Patents Assigned to Applied Biosystems, LLC.
  • Reagents, methods, and libraries for bead-based sequencing
    Patent number: 9493830
    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. The invention further provides sets of labeled extension probes containing phosphorothiolate linkages.
    Type: Grant
    Filed: October 18, 2013
    Date of Patent: November 15, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Multiplex compositions and methods for quantification of human nuclear DNA and human male DNA and detection of PCR inhibitors
    Patent number: 9481909
    Abstract: The invention relates to a method for simultaneous quantification of human nuclear DNA and human male DNA in a biological sample while also detecting the presence of PCR inhibitors in a single reaction. The multiplex quantification method also provides a ratio of human nuclear and male DNA present in a biological sample. Such sample characterization is useful for achieving efficient and accurate results in downstream molecular techniques such as genotyping.
    Type: Grant
    Filed: June 19, 2015
    Date of Patent: November 1, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Jaiprakash Shewale, Manohar Furtado, Pius Brzoska, Maura Barbisin, Rixun Fang, Michael Malicdem, Cristin O'Shea
  • Method of automated calibration and diagnosis of laboratory instruments
    Patent number: 9482652
    Abstract: Method and system providing an automated workflow for installing and/or calibrating laboratory equipment. The workflow empowers an end user to perform installation and calibration thereby reducing the costs associated with such activities. The automated workflow taught herein, can greatly reduce the incidence of calibration error by providing for verification of certain events during the calibration process.
    Type: Grant
    Filed: September 10, 2013
    Date of Patent: November 1, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Bruce E. DeSimas, Leslie A. Dow
  • Methods for multiplexing amplification reactions
    Patent number: 9481907
    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: June 12, 2014
    Date of Patent: November 1, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: John C. Gerdes, Elaine Best, Jeffrey M. Marmaro
  • Cooling in a thermal cycler using heat pipes
    Patent number: 9468927
    Abstract: A device for amplifying a nucleic acid sample may include a sample holder configured to receive a nucleic acid sample, a heating system configured to raise the temperature of the sample, a cooling system configured to lower the temperature of the sample, and a controller configured to operably control the heating system and the cooling system to cycle the device through a desired time-temperature profile. The cooling system may include at least one heat pipe and a heat sink and the at least one heat pipe may include a first portion disposed proximate to the sample holder and a second portion disposed proximate to the heat sink.
    Type: Grant
    Filed: April 8, 2013
    Date of Patent: October 18, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Alexander Dromaretsky, Thomas C. Au
  • Modified surfaces as solid supports for nucleic acid purification
    Patent number: 9464315
    Abstract: The invention relates to methods of separating polynucleotides, such as DNA, RNA and PNA, from solutions containing polynucleotides by reversibly binding the polynucleotides to a solid surface, such as a magnetic microparticle.
    Type: Grant
    Filed: March 25, 2013
    Date of Patent: October 11, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Gary Latham, Xingwang Fang, Richard Conrad, Jon Kemppainen, Robert Setterquist, Brittan Pasloske
  • Methods for placing, accepting, and filling orders for products and services
    Patent number: 9464320
    Abstract: Methods and systems for ordering assays which detect SNPs or gene expression are provided. The methods use PCR and RT-PCR procedures. Collections of stock assays are assembled using pre- and post-manufacturing quality control procedures and made available to consumers via the Internet. In addition, custom assays are prepared upon order from the consumer and these assays are also prepared using pre- and post-manufacturing quality control procedures. The assays are then delivered to the consumer.
    Type: Grant
    Filed: April 27, 2012
    Date of Patent: October 11, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Ryan T. Koehler, Kenneth J. Livak, Junko Stevens, Francisco M. De La Vega, Michael Rhodes, Laurent R. Bellon, Julie Williams, Dawn Madden, Dennis A. Gilbert, Yu N. Wang, Eugene G. Spier, Xiaoqing You, Lily Xu, Jeremy Heil, Stephen Glanowski, Emily S. Winn-Deen, Ivy McMullen, Leila G. Smith
  • Device for carrying out chemical or biological reactions
    Patent number: 9457351
    Abstract: The invention relates to a device for carrying out of chemical or biological reactions with a reaction vessel receiving element for receiving a microtiter plate with several reaction vessels, wherein the reaction vessel receiving element has several recesses arranged in a regular pattern to receive the respective reaction vessels, a heating device for heating the reaction vessel receiving element, and a cooling device for cooling the reaction vessel. The invention is characterized by the fact that the reaction vessel receiving element is divided into several segments. The individual segments are thermally decoupled from one another, and each segment is assigned a heating device which may be actuated independently of the others. By means of the segmentation of the reaction vessel receiving element, it is possible for zones to be set and held at different temperatures.
    Type: Grant
    Filed: March 12, 2014
    Date of Patent: October 4, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Lim Hi Tan, Jew Kwee Ngui, Hon Siu Shin, Ui Leng Soh, Yang Hooi Kee, Hock Lai Khoo, Mark T. Reed, Wolfgang Heimberg
  • Achromatic lens array
    Patent number: 9448103
    Abstract: A luminescence detection system may include an excitation light source, a single element achromat, and a detector. The single element achromat may be configured to regulate the excitation light from the light source and direct the regulated light to a target, and the detector may be configured to detect luminescence generated by the target. The single element achromat may be configured to regulate the emission light from the target and direct the regulated light to a detector, and the excitation light source may be configured to direct the excitation light to the target. The single element achromat may be configured to regulate both the excitation light from the light source and the emission light from the target and direct the regulated light to, respectively, the target and a detector.
    Type: Grant
    Filed: October 9, 2015
    Date of Patent: September 20, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventor: Steven J. Boege
  • Methods of detecting target nucleic acids
    Patent number: 9434982
    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: July 2, 2015
    Date of Patent: September 6, 2016
    Assignee: Applied Biosystems LLC
    Inventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
  • Analyzing messenger RNA and micro RNA in the same reaction mixture
    Patent number: 9422603
    Abstract: The present teachings provide methods, compositions, and kits for performing primer extension reactions on at least two target polynucleotides in the same reaction mixture. In some embodiments, a reverse transcription reaction is performed on a first target polynucleotide with a hot start primer comprising a self-complementary stem and a loop, and extension products form at high temperatures but extension products form less so at low temperatures since the self-complementary stem of the hot start primer prevents hybridization of the target specific region to the target. However, non-hot start primers with free target specific regions can hybridize to their corresponding targets at the low temperature and extension can happen at the low temperature.
    Type: Grant
    Filed: February 20, 2015
    Date of Patent: August 23, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Kai Qin Lao, Neil A. Straus
  • nucleic acid polymerases
    Patent number: 9416412
    Abstract: The invention provides novel nucleic acid polymerases from strains GK24 and RQ-1 of Thermus thermophilus, and nucleic acids encoding those polymerases, as well as methods for using the polymerases and nucleic acids.
    Type: Grant
    Filed: March 12, 2015
    Date of Patent: August 16, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: James Rozzelle, Elena Bolchakova
  • Amplification and detection of ribonucleic acids
    Patent number: 9416406
    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: December 15, 2014
    Date of Patent: August 16, 2016
    Assignee: Applied Biosystems, LLC
    Inventor: R. Scott Kuersten
  • Method and system for multiplex genetic analysis
    Patent number: 9410889
    Abstract: The present disclosure provides apparatus, systems and method for detecting separately and substantially simultaneously light emissions from a plurality of localized light-emitting analytes. A system according to exemplary embodiments of the present disclosure comprises a sample holder having structures formed thereon for spatially separating and constraining a plurality of light-emitting analytes each having a single nucleic acid molecule or a single nucleic acid polymerizing enzyme, a light source configured to illuminate the sample holder, an optical assembly configured to collect and detect separately and substantially simultaneously light emissions associated with the plurality of light emitting analytes. The system may further include a computer system configured to analyze the light emissions to determine the structures or properties of a target nucleic acid molecule associated with each analyte.
    Type: Grant
    Filed: June 9, 2006
    Date of Patent: August 9, 2016
    Assignee: Applied Biosystem, LLC
    Inventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
  • Alternative nucleic acid sequencing methods
    Patent number: 9404155
    Abstract: Embodiments are provided that provide for parallel sequencing of nucleic acid segments. In some embodiments, a single sequence is sequenced by at least two different sequencing techniques and the results compared, allowing for deficiencies or strengths of one technique to be complemented by the second technique.
    Type: Grant
    Filed: April 11, 2013
    Date of Patent: August 2, 2016
    Assignee: Applied Biosystems, LLC
    Inventor: Scott Bortner
  • Linear amplification of short nucleic acids
    Patent number: 9394557
    Abstract: The present teachings provide novel methods for amplifying short nucleic acids. In some embodiments, the present teachings provide novel methods for linearly amplifying a collection of micro RNAs by using temperature cycling during a reverse transcription reaction. The cycling can comprise at least 20 cycles of an annealing temperature segment of 10° C.-30° C., and a denaturation temperature segment of 35° C.-60° C. In some embodiments, the temperature cycled reaction can comprise an osmolyte.
    Type: Grant
    Filed: December 20, 2013
    Date of Patent: July 19, 2016
    Assignee: Applied Biosystems, LLC
    Inventor: Will Bloch
  • nucleic acid polymerases
    Patent number: 9382522
    Abstract: The invention provides nucleic acids and polypeptides for a nucleic acid polymerase from a thermophilic organism, Thermus scotoductus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Grant
    Filed: August 19, 2009
    Date of Patent: July 5, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Elena V. Bolchakova, James E. Rozzelle
  • Apparatus and method for transporting sample well trays
    Patent number: 9347963
    Abstract: An apparatus for transporting sample well trays with respect to a heating device is provided. The apparatus includes a sample well tray holder, a rotational actuator, and a biasing mechanism. The sample well tray holder includes a plate in which a sample well tray may be positioned. The sample well tray holder is configured to rotate about a first rotational axis. The rotational actuator is configured to rotate the sample well tray holder about the first rotational axis. The biasing mechanism is configured to urge the sample well tray holder in a generally upward direction along the first rotational axis.
    Type: Grant
    Filed: April 21, 2011
    Date of Patent: May 24, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Jessica E. Barzilai, Donald R. Sandell
  • Methods and kits using extended rhodamine dyes
    Patent number: 9309561
    Abstract: Extended rhodamine compounds exhibiting favorable fluorescence characteristics having the structure are disclosed. In addition, novel intermediates for synthesis of these dyes are disclosed, such intermediates having the structure In addition, methods of making and using the dyes as fluorescent labels are disclosed.
    Type: Grant
    Filed: December 5, 2013
    Date of Patent: April 12, 2016
    Assignee: Applied Biosystems, LLC
    Inventors: Joe Y. L. Lam, Scott C. Benson, Steven M. Menchen
  • Lens assembly for biological testing
    Patent number: 9310301
    Abstract: The invention relates to an optical detection system for a thermal cycling device including at least one light source, a light detection device for detecting light received from a plurality of biological samples, and a lens having first and second surfaces formed on the lens, the second surface substantially opposed to the first surface. The first surface may be configured to collimate light and the second surface may be configured to direct light into each of the plurality of biological samples.
    Type: Grant
    Filed: May 10, 2012
    Date of Patent: April 12, 2016
    Assignee: APPLIED BIOSYSTEMS, LLC
    Inventors: Donald Sandell, Eugene Young, Steven Boege