Nucleotides Or Polynucleotides, Or Derivatives Thereof Patents (Class 506/16)
  • Patent number: 11391734
    Abstract: Bistable devices are constructed using a polynucleotide platform for sensing molecular events such as binding or conformational changes of target molecules. Uses include measurement of target concentration, measuring the effect of environmental condition (such as heat, light, or pH) on the target, or screening a library for molecules that bind the target or modulate its biological function. Devices comprise three regions: a top lid, bottom lid, and flexible linker or hinge between them. A device has an open configuration in which the top and bottom lid are separated, and a closed configuration they are bound close together. Binding domains or variations of the target molecule are fixed to a device so that when the molecular event occurs, the device switches from open to closed, or vice versa, which generates a signal. Optimal device design is determined by the signal modality (optical or electronic) used to measure closure of surface-immobilized devices.
    Type: Grant
    Filed: March 28, 2019
    Date of Patent: July 19, 2022
    Assignee: CALIFORNIA INSTITUTE OF TECHNOLOGY
    Inventors: Ashwin Gopinath, Paul W. K. Rothemund
  • Patent number: 11365381
    Abstract: Systems, methods and kits are described for culturing one or more biological cells in a microfluidic device, including provision of nutrients and gaseous components configured to enhance cell growth, viability, portability, or any combination thereof. In some embodiments, culturing a single cell may produce a clonal population in the microfluidic device.
    Type: Grant
    Filed: July 2, 2020
    Date of Patent: June 21, 2022
    Assignee: Berkeley Lights, Inc.
    Inventors: Randall D. Lowe, Jr., Kristin G. Beaumont, Aathavan Karunakaran, Natalie C. Marks, Jason M. McEwen, Mark P. White, J. Tanner Nevill, Gang F. Wang, Andrew W. McFarland, Daniele Malleo, Keith J. Breinlinger, Xiao Guan, Kevin T. Chapman
  • Patent number: 11359235
    Abstract: Labeled nucleotide analogs comprising at least one avidin protein, at least one dye-labeled compound, and at least one nucleotide compound are provided. The analogs are useful in various fluorescence-based analytical methods, including the analysis of highly multiplexed optical reactions in large numbers at high densities, such as single molecule real time nucleic acid sequencing reactions. The analogs are detectable with high sensitivity at desirable wavelengths. They contain structural components that modulate the interactions of the analogs with DNA polymerase, thus decreasing photodamage and improving the kinetic and other properties of the analogs in sequencing reactions. Also provided are nucleotide and dye-labeled compounds of the subject analogs, as well as intermediates useful in the preparation of the compounds and analogs. Compositions comprising the compounds, methods of synthesis of the intermediates, compounds, and analogs, and mutant DNA polymerases are also provided.
    Type: Grant
    Filed: June 13, 2019
    Date of Patent: June 14, 2022
    Assignee: Pacific Biosciences of California, Inc.
    Inventors: Gene Shen, Stephen Yue, Lubomir Sebo, Louis Brogley
  • Patent number: 11352669
    Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.
    Type: Grant
    Filed: June 30, 2021
    Date of Patent: June 7, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Xiaoliang Sunney Xie, Katsuyuki Shiroguchi, Peter A. Sims, Tony Z. Jia
  • Patent number: 11351539
    Abstract: A multi-level microfluidic device is provided. The device includes a silicon wafer substrate and a stack of layers arranged on the silicon wafer substrate. The stack comprises a plurality of fluidic silicon layers, wherein each fluidic silicon layer includes a microfluidic structure at least one intermediate layer. The at least one intermediate layer is arranged between two fluidic silicon layers, and a fluid inlet and a fluid outlet in fluid connection with at least one of the fluidic silicon layers. Each layer in the stack is formed by deposition or growth. Methods for manufacturing microfluidic devices is also provided.
    Type: Grant
    Filed: December 6, 2019
    Date of Patent: June 7, 2022
    Assignee: IMEC VZW
    Inventor: Silvia Lenci
  • Patent number: 11345931
    Abstract: CRISPR/Cas Systems are provided where a tuned guide RNA is used to discriminate between two protospacer sequences of same length that differ by one nucleotide.
    Type: Grant
    Filed: December 14, 2016
    Date of Patent: May 31, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Alejandro Chavez, Benjamin W. Pruitt
  • Patent number: 11345961
    Abstract: Embodiments may include a method of determining a nucleic acid sequence. The nucleic acid may be DNA. The method may include forming, by a polymerase, a double-stranded nucleic acid molecule from a first nucleic acid strand and a second nucleic acid strand. Forming the double-stranded nucleic acid molecule may include adding a first compound to the second nucleic acid strand. The first compound may include a nucleotide attached to a third nucleic acid strand. The third nucleic acid strand may be attached to a moiety. The method may also include detaching the nucleotide from the third nucleic acid strand and the moiety. The method may further include measuring a change in an electrical characteristic of a transistor resulting from the moiety. Additionally, the method may include identifying the nucleotide based on the measured change in the electrical characteristic.
    Type: Grant
    Filed: September 28, 2017
    Date of Patent: May 31, 2022
    Assignee: Roche Sequencing Solutions, Inc.
    Inventor: Yann Astier
  • Patent number: 11339399
    Abstract: The present invention provides cell lines for high efficiency genome editing using cas/CRISPR systems, methods of generating such cells lines, and methods of generating mutations in the genome of an organism using such cell lines.
    Type: Grant
    Filed: December 31, 2015
    Date of Patent: May 24, 2022
    Assignee: Viridos, Inc.
    Inventors: John Verruto, Eric Moellering
  • Patent number: 11326200
    Abstract: A method of preparing a sample may include depositing an aqueous solution comprising copies of a primer into a layer of hydrophobic liquid on a substrate with a thermal inkjet device. A sample may include: a substrate; a layer of hydrophobic liquid on the substrate, the layer of hydrophobic liquid comprising a plurality of droplets of aqueous solution distributed in the layer, wherein the plurality of droplets contain: primers; a polymerase enzyme; deoxynucleotide triphosphates (dNTPs); and a target sequence for replication; and a cover, the cover contacting and covering the layer of hydrophobic liquid.
    Type: Grant
    Filed: July 22, 2016
    Date of Patent: May 10, 2022
    Assignee: Hewlett-Packard Development Company, L.P.
    Inventors: Michael W. Cumbie, Devin Alexander Mourey, Si-Iam Choy
  • Patent number: 11286523
    Abstract: Methods and compositions for digital profiling of nucleic acid sequences present in a sample are provided.
    Type: Grant
    Filed: January 28, 2020
    Date of Patent: March 29, 2022
    Assignee: President and Fellows of Harvard College
    Inventors: Xiaoliang Sunney Xie, Katsuyuki Shiroguchi, Peter A. Sims, Tony Z. Jia
  • Patent number: 11278901
    Abstract: A microfluidic emulsion droplet generation system and methods of use thereof are provided. The system may include a microfluidic substrate having a flow path configured and arranged for emulsion droplet generation, at least one textured surface in the flow path configured and arranged for inducing surface-mediated coalescence of emulsion droplets; and at least one channel junction in the flow path for emulsion droplet formation.
    Type: Grant
    Filed: May 29, 2020
    Date of Patent: March 22, 2022
    Assignee: 10x Genomics, Inc.
    Inventors: Rajiv Bharadwaj, Tobias Daniel Wheeler, Kevin Ness, Benjamin Hindson
  • Patent number: 11278941
    Abstract: Provided herein is a hierarchical superhydrophobic surface comprising an array of first geometrical features disposed on a substrate comprising a first material, and an array of second geometrical features disposed on the first features to form a hierarchical structure and a terminal level disposed on the second features, wherein the terminal level comprises a second material, the second material being different from the first material. The second material has a hydrophilicity different from the hydrophilicity of at least one of 1) the hydrophilicity of the second material and 2) hydrophilicity induced by the hierarchical structure. The present disclosure further methods of preparing hierarchical superhydrophobic surfaces and medical devices comprising the hierarchical superhydrophobic surfaces.
    Type: Grant
    Filed: July 16, 2018
    Date of Patent: March 22, 2022
    Assignee: BVW Holding AG
    Inventors: Michael Milbocker, Lukas Bluecher
  • Patent number: 11280740
    Abstract: A luminescence-enhancement system can include a luminescence-enhancement sensor having a substrate and a group of nanofingers with individual nanofingers that can be flexible and include a support end attached to the substrate, a distal tip positioned distally with respect to the substrate, and a middle portion between the support end and the distal tip. A coating of a metal or metal alloy can be applied to the substrate and the distal tip that is conductively continuous. The middle portion can be devoid of the coating or the coating at the middle portion is conductively discontinuous. A liquid ejector can be present and can include a jetting nozzle to eject a liquid droplet having a volume of 2 pL to 10 ?L. The group of nanofingers and the jetting nozzle can be positionable relative to one another for the droplet to be deposited on the group of nanofingers.
    Type: Grant
    Filed: April 6, 2018
    Date of Patent: March 22, 2022
    Assignee: Hewlett-Packard Development Company, L.P.
    Inventors: Steven Barcelo, Anita Rogacs, Raghuvir N. Sengupta
  • Patent number: 11268117
    Abstract: In some embodiments, the disclosure relates generally to methods, as well as related compositions and kits for recombinase-mediated nucleic acid amplification, such as recombinase-polymerase amplification (RPA), of a nucleic acid template using at least one blocked primer that contains a 5? domain, at least one nucleotide that is cleavable by an RNase H enzyme, a 3? domain, wherein the primer is not extendable by a polymerase, and wherein the 3? domain has a length of 7-100 nucleotides, for example 10-30 nucleotides. These methods and the use of a blocked primer reduce or eliminate non-specific amplification products, such as primer dimers, which are generated in RPA reactions.
    Type: Grant
    Filed: June 9, 2017
    Date of Patent: March 8, 2022
    Assignee: Life Technologies Corporation
    Inventors: Hua Yu, Theo Nikiforov, Abraham Rosenbaum
  • Patent number: 11256033
    Abstract: Light detection devices and corresponding methods are provided. The devices include a reaction structure to contain a reaction solution and at least one reaction site that generates light emissions in response to incident excitation light after treatment with the reaction solution. The devices also include a plurality of light sensors and device circuitry. The devices further include a plurality of light guides extending toward at least one corresponding light sensor from input regions that receive the excitation light and the light emissions from at least one corresponding reaction recess. The light guides comprise a first filter region that filters the excitation light and permits the light emissions of a first wavelength to pass to the at least one corresponding light sensor, and a second filter region that filters the excitation light and the permits light emissions of a second wavelength to pass to the at least one corresponding light sensor.
    Type: Grant
    Filed: May 6, 2020
    Date of Patent: February 22, 2022
    Assignee: ILLUMINA, INC.
    Inventor: Xiuyu Cai
  • Patent number: 11247209
    Abstract: Provided are methods and systems useful for screening large libraries of effector molecules. Such methods and systems are particularly useful in microfluidic systems and devices. The methods and systems provided herein utilize encoded effectors to screen large libraries of effectors.
    Type: Grant
    Filed: November 5, 2020
    Date of Patent: February 15, 2022
    Assignee: 1859, Inc.
    Inventors: Devon Cayer, Andrew MacConnell, Pavel Chubukov, Ramesh Ramji, Sean Stromberg
  • Patent number: 11247896
    Abstract: A material with a nanotexture comprising structures extending from a substrate. The structures are modified by coating the nanotexture with a protective coating and partially removing the coating, exposing a portion of the structure for functionalization.
    Type: Grant
    Filed: July 30, 2019
    Date of Patent: February 15, 2022
    Assignee: UChicago Argonne, LLC
    Inventors: Martyna Michalska, Philip D. Laible, Ralu Divan
  • Patent number: 11180810
    Abstract: This disclosure provides kits and methods for determining whether a subject is suffering from a liver disease, and/or whether the subject will be a responsive to a therapy for a liver disease. The disclosed methods comprise determining the miR profile of exosomes isolated from a body fluid of the subject.
    Type: Grant
    Filed: September 28, 2016
    Date of Patent: November 23, 2021
    Assignees: RESEARCH INSTITUTE AT NATIONWIDE CHILDREN'S HOSPITAL, BEIJING FRIENDSHIP HOSPITAL, CAPITAL MEDICAL UNIVERSITY
    Inventors: David Brigstock, Li Chen, Hong You, Min Cong
  • Patent number: 11180805
    Abstract: The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization. Such polynucleotide processing may be useful for a variety of applications, including analyte characterization by polynucleotide sequencing. The compositions, methods, systems, and devices disclosed herein generally describe barcoded oligonucleotides, which can be bound to a bead, such as a gel bead, useful for characterizing one or more analytes including, for example, protein (e.g., cell surface or intracellular proteins), genomic DNA, and RNA (e.g., mRNA or CRISPR guide RNAs). Also described herein, are barcoded labelling agents and oligonucleotide molecules useful for “tagging” analytes for characterization.
    Type: Grant
    Filed: October 29, 2020
    Date of Patent: November 23, 2021
    Assignee: 10X GENOMICS, INC
    Inventors: Michael Ybarra Lucero, Tarjei Sigurd Mikkelsen, Katherine Pfeiffer, Stephane Claude Boutet
  • Patent number: 11155862
    Abstract: The present invention discloses a method for rapidly constructing amplicon library including the following steps: 1. Synthesizing a primer combination for constructing an amplicon library of a DNA sample, the primer combination of the amplicon library used to construct the DNA sample includes: a forward fusion primer designed according to the target amplicon, a reverse fusion primer designed according to the target amplicon, a forward universal primer and a reverse universal primer; 2. Constructing a PCR reaction system for the DNA sample; 3. Performing PCR. The method according to the present invention can be used to construct an amplicon library in a simple and rapid manner, and since a barcode is introduced before the start of PCR, the possibility of cross-contamination between the sample and the library is greatly reduced.
    Type: Grant
    Filed: March 28, 2018
    Date of Patent: October 26, 2021
    Assignee: Genetron Health (Beijing) Co., Ltd.
    Inventors: Hai Yan, Sizhen Wang, Yuchen Jiao, Dayong Xu, Qiaosong Zheng, Xiao Shi
  • Patent number: 11118215
    Abstract: In one aspect, the present invention relates to a method for obtaining structural information about an encoded molecule. The encoded molecule may be produced by a reaction of a plurality of chemical entities and may be capable of being connected to an identifier oligonucleotide containing codons informative of the identity of the chemical entities which have participated in the formation of the encoded molecule. In a certain embodiment, primers are designed complementary to the codons appearing on the identifier oligonucleotide, and the presence, absence or relative abundance of a codon is evaluated by mixing a primer with the identifier oligonucleotide in the presence of a polymerase and substrate (deoxy)ribonucleotide triphosphates and measuring the extension reaction. In another aspect, the invention provides a method for selecting compounds which binds to a target.
    Type: Grant
    Filed: September 17, 2004
    Date of Patent: September 14, 2021
    Assignee: NUEVOLUTION A/S
    Inventors: Thomas Thisted, Mikkel Dybro Lundorf, Per-Ola Freskgard, Torben Ravn Rasmussen
  • Patent number: 11110450
    Abstract: A sample-reagent mixture is thermal cycled through a plurality of cycles. Each thermal cycle includes actuating a heater to heat the sample-reagent mixtures; and dispensing a fluid onto the sample-reagent mixture to cool the sample reagent mixture.
    Type: Grant
    Filed: January 29, 2016
    Date of Patent: September 7, 2021
    Assignee: Hewlett-Packard Development Company, L.P.
    Inventors: Bradley D. Chung, Alexander N. Govyadinov
  • Patent number: 11059865
    Abstract: Disclosed are catalytically active water-insoluble protein aggregates comprising fusion proteins which comprise a coiled-coil domain and a catalytic domain, methods of manufacturing such protein aggregates, and their use.
    Type: Grant
    Filed: July 22, 2016
    Date of Patent: July 13, 2021
    Assignee: evoxx technologies GmbH
    Inventors: Martina Pohl, Karl-Erich Jaeger, Martin Diener, Ulrich Krauss
  • Patent number: 11052368
    Abstract: The present invention generally relates to microfluidics and labeled nucleic acids. For example, certain aspects are generally directed to systems and methods for labeling nucleic acids within microfluidic droplets. In one set of embodiments, the nucleic acids may include “barcodes” or unique sequences that can be used to distinguish nucleic acids in a droplet from those in another droplet, for instance, even after the nucleic acids are pooled together. In some cases, the unique sequences may be incorporated into individual droplets using particles and attached to nucleic acids contained within the droplets (for example, released from lysed cells). In some cases, the barcodes may be used to distinguish tens, hundreds, or even thousands of nucleic acids, e.g., arising from different cells or other sources.
    Type: Grant
    Filed: May 29, 2018
    Date of Patent: July 6, 2021
    Assignees: Vilnius University, President and Fellows of Harvard College
    Inventors: David A. Weitz, Allon Moshe Klein, Ilke Akartuna, Linas Mazutis, Marc W. Kirschner
  • Patent number: 11038147
    Abstract: The present disclosure relates to an organic electroluminescence device with enhanced out-coupling efficiency. The electroluminescence device comprises a substrate, a first electrode disposed on the substrate, an organic layer and a second electrode. The organic layer is formed between the first electrode and the second electrode. The organic layer comprises one or more nanoparticles forming protrusion features on the organic layer thereby forming a topographical structured organic layer in the electroluminescence device. The electroluminescence device is capable of reducing the surface plasmon polariton loss thereby, enhancing the light out-coupling the electroluminescence device.
    Type: Grant
    Filed: April 26, 2017
    Date of Patent: June 15, 2021
    Assignee: Sumitomo Chemical Company Limited
    Inventors: Philip Benzie, Mark Herrington, Karen Alsop-Fox
  • Patent number: 11029291
    Abstract: A system for analyzing a sample includes a chromatographic device, an electrospray source, and a mass resolving device. The chromatographic device is configured to separate components of the sample as a function of retention time within a chromatographic column. The electrospray source is configured to direct a first portion of a flow from the chromatographic device via a waste outlet to a pressurized waste reservoir, direct a second portion of the flow to an electrospray ionization outlet to form a spray, and charge and desolvate the spray to form ions of the components of the sample. A flow rate of the second portion of the liquid flow is substantially determined by a pressure of the pressurized waste reservoir. The mass resolving device configured to receive the ions and characterize the mass-to-charge ratio of the ions.
    Type: Grant
    Filed: July 10, 2020
    Date of Patent: June 8, 2021
    Assignee: Thermo Finnigan LLC
    Inventors: Gary A. Schultz, R. Paul Atherton, Eloy R. Wouters
  • Patent number: 11008613
    Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.
    Type: Grant
    Filed: March 20, 2020
    Date of Patent: May 18, 2021
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
  • Patent number: 11001885
    Abstract: An apparatus suitable for single molecule sequencing. The apparatus includes at least one nanowell, a plurality of nucleic acid immobilization moieties, and a plurality of types of nucleic acid fragments. The nanowell has an observation zone. The nucleic acid immobilization moieties are disposed in or proximate to the observation zone. The nucleic acid fragments are immobilized to the nucleic acid immobilization moieties, respectively. At least one polymerase is disposed in the observation zone. A method of sequencing nucleic acid molecules using the above-mentioned apparatus is provided.
    Type: Grant
    Filed: June 12, 2018
    Date of Patent: May 11, 2021
    Assignee: Personal Genomics Taiwan, Inc.
    Inventors: Chung-Fan Chiou, Chao-Chi Pan, Ching-Wei Tsai, Bor-Huah Chen, Jian-Hao Ciou
  • Patent number: 11001815
    Abstract: The present disclosure provides methods, compositions, kits and systems for nucleic acid amplification. In some embodiments, nucleic acid amplification methods include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, nucleic acid amplification methods include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the nucleic acid amplification method employs an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel and/or in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components.
    Type: Grant
    Filed: June 14, 2019
    Date of Patent: May 11, 2021
    Assignee: Life Technologies Corporation
    Inventors: Chieh-Yuan Li, David Ruff, Shiaw-Min Chen, Jennifer O'Neil, Rachel Kasinskas, Jonathan Rothberg, Bin Li, Kai Qin Lao
  • Patent number: 10995369
    Abstract: The present invention is concerned with compositions and methods for improving the rate of correct sample identification in indexed nucleic acid library preparations for multiplex next generation sequencing by exonuclease treatment after protective adapters are ligated to target polynucleotides to degrade unincorporated adapters prior to amplification and sequencing.
    Type: Grant
    Filed: April 23, 2018
    Date of Patent: May 4, 2021
    Assignees: Illumina, Inc., Illumina Cambridge Limited
    Inventors: Eric Hans Vermaas, Mahdieh Khosroheidari, Angela Kalbande
  • Patent number: 10995367
    Abstract: Provided are a vesicular adaptor and a single-chain cyclic library constructed by using the adaptor. The library can be used for RNA sequencing and other sequencing platforms dependent on a single-stranded cyclic library, and has the advantage of high throughput sequencing, high accuracy and simple operations.
    Type: Grant
    Filed: September 19, 2019
    Date of Patent: May 4, 2021
    Assignee: MGI TECH CO., LTD.
    Inventors: Yuan Jiang, Jing Guo, Xiaojun Ji, Chunyu Geng, Kai Tian, Xia Zhao, Huaiqian Xu, Wenwei Zhang, Hui Jiang, Radoje Drmanac
  • Patent number: 10975426
    Abstract: The present disclosure relates to compositions and methods based on polypeptide-tagged nucleotide, and the use of such polypeptide-tagged nucleotides in nanopore devices and methods.
    Type: Grant
    Filed: August 26, 2016
    Date of Patent: April 13, 2021
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Frank Bergmann, Christoph Seidel, Andrew Trans, Dmitriy Gremyachinskiy, Hannes Kuchelmeister, Lars Hillringhaus
  • Patent number: 10947587
    Abstract: A short tandem repeat (STR) typing method and system are developed for forensic identification of individual cells. Agarose-in-oil droplets are produced with a high frequency using a microfluidic droplet generator. Statistically dilute single cells, along with primer-functionalized microbeads, are randomly compartmentalized in the droplets. Massively parallel single-cell droplet PCR is performed to transfer replicas of desired STR targets from the single-cell genomic DNA onto a coencapsulated microbead. These DNA-conjugated beads are subsequently harvested and reamplified under statistically dilute conditions for conventional capillary electrophoresis STR fragment size analysis. The methods and systems described herein are valuable for the STR analysis of samples containing mixtures of cells/DNA from multiple contributors and for low concentration samples.
    Type: Grant
    Filed: November 5, 2014
    Date of Patent: March 16, 2021
    Assignee: The Regents of the University of California
    Inventors: Tao Geng, Richard Novak, Richard A. Mathies
  • Patent number: 10947581
    Abstract: A system and method for target material capture, the method comprising: receiving a set of target cells into an array of wells defined at a surface plane of a substrate; receiving a set of particles into the array of wells, thereby co-capturing the set of target cells and the set of particles; achieving a desired state for the array of wells upon receiving a washing fluid into a cavity in communication with the array of wells; receiving a lysis buffer into the cavity; receiving a partitioning fluid into the cavity, thereby displacing the lysis buffer from the cavity and partitioning each of the array of wells from adjacent wells, at the surface plane; and retaining intercellular material of the set of target cells, individually with the set of particles within the array of wells.
    Type: Grant
    Filed: March 17, 2020
    Date of Patent: March 16, 2021
    Assignee: Bio-Rad Laboratories, Inc.
    Inventors: Kalyan Handique, John Stark, Yadwinder Deol, Vishal Sharma
  • Patent number: 10934636
    Abstract: The present invention provides a novel method for preparing a sequencing library and studying molecular interactions involving a nucleic acid. In particular, the invention relates to a method for preparing a sequencing library, the method comprising the addition of an agent binding to chromatin to a sample comprising a nucleic acid; isolating chromatin bound by said agent; addition of transposase to the isolated chromatin; isolating nucleic acid from chromatin; and obtaining a sequencing library. Moreover, the present invention relates to a method for mapping of molecular interactions involving a nucleic acid, the method comprising the addition of an agent binding to chromatin to a sample comprising a nucleic acid; isolating chromatin bound by said agent; addition of transposase to the isolated chromatin; isolating nucleic acid from chromatin; amplification of nucleic acid; sequencing of amplified nucleic acid; and identifying molecular interactions.
    Type: Grant
    Filed: August 11, 2016
    Date of Patent: March 2, 2021
    Assignee: CEMM—Forschungszentrum für Molekulare Medizin GmbH
    Inventors: Christoph Bock, Christian Schmidl
  • Patent number: 10894990
    Abstract: Disclosed are methods for screening biological samples for the presence unknown microbes, such as bacteria and archaea or unknown eukaryotes using rRNA gene sequences or other highly conserved genetic regions, across multiple biological samples using a unique sequence tag (barcode) corresponding to the sample. The screening process tracks the unknown microbe or eukaryote in a diluted sample where the DNA has been prepared using whole genome amplification. The whole genome of the unknown microbe or eukaryote is then sequenced and assembled.
    Type: Grant
    Filed: May 16, 2017
    Date of Patent: January 19, 2021
    Assignee: Shoreline Biome, LLC
    Inventors: Mark Driscoll, Thomas Jarvie
  • Patent number: 10876148
    Abstract: Methods and formulations for preparing low non-specific binding surfaces are described, and the prepared surface can provide improved performance for nucleic acid detection and base calling applications. The surface provides more accurate nucleic acid detection, enhanced contrast to noise ratio, and better data collection.
    Type: Grant
    Filed: January 10, 2020
    Date of Patent: December 29, 2020
    Assignee: ELEMENT BIOSCIENCES, INC.
    Inventors: Chunhong Zhou, Sinan Arslan, Molly Min He, Matthew Kellinger, Adeline Huizhen Mah, Michael Previte, Lei Sun
  • Patent number: 10858691
    Abstract: Focused acoustic treatment of samples may be used to differentially shear different fragment lengths of DNA or other nucleic acid portions of a sample. Relatively larger fragment lengths may be sheared while smaller fragment lengths are unaffected by the focused acoustic based shearing.
    Type: Grant
    Filed: April 17, 2018
    Date of Patent: December 8, 2020
    Assignee: Covaris, Inc.
    Inventors: Hans-Ulrich Thomann, James A. Laugharn, Jr.
  • Patent number: 10858695
    Abstract: In some embodiments, provided are methods for nucleic acid amplification include subjecting the nucleic acid to be amplified to partially denaturing conditions. In some embodiments, methods for nucleic acid amplification include amplifying without fully denaturing the nucleic acid that is amplified. In some embodiments, the methods for nucleic acid amplification employ an enzyme that catalyzes homologous recombination and a polymerase. In some embodiments, methods for nucleic acid amplification can be conducted in a single reaction vessel. In some embodiments, methods for nucleic acid amplification can be conducted in a single continuous liquid phase of a reaction mixture, without need for compartmentalization of the reaction mixture or immobilization of reaction components. In some embodiments, methods for nucleic acid amplification comprise a amplifying at least one polynucleotide onto a surface under isothermal amplification conditions, optionally in the presence of a polymer.
    Type: Grant
    Filed: October 23, 2018
    Date of Patent: December 8, 2020
    Assignee: Life Technologies Corporation
    Inventors: Chieh-Yuan Li, David Ruff, Jennifer O'Neil, Rachel Kasinskas, Shiaw-Min Chen, Jonathan M. Rothberg, Bin Li, Kai Qin Lao
  • Patent number: 10844435
    Abstract: The present disclosure relates to a method of treating a patient experiencing hypotension, comprising genotyping for a TT, AA, or AT genotype, and administering a therapeutically effective amount of vasopressin based on genotype to maintain a target blood pressure.
    Type: Grant
    Filed: July 17, 2020
    Date of Patent: November 24, 2020
    Assignee: PAR PHARMACEUTICAL, INC.
    Inventor: Saji Vijayan
  • Patent number: 10815536
    Abstract: The present invention provides novel methods, systems, tools, and kits for the simultaneous detection, identification and/or characterization of all viruses known or suspected to infect vertebrates. The methods, systems, tools, and kits described herein are based upon the virome capture sequencing platform (“VirCapSeq-VERT”), a novel platform developed by the inventors. The invention also provides methods and kits for designing and constructing of the virome capture sequencing platform.
    Type: Grant
    Filed: September 19, 2016
    Date of Patent: October 27, 2020
    Assignee: THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK
    Inventors: Walter Ian Lipkin, Omar Jabado, Thomas Briese, Amit Kapoor, Jan Gogarten, Komal Jain, Nischay Mishra
  • Patent number: 10792638
    Abstract: Droplet generation devices and systems that parallelize droplet generation devices are provided. The droplet generation devices can include a symmetric block-and-break system and a tapered droplet generation zone. The symmetric block-and-break system can include a pair of break channels and a pair of bypass channels symmetrically arranged with respect to the dispersed-phase input channel and the output channel. The droplet generation devices can generate monodisperse droplets with a predefined volume over a range of flow rates, pressures, and fluid properties. The droplet generation devices are therefore capable of parallelization to achieve large-capacity droplet generation, e.g. greater than 1 L/hr, with small overall coefficients of variation.
    Type: Grant
    Filed: October 7, 2016
    Date of Patent: October 6, 2020
    Assignee: KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY
    Inventors: David Conchouso Gonzalez, Armando Arpys Arevalo Carreno, Ian G. Foulds
  • Patent number: 10751717
    Abstract: A microfluidic chip for collecting dielectric particles in a fluid sample to be tested includes an insulating substrate, a first interdigitated electrode, a second interdigitated electrode, and a dielectric layer. The dielectric layer is formed on the first and second interdigitated electrodes and is made from a semiconductive inorganic material having a dielectric constant of from 3.7 F/m to 80 F/m.
    Type: Grant
    Filed: June 4, 2018
    Date of Patent: August 25, 2020
    Assignee: National Cheng Kung University
    Inventors: Hsien-Chang Chang, Tien-Chun Tsai, Yen-Liang Cho, Zong-Zhan Wu, Peng-Ting Chen
  • Patent number: 10722858
    Abstract: The invention relates to methods of tagging analytes in a sample.
    Type: Grant
    Filed: July 23, 2018
    Date of Patent: July 28, 2020
    Assignee: Lineage Biosciences, Inc.
    Inventors: Hei-Mun Christina Fan, Edward A. Hutchins
  • Patent number: 10718016
    Abstract: Short Tandem Repeats are currently used by law enforcement and others, for example, for the identification of individuals by DNA matching. A method is described herein that uses WPD to classify and identify repeating sequences in nucleotide sequences from the position and frequency information contained within nucleotide sequences. This decomposition allows for the quick classification of nucleotide sequences (i.e., reads) into two different classes, including, for example, one class that contains sequencer reads that contain a repeat motif with non-repeat sequence on either flank, and another class that contains sequencer reads that do not contain any repeat sequence.
    Type: Grant
    Filed: June 16, 2017
    Date of Patent: July 21, 2020
    Assignee: BATTELLE MEMORIAL INSTITUTE
    Inventors: Joseph J. Regensburger, Aaron J. Sander, Jared M. Schuetter, Daniel M. Bornman, Seth A. Faith, Scott C. Nelson, Brian A. Young
  • Patent number: 10711271
    Abstract: This disclosure provides, among other things, a method for making a cDNA library. In some embodiments the method may comprise reverse transcribing mRNA to produce DNA:mRNA hybrids, treating the DNA:mRNA hybrids with RNAseH to produce mRNA fragments, and reverse transcribing the mRNA fragments.
    Type: Grant
    Filed: November 20, 2017
    Date of Patent: July 14, 2020
    Assignee: BIOO SCIENTIFIC CORPORATION
    Inventors: Kevin Allen, Adam Morris
  • Patent number: 10679724
    Abstract: A method of modeling a background signal when sequencing a polynucleotide strand using sequencing-by-synthesis includes: flowing a series of nucleotide flows onto a reactor array having multiple reaction confinement regions, one or more copies of the polynucleotide strand being located in a loaded reaction confinement region of the reactor array, the loaded reaction confinement region being located in a vicinity of one or more neighboring reaction confinement regions that may or may not be loaded; receiving output signals from the reactor array; and modeling a background signal for the loaded reaction confinement region using the received output signals and a model adapted to account at least for an exchange of ions between the one or more neighboring reaction confinement regions and a headspace adjacent the loaded reaction confinement region and the one or more neighboring reaction confinement regions.
    Type: Grant
    Filed: April 27, 2017
    Date of Patent: June 9, 2020
    Assignee: Life Technologies Corporation
    Inventor: Todd Rearick
  • Patent number: 10669538
    Abstract: The present invention relates to a method for synthesising templated molecules. In one aspect of the invention, the templated molecules are linked to the template which templated the synthesis thereof. The invention allows the generation of libraries which can be screened for e.g. therapeutic activity.
    Type: Grant
    Filed: October 13, 2016
    Date of Patent: June 2, 2020
    Assignee: NUEVOLUTION A/S
    Inventors: Henrik Pedersen, Alex Haahr Gouliaev, Thomas Franch, Christian Klarner Sams, Eva Kampmann Olsen, Frank Abilgaard Slok, Gitte Nystrup Husemoen, Jakob Felding, Lene Hyldtoft, Mads Norregaard-Madsen, Michael Anders Godskesen, Sanne Schroder Glad, Thomas Thisted, Per-Ola Freskgard, Anette Holtmann
  • Patent number: 10669580
    Abstract: The present disclosure relates to compounds comprising a negatively-charged polymer moiety which is capable of entering a nanopore and upon entering a nanopore in the presence of positive ions results in an increased flow of the positive ions through the nanopore. The present disclosure provides methods of preparing the compounds and for their use as nanopore-detectable tags, in particular, for nanopore-based nucleic acid detection and sequencing.
    Type: Grant
    Filed: August 23, 2017
    Date of Patent: June 2, 2020
    Assignee: Roche Sequencing Solutions, Inc.
    Inventors: Dmitriy Gremyachinskiy, Peter Crisalli, Andrew Trans, Ashwini Bhat
  • Patent number: 10655170
    Abstract: Methods of coupling adaptors to a target nucleic acid include coupling a first adaptor to a first end of the target nucleic acid to form a coupled first adaptor. A portion of a second adaptor is hybridized to a portion of the coupled first adaptor to form a hybridized second adaptor having a single-stranded 3?-end. The hybridized second adaptor is coupled to a second end of the target nucleic acid to form an adaptor-flanked product having at least a part of the first adaptor coupled to the first end of the target nucleic acid and at least a part of the second adaptor coupled to the second end of the target nucleic acid. These methods can minimize the formation of adaptor-dimers that may be problematic in subsequent complementary nucleic acid strand synthesis, amplification, and sequencing.
    Type: Grant
    Filed: July 5, 2017
    Date of Patent: May 19, 2020
    Assignee: Takara Bio USA, Inc.
    Inventors: Konstantinos Charizanis, Marta Gonzalez-Hernandez, Amanda McNulty, Karl Hecker, Emmanuel Kamberov, John Langmore