shorter oligonucleotides synthesized in situ on a microarray platform. Specifically, there is disclosed a process for in situ synthesis of oligonucleotide fragments on a solid phase microarray platform and subsequent, “on device” assembly of larger polynucleotides composed of a plurality of shorter oligonucleotide fragments.
    Type: Grant
    Filed: February 23, 2017
    Date of Patent: May 5, 2020
    Assignee: Gen9, Inc.
    Inventor: Andrew V. Oleinikov
  • Patent number: 10641688
    Abstract: A single dissolving compound forms plural azeotropes, which can be azeotropically vaporized off at various stages of the treatment process, thus maintaining predictable concentrations of the chemicals present. The treatment process can be performed in the absence of formalin or related compounds which can interfere with the preservation of genetic material. A process for preserving a specimen includes using a dissolving compound that can form a plural number of azeotropes, at least one azeotrope being formed between one or more components of the dissolving compound and specimen-supplied water, and at least one azeotrope being formed between different components of the dissolving compound; successively and azeotropically vaporizing off formed azeotropes; and impregnating the specimen with a support medium.
    Type: Grant
    Filed: February 23, 2017
    Date of Patent: May 5, 2020
    Inventor: Steven Wheeler
  • Patent number: 10641764
    Abstract: Droplet-interface bilayer and lipid bilayer membrane compositions stabilized with an amphiphilic polymer are disclosed. Methods of making and using the compositions are also disclosed.
    Type: Grant
    Filed: July 1, 2016
    Date of Patent: May 5, 2020
    Assignee: THE UNIVERSITY OF MASSACHUSETTS
    Inventors: Matthew A. Holden, Max J. Lein, Arash Manafirad, Dan Ezra Aurian-Blajeni
  • Patent number: 10640815
    Abstract: The present disclosure relates to a set of at least 100 single-stranded oligonucleotide probes directed against (or complementary to) portions of a genomic target sequence of interest. The present disclosure also relates to a method of detecting a genomic target sequence of interest using the set of oligonucleotide probes and a method of generating the set of oligonucleotide probes. Further the present disclosure relates to a kit comprising the set of oligonucleotide probes and at least one further component.
    Type: Grant
    Filed: April 22, 2016
    Date of Patent: May 5, 2020
    Assignee: Roche Molecular Systems, Inc.
    Inventors: Frank Bergmann, Walter Eberle, Thomas Fischer, Herbert von der Eltz
  • Patent number: 10633665
    Abstract: The present disclosure generally relates to novel polynucleotide molecules for use in regulating gene expression in recombinant cells, such as labyrinthulomycetes cells. The disclosure further relates to nucleic acid constructs, such as vectors and expression cassettes, containing a regulatory element operably linked to a heterologous nucleotide sequence. The disclosure further relates to methods for stably transforming a host cell, such as a labyrinthulomycetes cell with transgenes. Stably transformed recombinant cells, progeny, biomaterials derived therefrom, and methods for preparing and using the same are also provided.
    Type: Grant
    Filed: March 8, 2018
    Date of Patent: April 28, 2020
    Assignee: Conagen Inc.
    Inventors: Nicky C. Caiazza, Maung Nyan Win, Jun Urano
  • Patent number: 10626436
    Abstract: A method of determining variation between a query cell culture media and a reference cell culture media is provided. The method comprises the steps of incubating a reference cell with an aliquot of the query culture media and at least three chemical cell stressors in wells of a microtitre plate and determining an environmental response of the reference cell in the presence of the query cell culture media and each of the plurality of chemical cell stressors. A query cell culture media specific environmental response fingerprint is generated comprising the plurality of chemical cell stressor specific environmental responses. The query cell culture media-specific environmental response fingerprint is compared with a reference media-specific environmental response fingerprints corresponding to a reference cell culture media and generated using the reference cell.
    Type: Grant
    Filed: April 1, 2016
    Date of Patent: April 21, 2020
    Assignee: Valitacell Limited
    Inventors: Jerry Clifford, David James, Ben Thompson
  • Patent number: 10626401
    Abstract: The invention relates to non-CpG single-stranded oligonucleotides (ssONs) for use in the treatment or prophylaxis of disorders of the skin and/or subcutaneous tissue, including pruritus, in a suitable formulation or in combination with other immunomodulatory treatments. The said ssONs have a length of at least 25 nucleotides and are stabilized by phosphorothioate internucleotide linkages and/or 2?-O-Methyl modifications.
    Type: Grant
    Filed: June 14, 2016
    Date of Patent: April 21, 2020
    Assignee: TIRMED PHARMA AB
    Inventors: Anna-Lena Spetz, Peter Jarver, Annette Skold
  • Patent number: 10626447
    Abstract: The detection and quantification of nucleic acid sequences can be done using template catalyzed TARA transfer reactions without enzyme and PCR. It comes with the novel chemistry platform technology using Template Assisted Rapid Assay (TARA), an enzyme-free, PCR-less and rapid transfer reaction assay directly from samples from nasopharyngeal swab, nasal aspirate, oropharyngeal swab or blood. The procedures of the detection and quantification of nucleic acid sequences include utilizing two or more oligonucleotide probes that reversibly bind a target nucleic acid in close proximity to each other and possess complementary reactive TARA reaction moieties. In addition, various methods, reagents, and kits for detecting and quantifying nucleic acid sequences and for determining the sequence of nucleic acids are provided.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: April 21, 2020
    Assignee: CROSSLIFE TECHNOLOGIES INC.
    Inventors: HyunDae Cho, Chang Hee Kim
  • Patent number: 10626390
    Abstract: Provided herein are compositions, systems, and methods using multiple ligases, wherein at least one of the ligases is an adenylation-deficient ATP-dependent ligase or an un-adenylated ATP-dependent ligase (e.g., present in an ATP free mixture). In certain embodiments, multiple ligases are used to ligate a pre-adenylated double stranded sequence to a non-adenylated double stranded sequence (e.g., the adenylation-deficient ATP-dependent ligase or un-adenylated ATP-dependent ligase ligates the first strand, and a second ligase ligates the second strand). In other embodiments, provided herein are mutant T4 ligases (e.g., K159S mutant or K159C mutant).
    Type: Grant
    Filed: February 7, 2017
    Date of Patent: April 21, 2020
    Assignee: RGENE, INC.
    Inventors: Yu Zheng, Manqing Hong
  • Patent number: 10626473
    Abstract: Provided herein is a highly sensitive and robust method for Zika detection in semen, as well as related compositions. The method can include: (a) extracting nucleic acids from a human semen sample; (b) detecting Zika virus nonstructural protein 5 (NS5) mRNA using real-time reverse-transcription polymerase chain reaction (rRT-PCR); and (c) simultaneously, in the rRT-PCR, detecting human beta-actin mRNA as positive control.
    Type: Grant
    Filed: October 3, 2017
    Date of Patent: April 21, 2020
    Assignee: Genetics & IVG Institute, Inc.
    Inventors: Brian D. Mariani, Harvey J. Stern
  • Patent number: 10612082
    Abstract: A method for amplification of nucleic acids in which substantially use is made of the fact that a pre-defined nucleic acid chain (target sequence) can be multiplied/amplified in the presence of a target sequence-specific activator oligonucleotide. The target sequence-specific activator oligonucleotide causes the separation of re-synthesized complementary primer extension products by strand displacement, so that a new primer oligonucleotide can attach to the respective template strand. The thus formed complex of a primer oligonucleotide and a template strand can initiate a new primer extension reaction. The thus formed primer extension products in turn function as templates, so that an exponential amplification reaction results.
    Type: Grant
    Filed: August 21, 2017
    Date of Patent: April 7, 2020
    Assignee: AGCT GmbH
    Inventors: Dmitry Cherkasov, Norbert Basler, Claus Becker, Hans-Joerg Hess, Andreas Mueller-Hermann
  • Patent number: 10612091
    Abstract: The invention relate to systems and methods for sequencing polynucleotides, as well as detecting reactions and binding events involving other biological molecules. The systems and methods may employ chamber-free devices and nanosensors to detect or characterize such reactions in high-throughput. Because the system in many embodiments is reusable, the system can be subject to more sophisticated and improved engineering, as compared to single use devices.
    Type: Grant
    Filed: February 22, 2019
    Date of Patent: April 7, 2020
    Assignee: GENAPSYS, INC.
    Inventors: Hesaam Esfandyarpour, Kosar Baghbani Parizi, Mark F. Oldham, Eric S. Nordman, Richard T. Reel, Susanne Baumhueter, Cheryl Heiner, Frank Lee
  • Patent number: 10612088
    Abstract: A method for parallel sequencing target RNA from samples from multiple sources while maintaining source identification is provided. The method includes providing samples of RNA comprising target RNA from two or more sources; labeling, at the 3? end, the RNA from the two or more sources with a first nucleic acid adaptor that comprises a nucleic acid sequence that differentiates between the RNA from the two or more sources; reverse transcribing the two or more sources to create a single stranded DNA comprising the nucleic acid sequence that differentiates between the RNA from the two or more sources; amplifying the single stranded DNA to create DNA amplification products that comprise the nucleic acid sequence that differentiates between the RNA from the two or more sources; sequencing the DNA amplification products thereby parallel sequencing target RNA from samples from multiple sources while maintaining source identification.
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: April 7, 2020
    Assignees: THE BROAD INSTITUTE, INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY
    Inventors: Alexander A. Shishkin, Mitchell Guttman, Christine F. Surka, Eric S. Lander
  • Patent number: 10612077
    Abstract: In certain aspects, the invention disclosed herein relates to the isothermal amplification of probe linkage products to generate specific amplified signals. In some aspects, the invention provides methods, reagents, and kits for carrying out such amplification via the isothermal chain reaction (ICR).
    Type: Grant
    Filed: October 22, 2015
    Date of Patent: April 7, 2020
    Inventor: Ricardo Mancebo
  • Patent number: 10604789
    Abstract: System, including methods, apparatus, and compositions, for performing amplification assays with an amplification reporter including a first oligomer and a second oligomer capable of base-pairing with one another below a melting temperature of the reporter. The reporter may have a detectable photoluminescence that is affected, such as reduced, by base-pairing of the first and second oligomers with one another. A target, such as a nucleic acid target sequence, may be amplified in at least one volume, such as a plurality of partitions, above the melting temperature, and photoluminescence of the reporter may be detected from the at least one volume below the melting temperature. A property of the target, such as a concentration of the target, may be determined based on the photoluminescence detected.
    Type: Grant
    Filed: January 20, 2017
    Date of Patent: March 31, 2020
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: John F. Regan, Dianna Maar, Dawne N. Shelton, Tina C. Legler, Samantha Cooper, Wei Yang, Eli A. Hefner, Niels Klitgord
  • Patent number: 10604791
    Abstract: Provided herein are products and processes for detecting the presence or absence of multiple target nucleic acids. Certain methods include amplifying the target nucleic acids, or portion thereof; extending oligonucleotides that specifically hybridize to the amplicons, where the extended oligonucleotides include a capture agent; capturing the extended oligonucleotides to a solid phase via the capture agent; releasing the extended oligonucleotide by competition with a competitor; detecting the extended oligonucleotide, and thereby determining the presence or absence of each target nucleic acid by the presence or absence of the extended oligonucleotide.
    Type: Grant
    Filed: July 17, 2012
    Date of Patent: March 31, 2020
    Assignee: Agena Bioscience, Inc.
    Inventors: Christiane Honisch, Dirk Johannes Van Den Boom, Michael Mosko, Anders Nygren
  • Patent number: 10604574
    Abstract: Described herein are pseudotyped oncolytic viruses comprising nucleic acids encoding an engager molecule. In some embodiments, the pseudotyped oncolytic viruses comprises nucleic acids encoding an engager molecule and one or more therapeutic molecules. Pharmaceutical compositions containing the pseudotyped oncolytic virus and methods of treating cancer using the pseudotyped oncolytic viruses are further provided herein.
    Type: Grant
    Filed: October 25, 2018
    Date of Patent: March 31, 2020
    Assignee: ONCORUS, INC.
    Inventor: Luke Evnin
  • Patent number: 10597701
    Abstract: The present invention relates to a proximity-probe based detection assay for detecting an analyte in a sample and in particular to a method that comprises the use of at least one set of at least first and second proximity probes, which probes each comprise an analyte-binding domain and a nucleic acid domain and can simultaneously bind to the analyte directly or indirectly, wherein the nucleic acid domain of at least one of said proximity probes comprises a hairpin structure that can be unfolded by cleavage of the nucleic acid domain to generate at least one ligatable free end or region of complementarity to another nucleic acid molecule in said sample, wherein when the probes bind to said analyte unfolding said hairpin structure allows the nucleic acid domains of said at least first and second proximity probes to interact directly or indirectly.
    Type: Grant
    Filed: December 9, 2016
    Date of Patent: March 24, 2020
    Assignee: NAVINCI DIAGNOSTICS AB
    Inventors: Ulf Landegren, Rachel Yuan Nong, Ola Söderberg, Irene Helbing
  • Patent number: 10597737
    Abstract: Methods and kits for detecting a genetic variation in a polynucleotide analyte in a sample. A fluorophore is attached to a first primer, a quencher is attached to a second primer, and the first primer and the second primer are specific for the polynucleotide analyte. At least one of the primers is configured to hybridize to a region of the polynucleotide analyte encoding the genetic variation. The primers are configured to amplify the polynucleotide analyte having the genetic variation and a corresponding polynucleotide analyte lacking the generic variation. There is a detectable difference between a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the polynucleotide analyte with the genetic variation, and a change in signal generated by the fluorophore and quencher when using the first and second primers to amplify the corresponding polynucleotide analyte lacking the genetic variation.
    Type: Grant
    Filed: August 22, 2018
    Date of Patent: March 24, 2020
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Aditya Rajagopal, Mark D. Goldberg, Erika F. Garcia, Xiomara L. Madero, Thomas A. Tombrello, Axel Scherer
  • Patent number: 10597651
    Abstract: The present disclosure relates to nucleic acid extraction and purification methods and devices to accomplish the same. The present disclosure proposes a novel approach to this problem wherein cell isolation and nucleic acid purification can be integrated in a single “step,” by using the same solid phase for both cell adsorption and nucleic acid purification. This is achieved by binding the cells to a solid support as a first step. The same solid support is then used under conditions that lyse the bound cells, and then subsequently enable the nucleic acid to bind to the support. Methods of the present disclosure relate to the isolation of nucleic acid, and especially to a method for isolating DNA from cells, biological or environmental samples using antibiotics, which bind nucleic acids.
    Type: Grant
    Filed: April 29, 2015
    Date of Patent: March 24, 2020
    Assignee: Accudx Corporation
    Inventor: Raveendran Pottathil
  • Patent number: 10597642
    Abstract: Provided herein are compositions and systems for use in polymerase-dependent, nucleotide transient-binding methods. The methods are useful for deducing the sequence of a template nucleic acid molecule and single nucleotide polymorphism (SNP) analyses. The methods rely on the fact that the polymerase transient-binding time for a complementary nucleotide is longer compared to that of a non-complementary nucleotide. The labeled nucleotides transiently-binds the polymerase in a template-dependent manner, but does not incorporate. The methods are conducted under any reaction condition that permits transient binding of a complementary or non-complementary nucleotide to a polymerase, and inhibits nucleotide incorporation.
    Type: Grant
    Filed: August 30, 2017
    Date of Patent: March 24, 2020
    Assignee: Life Technologies Corporation
    Inventors: Peter Vander Horn, Cheng-Yao Chen, Guobin Luo, Michael Previte, Jamshid Temirov, Theo Nikiforov, Zhaohui Zhou, Hongye Sun, Yufang Wang, Stefanie Yukiko Nishimura, Hongyi Wang, Marian Peris, Barnett Rosenblum, Michael Phelan
  • Patent number: 10590244
    Abstract: The present disclosure provides systems and methods for making a hydrogel comprising a cell, cell nucleus, or one or more components derived from a cell or cell nucleus. A method for making a hydrogel may comprise providing a cell or cell nucleus, a first polymer, wherein the first polymer comprises a plurality of first crosslink precursors, each of the plurality of first crosslink precursors comprising an azide group; providing a second polymer, wherein the second polymer comprises a plurality of second crosslink precursors, each of the plurality of second crosslink precursors comprising an alkyne group; and crosslinking the first polymer and the second polymer via a reaction between a first section of the first crosslink precursors and a second section of the second crosslink precursors, thereby providing the hydrogel comprising the cell or cell nucleus.
    Type: Grant
    Filed: November 1, 2018
    Date of Patent: March 17, 2020
    Assignee: 10X GENOMICS, INC.
    Inventors: Joshua Delaney, Shalini Gohil, Christopher Hindson, Adam Lowe, Andrew D. Price
  • Patent number: 10590483
    Abstract: Provided herein are methods and composition for immune repertoire sequencing and single cell barcoding. The methods and compositions can be used to pair any two sequences originating from a single cell, such as heavy and light chain antibody sequences, alpha and beta chain T-cell receptor sequences, or gamma and delta chain T-cell receptor sequences, for antibody and T-cell receptor discovery, disease and immune diagnostics, and low error sequencing.
    Type: Grant
    Filed: September 15, 2015
    Date of Patent: March 17, 2020
    Assignee: AbVitro LLC
    Inventors: Francois Vigneault, Adrian Wrangham Briggs, Christopher Ryan Clouser, Stephen Jacob Goldfless, Sonia Timberlake
  • Patent number: 10583415
    Abstract: De novo synthesized large libraries of nucleic acids are provided herein with low error rates. Further, devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Longer nucleic acids can be synthesized in parallel using microfluidic assemblies. Further, methods herein allow for the fast construction of large libraries of long, high-quality genes. Devices for the manufacturing of large libraries of long and high-quality nucleic acids are further described herein.
    Type: Grant
    Filed: May 10, 2019
    Date of Patent: March 10, 2020
    Assignee: Twist Bioscience Corporation
    Inventors: William Banyai, Bill James Peck, Andres Fernandez, Siyuan Chen, Pierre Indermuhle
  • Patent number: 10586610
    Abstract: The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.
    Type: Grant
    Filed: March 16, 2016
    Date of Patent: March 10, 2020
    Assignee: Verinata Health, Inc.
    Inventors: Richard P. Rava, Anupama Srinivasan
  • Patent number: 10584375
    Abstract: A method for identifying target alleles, that includes steps of (a) forming a plurality of stabilized ternary complexes at a plurality of features on an array, wherein the stabilized ternary complexes each has a polymerase, a template nucleic acid having a target allele of a locus, a primer hybridized to the locus, and a next correct nucleotide having a cognate in the locus, wherein either (i) the primer is an allele-specific primer having a 3? nucleotide that is a cognate nucleotide for the target allele, or (ii) the primer is a locus-specific primer and the next correct nucleotide hybridizes to the target allele; and (b) detecting stabilized ternary complexes at the features, thereby identifying the target alleles.
    Type: Grant
    Filed: February 20, 2018
    Date of Patent: March 10, 2020
    Assignee: OMNIOME, INC.
    Inventors: Corey M. Dambacher, Michael Van Nguyen
  • Patent number: 10577388
    Abstract: The present invention relates to the field of oligonucleotide conjugates and to methods of synthesis thereof. In the present method a low-water content solvent environment allows a more efficient conjugation, reducing the amount of conjugate moiety needed and increasing the conjugation reaction speed.
    Type: Grant
    Filed: September 29, 2016
    Date of Patent: March 3, 2020
    Assignee: Roche Innovation Center Copenhagen A/S
    Inventors: Dennis Jul Hansen, Christoph Rosenbohm, Michael Meldgaard
  • Patent number: 10577653
    Abstract: A method of analyzing a molecule is disclosed. A lipid bilayer is formed such that it divides a first reservoir characterized by a first reservoir osmolarity from a second reservoir characterized by a second reservoir osmolarity. An electrolyte solution is flowed to the first reservoir that tends to make a first change to a ratio of the first reservoir osmolarity to the second reservoir osmolarity. A voltage is applied across the lipid bilayer, wherein the lipid bilayer is inserted with a nanopore, and wherein a net transfer of ions between the first reservoir and the second reservoir tends to make a second change to the ratio of the first reservoir osmolarity to the second reservoir osmolarity, and wherein the first change to the ratio and the second change to the ratio tends to counter-balance each other.
    Type: Grant
    Filed: June 22, 2017
    Date of Patent: March 3, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Geoffrey Barrall, Jason Komadina, Marcin Rojek
  • Patent number: 10577652
    Abstract: This invention provides methods for attaching a nucleic acid to a solid surface and for sequencing nucleic acid by detecting the identity of each nucleotide analogue after the nucleotide analogue is incorporated into a growing strand of DNA in a polymerase reaction. The invention also provides nucleotide analogues which comprise unique labels attached to the nucleotide analogue through a cleavable linker, and a cleavable chemical group to cap the —OH group at the 3?-position of the deoxyribose.
    Type: Grant
    Filed: November 26, 2018
    Date of Patent: March 3, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Jingyue Ju, Zengmin Li, John Robert Edwards, Yasuhiro Itagaki
  • Patent number: 10570462
    Abstract: Provided herein are kits for performing for nucleic acid sequences.
    Type: Grant
    Filed: May 27, 2016
    Date of Patent: February 25, 2020
    Assignee: Brandeis University
    Inventors: Lawrence J. Wangh, John E. Rice, J. Aquiles Sanchez, Arthur H. Reis, Jr.
  • Patent number: 10570445
    Abstract: FRET-labeled compounds are provided for use in analytical reactions. In certain embodiments, FRET-labeled nucleotide analogs are used in place of naturally occurring nucleoside triphosphates or other analogs in analytical reactions comprising nucleic acids, for example, template-directed nucleic acid synthesis, DNA sequencing, RNA sequencing, single-base identification, hybridization, binding assays, and other analytical reactions.
    Type: Grant
    Filed: July 30, 2018
    Date of Patent: February 25, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Xiangxu Kong, Gene Shen
  • Patent number: 10570463
    Abstract: In some aspects, the disclosure provides compounds comprising nucleic acid modifying moieties, such as nucleic acid binding dyes comprising activatable groups. In some aspects, the disclosure provides nucleic acid probes comprising compounds of the disclosure, and methods of making the same. In some aspects, the disclosure provides methods of using compounds of the disclosure, such as methods of labeling and/or detecting non-viable organisms or non-viable cells, and methods of detecting contamination or infection.
    Type: Grant
    Filed: October 29, 2015
    Date of Patent: February 25, 2020
    Assignee: BIOTIUM, INC.
    Inventors: Fei Mao, Patrick Gordon McGarraugh, Alexis Spain Madrid, Wai-Yee Leung, Lori M. Roberts
  • Patent number: 10571479
    Abstract: The present invention provides a method of measuring a vitamin D. Specifically, the present invention provides a method of measuring a vitamin D, comprising: (1) treating a sample with a surfactant having a steroid skeleton; and (2) detecting the vitamin D in the treated sample. The present invention also provides a kit for measuring a vitamin D, comprising: (1) a surfactant having a steroid skeleton; and (2) an affinity substance for a vitamin D and/or a vitamin D standard. Examples of the surfactant having the steroid skeleton may include a bile acid or a derivative thereof or a salt thereof.
    Type: Grant
    Filed: January 20, 2014
    Date of Patent: February 25, 2020
    Assignee: FUJIREBIO INC.
    Inventors: Yoshiaki Uchida, Takuya Sakyu, Kazuya Omi
  • Patent number: 10568901
    Abstract: Provided are compositions and methods for treating cancer, particularly solid tumors, and cancer metastasis, using micro-RNAs mi R-96 and/or mi R-182.
    Type: Grant
    Filed: July 14, 2016
    Date of Patent: February 25, 2020
    Assignees: TEL HASHOMER MEDICAL RESEARCH INFRASTRUCTURE AND SERVICES LTD., RAMOT AT TEL AVIV UNIVERSITY LTD.
    Inventors: Avital Gilam, Noam Shomron, Eitan Friedman
  • Patent number: 10571400
    Abstract: A method for detecting a target cell surface molecule and classifying cell types in a fluid sample. The method involves the addition of a reagent to the fluid sample. The reagent includes nanoparticles with optical plasmonic resonances, and at least one fluorescent probe. The nanoparticles are a bio-optical probe for the target cell surface molecule. Each fluorescent probe targets a cell classification marker. The method further involves the acquisition of an image using dark field microscopy and fluorescence microscopy to detect and quantify the presence or absence of any cells in the fluid sample having the target cell surface molecule or having the cell classification marker.
    Type: Grant
    Filed: March 11, 2016
    Date of Patent: February 25, 2020
    Assignee: The General Hospital Corporation
    Inventors: Conor L. Evans, W. Peter Hansen, Robert A. Hoffman, Petra B. Krauledat, Daniel W. Cramer
  • Patent number: 10563247
    Abstract: A single-molecule mechanoanalytical real-time sensing device (SMART) comprising a molecular trawl and a DNA stem-loop structure that serves as a molecular dipstick, said trawl and said DNA stem-loop structure anchored by handles to two optically-trapped bead templates; said molecular trawl comprising multiple analyte recognition elements that exist in each of two separate DNA (pair) strands that act as two pincers, said pincers each having a nucleobase capable of catching an analyte in a media; said DNA stem-loop structure comprising a plurality of nucleotides in said loop and multiple base pairs in said stem; and wherein said DNA stem-loop is located generally opposite to said molecular trawl that is capable of reporting an amount of bound analyte target via mechanochemical transient events.
    Type: Grant
    Filed: April 20, 2017
    Date of Patent: February 18, 2020
    Assignee: KENT STATE UNIVERSITY
    Inventors: Hanbin Mao, Shankar Mandal
  • Patent number: 10563255
    Abstract: Methods, devices, and systems for performing intermittent detection during analytical reactions are provided. Such methods facilitate collection of reaction data from disparate reaction times. Further, such methods are useful for reducing photo-induced damage of one or more reactants in an illuminated analytical reaction at a given reaction time. In preferred embodiments, the reaction mixture is subjected to at least one illuminated and non-illuminated period and allowed to proceed such that the time in which the reaction mixture is illuminated is less than a photo-induced damage threshold period.
    Type: Grant
    Filed: June 23, 2017
    Date of Patent: February 18, 2020
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Stephen Turner, Jon Sorenson, Kenneth Mark Maxham, John Eid
  • Patent number: 10557851
    Abstract: Disclosed herein are embodiments of a signaling conjugate, embodiments of a method of using the signaling conjugates, and embodiments of a kit comprising the signaling conjugate. The disclosed signaling conjugate comprises a latent reactive moiety and a chromogenic moiety that may further comprise a linker suitable for coupling the latent reactive moiety to the chromogenic moiety. The signaling conjugate may be used to detect one or more targets in a biological sample and are capable of being covalently deposited directly on or proximally to the target. Particular disclosed embodiments of the method of using the signaling conjugate comprise multiplexing methods.
    Type: Grant
    Filed: July 18, 2018
    Date of Patent: February 11, 2020
    Assignee: Ventana Medical Systems, Inc.
    Inventors: Nelson Alexander, William Day, Jerome W. Kosmeder, II, Mark Lefever, Larry Morrison, Anne M. Pedata, Stacey Stanislaw