Patents Assigned to Applied Biosystems, LLC.
  • Patent number: 10329564
    Abstract: Modification formats having modified nucleotides are provided for siRNA. Short interfering RNA having modification formats and modified nucleotides provided herein reduce off-target effects in RNA interference of endogenous genes. Further modification formatted siRNAs are demonstrated to be stabilized to nuclease-rich environments. Unexpectedly, increasing or maintaining strand bias, while necessary to maintain potency for endogenous RNA interference, is not sufficient for reducing off-target effects in cell biology assays.
    Type: Grant
    Filed: September 5, 2017
    Date of Patent: June 25, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Nitin Puri, Irudaya Charles, Susan Maylin Magdaleno, Alexander Vlassov, Christopher Burnett
  • Patent number: 10323277
    Abstract: The present invention provides methods for determining a nucleic acid sequence by performing successive cycles of duplex extension along a single stranded template. The cycles comprise steps of extension, ligation, and, preferably, cleavage. In certain embodiments the methods make use of extension probes containing phosphorothiolate linkages and employ agents appropriate to cleave such linkages. The invention provides methods of determining information about a sequence using at least two distinguishably labeled probe families. In certain embodiments the methods acquire less than 2 bits of information from each of a plurality of nucleotides in the template in each cycle. In certain embodiments the sequencing reactions are performed on templates attached to immobilized beads.
    Type: Grant
    Filed: October 12, 2016
    Date of Patent: June 18, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Patent number: 10253361
    Abstract: A thermal cycling device for thermally cycling samples of biological material contained in a microcard having a top and bottom surface. The thermal cycling device can include a sample block having an upper surface configured for engaging the bottom surface of a microcard, a vacuum device, and a temperature control system operatively connected with the sample block. The upper surface of the sample block may include a plurality of channels, the channels defining spaces between the sample block and the bottom surface of a microcard that may be positioned thereon. The vacuum device may be in fluid communication with the sample block for drawing gas out of the spaces defined by the channels in the sample block. The vacuum device may be configured for substantially maintaining a vacuum between the sample block and microcard so that a retention force is imparted on the microcard to urge the microcard toward the sample block.
    Type: Grant
    Filed: August 21, 2013
    Date of Patent: April 9, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: Adrian Fawcett
  • Patent number: 10240191
    Abstract: Compositions, methods, and kits for detecting one or more species of RNA molecules are disclosed. In one embodiment, a first adaptor and a second adaptor are ligated to the RNA molecule using a polypeptide comprising double-strand specific RNA ligase activity, without an intervening purification step. The ligated product is reverse transcribed, then at least some of the ribonucleosides in the reverse transcription product are removed. Primers are added and amplified products are generated. In certain embodiments, the sequence of at least part of at least one species of amplified product is determined and at least part of the corresponding RNA molecule is determined. In some embodiments, at least some of the amplified product species are detected, directly or indirectly, allowing the presence and/or quantity of the RNA molecule of interest to be determined.
    Type: Grant
    Filed: November 3, 2017
    Date of Patent: March 26, 2019
    Assignee: Applied Biosystems, LLC
    Inventor: R. Scott Kuersten
  • Patent number: 10233444
    Abstract: The invention relates to methods for the detection of a specific sequence of RNA in a cell or tissue sample. The invention also relates to methods to enzymatically manipulate the RNA in a crude cell lysate in a number of applications.
    Type: Grant
    Filed: June 6, 2018
    Date of Patent: March 19, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Brittan Pasloske, Quoc Hoang
  • Publication number: 20190064108
    Abstract: The invention provides compositions, methods and kits for high speed, high resolution of analytes by capillary electrophoresis starting with uncoated capillaries. The compositions comprise a sieving component, comprising a non-crosslinked acrylamide polymer, and a surface interaction component, comprising at least one uncharged and non-crosslinked water-soluble silica-adsorbing polymer. Methods for employing the novel compositions in capillary electrophoresis are provided. Kits comprising the novel compositions for use in the novel methods are also provided.
    Type: Application
    Filed: April 24, 2018
    Publication date: February 28, 2019
    Applicant: Applied Biosystems, LLC
    Inventors: Karl O. Voss, Aldrich N.K. Lau
  • Patent number: 10215730
    Abstract: A method for dispensing liquid for use in biological analysis may comprise positioning liquid to be dispensed via electrowetting. The positioning may comprise aligning the liquid with a plurality of predetermined locations. The method may further comprise dispensing the aligned liquid from the plurality of predetermined locations through a plurality of openings respectively aligned with the predetermined locations. The dispensing may be via electrowetting.
    Type: Grant
    Filed: June 5, 2017
    Date of Patent: February 26, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Charles S. Vann, Debjyoti Banerjee, Timothy G. Geiser, James C. Nurse, Nigel P. Beard
  • Patent number: 10196680
    Abstract: The present disclosure relates to methods of identifying target nucleic acids by using coded molecules and its analysis by translocation through a nanopore. Generally, coded molecules are subject to a target polynucleotide dependent modification. The modified coded molecule is detected by isolating the modified coded molecules from the unmodified coded molecules prior to analysis through the nanopore or by detecting a change in the signal pattern of the coded molecule when analyzed through the nanopore.
    Type: Grant
    Filed: June 5, 2017
    Date of Patent: February 5, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Patent number: 10190164
    Abstract: The present disclosure relates to methods and compositions for making paired tags and paired tag libraries.
    Type: Grant
    Filed: April 24, 2017
    Date of Patent: January 29, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Bin Li, Lei Xi, Swati Ranade, Yangzhou Wang
  • Patent number: 10184149
    Abstract: A device for performing biological sample reactions may include a plurality of flow cells configured to be mounted to a common microscope translation stage, wherein each flow cell is configured to receive at least one sample holder containing biological sample. Each flow cell also may be configured to be selectively placed in an open position for positioning the at least one sample holder into the flow cell and a closed position for reacting biological sample contained in the at least one sample holder. The plurality of flow cells may be configured to be selectively placed in the open position and the closed position independently of each other.
    Type: Grant
    Filed: January 18, 2016
    Date of Patent: January 22, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Dennis Lehto, Steven J. Boege
  • Patent number: 10180428
    Abstract: There is disclosed a system for electrical charge detection comprising a nanoFET device. Also disclosed is a method of electrical charge detection for single molecule sequencing. The method includes attaching a macromolecule or assemblies thereof to a gate of a nanoFET device and flowing in a solution of charge tags, where a charge tag includes a nucleotide attached to a charge complex. The method also includes incorporating one charge tag into the macromolecule or assemblies thereof and cleaving the charge tags from the macromolecule or assemblies thereof. The method further includes detecting at least one of current and voltage from the nanoFET device.
    Type: Grant
    Filed: September 24, 2015
    Date of Patent: January 15, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Mark F. Oldham, Eric S. Nordman
  • Patent number: 10181010
    Abstract: A genetic surveillance system comprises a communications network and at least one reader-analyzer instrument. The reader-analyzer instrument has a communication interface to communicate over the network. The reader-analyzer instrument is adapted to perform genetic assay analysis of a sample obtained from a member of a population and to generate detection-related data based upon the analysis. The reader-analyzer instrument is adapted to associate qualifying information with the detection-related data and to communicate the associated qualifying information and detection-related data over the network.
    Type: Grant
    Filed: December 10, 2014
    Date of Patent: January 15, 2019
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Chirag Patel, Hans Fuernkranz, Michael Greenstein
  • Patent number: 10138475
    Abstract: The present invention concerns the use of methods and compositions for the isolation of small RNA molecules (100 nucleotides or fewer), such as microRNA and siRNA molecules. Such molecules are routinely lost in commonly used isolation procedures and therefore the present invention allows for a much higher level of enrichment or isolation of these small RNA molecules.
    Type: Grant
    Filed: October 19, 2015
    Date of Patent: November 27, 2018
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: Richard Conrad
  • Publication number: 20180314788
    Abstract: Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.
    Type: Application
    Filed: April 27, 2018
    Publication date: November 1, 2018
    Applicant: Applied Biosystems, LLC
    Inventor: Francis T. Cheng
  • Patent number: 10106845
    Abstract: A two-step multiplex amplification reaction includes a first step which truncates the standard initial multiplex amplification round to “boost” the sample copy number by only a 100-1000 fold increase in the target. Following the first step the product is divided into optimized secondary single amplification reactions, each containing one of the primer sets that were used previously in the first or multiplexed booster step. The booster step can occur using an aqueous target nucleic acid or using a solid phase archived nucleic acid. In particular, nucleic acid sequences that uniquely identify E. Coli were identified using the multiplex amplification method.
    Type: Grant
    Filed: October 14, 2016
    Date of Patent: October 23, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: John Gerdes, Elaine Best, Jeffrey M. Marmaro
  • Patent number: 10041113
    Abstract: Various embodiments of the teachings relate to a system or method for sample preparation or analysis in biochemical or molecular biology procedures. The sample preparation can involve small volume processed in discrete portions or segments or slugs, herein referred to as discrete volumes. A molecular biology procedure can be nucleic acid analysis. Nucleic acid analysis can be an integrated DNA amplification/DNA sequencing procedure.
    Type: Grant
    Filed: October 28, 2015
    Date of Patent: August 7, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: Linda G. Lee, Sam L. Woo, Congcong Ma, Richard T. Reel, Mark F. Oldham, David M. Cox, Benjamin G. Schroeder, Jon M. Sorenson, Willy Wiyatno
  • Patent number: 10010887
    Abstract: An apparatus and method for rapid thermal cycling including a thermal diffusivity plate. The thermal diffusivity plate can provide substantial temperature uniformity throughout the thermal block assembly during thermal cycling by a thermoelectric module. An edge heater can provide substantial temperature uniformity throughout the thermal block assembly during thermal cycling.
    Type: Grant
    Filed: October 10, 2014
    Date of Patent: July 3, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: Hon Siu Shin, Jew Kwee Ngui, Chee Kiong Lim, Ching Ong Lau, Lim Hi Tan, Yang Hooi Kee
  • Patent number: 10011831
    Abstract: The invention relates to methods for the detection of a specific sequence of RNA in a cell or tissue sample. The invention also relates to methods to enzymatically manipulate the RNA in a crude cell lysate in a number of applications.
    Type: Grant
    Filed: March 22, 2017
    Date of Patent: July 3, 2018
    Assignee: Applied Biosystems, LLC
    Inventors: Brittan Pasloske, Quoc Hoang
  • Patent number: 10002229
    Abstract: The invention discloses a system and methods for quantitating the presence of nucleic acid sequences by evaluation of amplification data generated using real-time PCR. In one aspect, the methods may be adapted to identify a threshold and threshold cycle for one or more reactions based upon evaluation of exponential and baseline regions for each amplification reaction. The methodology used in the analysis may be readily automated such that subjective user interpretation of the data is substantially reduced or eliminated.
    Type: Grant
    Filed: October 7, 2013
    Date of Patent: June 19, 2018
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: David C. Woo, Clinton Lewis, Nasser M. Abbasi
  • Patent number: 9977860
    Abstract: Systems and methods are provided for processing a melting or dissociation curve of a DNA or other sample, for example, during PCR processing. In some embodiments, detection of the melting point and melting curve behavior can be enhanced by taking a derivative of the curve, and detecting peaks in the differential dissociation curve. In some embodiments, the derivative operation can comprise the use of edge-processing, or other detection algorithms. In some embodiments, the dissociation analysis can comprise removing low-frequency (or pedestal) components of the differential dissociation curve. In some embodiments, the differential dissociation curve can exhibit a smoothed or more regular appearance than the raw detected data.
    Type: Grant
    Filed: April 22, 2014
    Date of Patent: May 22, 2018
    Assignee: Applied Biosystems, LLC
    Inventor: Francis T. Cheng