Patents Assigned to Applied Biosystems
  • EXPRESSION SIGNATURE IN PERIPHERAL BLOOD FOR DETECTION OF AORTIC ANEURYSM
    Publication number: 20130006342
    Abstract: We hypothesized that gene expression patterns in peripheral blood cells may correlate with TAA disease status, and carried out a comprehensive gene expression survey on peripheral blood cells obtained from TAA patients and normal individuals. A distinct gene expression profile in peripheral blood cells can classify TAA patients from normal individuals. The genes provided by the present teachings define a set of diagnostic markers, thus providing a blood-based gene expression test to facilitate early detection of TAA disease. Methods of distinguishing ascending from descending TAA are also provided, as are methods of distinguishing familial from sporadic TAA.
    Type: Application
    Filed: September 12, 2012
    Publication date: January 3, 2013
    Applicant: Applied BioSystems, LLC
    Inventors: Yulei WANG, Catalin Barbacioru, Raymond R. Samaha, John A. Elefteriades
  • Preparation and isolation of 5? capped MRNA
    Patent number: 8344118
    Abstract: The synthesis of capped/tagged RNA, methods of use and kits providing same are contemplated. Tagged RNA permits isolation of RNA transcripts in vitro. The ability to isolate and purify capped RNA results in improved transcription and translation and provides a tool for identifying RNA-protein interactions. Such capped RNA finds use in therapeutic applications, diagnosis and prognosis and in the treatment of cancers and HIV.
    Type: Grant
    Filed: December 13, 2011
    Date of Patent: January 1, 2013
    Assignee: Applied Biosystems, LLC
    Inventors: Anilkumar Kore, Shanmugasundaram Muthian, Irudaya Charles
  • Sample distribution devices and methods
    Patent number: 8337777
    Abstract: A device and methods for sample distribution through a channel in which an expandable valve provides a mechanism to regulate flow through the channel. The valve may be configured to exert a force on a membrane layer so as to substantially block a portion of the channel to retain the sample in a desired location and prevent flow past the valve mechanism between the channel and a chamber.
    Type: Grant
    Filed: June 25, 2007
    Date of Patent: December 25, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: James C. Nurse, Douglas P. Greiner, Nigel P. Beard
  • Reagents, methods, and libraries for bead-based sequencing
    Patent number: 8329404
    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: March 2, 2012
    Date of Patent: December 11, 2012
    Assignee: Applied Biosystems LLC
    Inventors: Kevin McKernan, Alan Blanchard, Lev Kotler, Gina Costa
  • Multiplex amplification of polynucleotides
    Patent number: 8323897
    Abstract: The present invention provides methods, reagents and kits for carrying out a variety of assays suitable for analyzing polynucleotides or samples that include an amplification step performed in a multiplex fashion. Also provided are methods for analyzing and improving the efficiency of amplification and for carrying out gene expression analysis.
    Type: Grant
    Filed: November 26, 2003
    Date of Patent: December 4, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Mark R. Andersen, David W. Ruff
  • nucleic acid polymerases
    Patent number: 8318469
    Abstract: The invention provides nucleic acids and polypeptides for nucleic acid polymerases from a thermophilic organism, Thermus brockianus. The invention also provides methods for using these nucleic acids and polypeptides.
    Type: Grant
    Filed: December 13, 2005
    Date of Patent: November 27, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: James E. Rozzelle, Elena V. Bolchakova
  • Dissolvable valve in a fluid processing device
    Patent number: 8312890
    Abstract: A fluid processing device, system, and method for processing a fluid, are provided. The device includes a substrate, a plurality of fluid retainment regions formed in or on the substrate, and a barrier at least partially separating two or more of the fluid retainment regions, wherein the barrier can include a solvent-dissolvable, LCST-free material.
    Type: Grant
    Filed: October 18, 2005
    Date of Patent: November 20, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Aldrich N. K. Lau
  • Methods for multiplexing amplification reactions
    Patent number: 8304214
    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: November 21, 2007
    Date of Patent: November 6, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: John C. Gerdes, Elaine A. Best, Jeffrey M. Marmaro
  • Emulsion PCR and amplicon capture
    Patent number: 8293502
    Abstract: Compositions and methods of use are disclosed for clonally amplifying target polynucleotide sequences in solution and attaching the amplicons to a surface by activation of a masked binding moiety. In an embodiment, the amplicons comprise the masked binding moiety and the surface comprises a binding partner of the binding moiety. Upon activation of the binding moiety, the amplicons bind to the binding partner on the surface. In a non-limiting example, the masked binding moiety is caged biotin or caged fluorescein, while the corresponding binding partner is avidin or an anti-fluorescein antibody.
    Type: Grant
    Filed: April 14, 2011
    Date of Patent: October 23, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Benjamin Schroeder
  • Sample preparation for in situ nucleic acid analysis, methods and compositions therefor
    Patent number: 8288106
    Abstract: Sample preparation processes for in situ RNA or DNA analysis, methods and compositions therefor are provided. Processes provided herein allow DNA or RNA analysis to be carried out in the same tube or on an aliquot of the prepared sample without centrifugation or extraction. The preparation process can be carried out at room temperature in as little as seven minutes and is amenable to high throughput processing using manual or robotic platforms.
    Type: Grant
    Filed: June 10, 2011
    Date of Patent: October 16, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Richard A. Fekete, Annalee Nguyen
  • System and method for interpolative calibration
    Patent number: 8285492
    Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.
    Type: Grant
    Filed: August 3, 2009
    Date of Patent: October 9, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Stephen J. Gunstream
  • Method for measuring luminescence at a luminescence detection workstation
    Patent number: 8278114
    Abstract: A luminescence detecting apparatus and method for analyzing luminescent samples is disclosed. A detecting apparatus may be configured so that light from luminescent samples pass through a collimator, a a first lens, a filter, and a camera lens, whereupon an image is created by the optics on the charge-coupled device (CCD) camera. The detecting apparatus may further include central processing control of all operations, multiple wavelength filter wheel, and/or a robot for handling of samples and reagents.
    Type: Grant
    Filed: March 2, 2010
    Date of Patent: October 2, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Michael Gambini, Jeff Levi, John Voyta, John Atwood, Susan Atwood-Stone, legal representative, Bruce De Simas, Edward Lakatos, Israel Metal, George Sabak, Yongdong Wang
  • High density plate filler
    Patent number: 8277760
    Abstract: A filling apparatus for filling a microplate. The microplate having a plurality of wells each sized to receive an assay. The filling apparatus can comprise an assay input layer having a first surface and an opposing second surface. The assay input layer can comprise an assay input port extending from the first surface to the second surface and at least one pressure nodule extending from the second surface. An output layer can comprise a plurality of staging capillaries each having an inlet and an outlet. The output layer can further comprise a capillary plane disposed above the plurality of staging capillaries in fluid communication with the assay input port. The capillary plane can be sized to draw the assay from the assay input port to generally flood fill the plurality of staging capillaries.
    Type: Grant
    Filed: March 30, 2006
    Date of Patent: October 2, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Dennis A. Lehto
  • Method for detecting the presence of a single target nucleic acid in a sample
    Patent number: 8278071
    Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.
    Type: Grant
    Filed: August 13, 2007
    Date of Patent: October 2, 2012
    Assignees: Applied Biosystems, LLC, The United States Department of Health and Human Service
    Inventors: James F. Brown, Jonathan E. Silver
  • Signal noise reduction for imaging in biological analysis
    Patent number: 8274650
    Abstract: A system and method for characterizing contributions to signal noise associated with charge-coupled devices adapted for use in biological analysis. Dark current contribution, readout offset contribution, photo response non-uniformity, and spurious charge contribution can be determined by the methods of the present teachings and used for signal correction by systems of the present teachings.
    Type: Grant
    Filed: May 6, 2010
    Date of Patent: September 25, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Austin B. Tomaney, Mark F. Oldham
  • Internal calibration standards for electrophoretic analyses
    Patent number: 8268558
    Abstract: The present teachings relate, among other things, to polynucleotide sequencing, fragment analysis and sample/lane tracking, and to polynucleotide sequencers and analyzers that employ optical detection techniques. Embodiments of the present teachings are described which include, for example, the addition of a calibration standard to a sequencing reaction. Information such as peak spacing and peak shape can be extracted from the standard.
    Type: Grant
    Filed: September 17, 2009
    Date of Patent: September 18, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Timothy Hunkapiller, Cheryl Heiner, Curtis Gehman, James Labrenz, Shiaw-Min Chen
  • Reverse transcription primers and methods of design
    Patent number: 8268987
    Abstract: The present invention provides novel algorithms for designing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts. Such oligonucleotides are particularly useful as primers for reverse transcription. The invention also provides compositions containing oligonucleotides that do not substantially hybridize to a small group of unwanted transcripts, while hybridizing to most other transcripts.
    Type: Grant
    Filed: November 19, 2010
    Date of Patent: September 18, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Robert Setterquist, Xiaohui Wang, Xiaowei Wang
  • Modified oligonucleotides and applications thereof
    Patent number: 8268978
    Abstract: Disclosed, among other things, are primers containing certain modified nucleobases in the 3? terminal region of the primers that provide reduced formation of primer-dimers during amplification reactions, and various methods of use thereof.
    Type: Grant
    Filed: September 23, 2010
    Date of Patent: September 18, 2012
    Assignee: Applied Biosystems, LLC
    Inventors: Khairuzzaman Bashar Mullah, Zhaochun Ma
  • Systems and methods for baseline correction using non-linear normalization
    Patent number: 8265883
    Abstract: Systems and methods are provided for calibrating emission data or other information signals collected during a polymerase chain reaction (PCR), amplification reaction, assay, process, or other reaction. Calibration of multiple detectable materials can be achieved during a single cycle or run, or during a plurality of runs of the reaction. A reading from every well, container, or other support region of a sample support does not have to be taken. Interpolation can be used to determine values for emission data or other information signals that were not taken, or are unknown, using detected emission data, or other detected information signals. By calibrating the detected emission data and the interpolated data, a more accurate reading of emission data or information signal can be obtained.
    Type: Grant
    Filed: March 23, 2011
    Date of Patent: September 11, 2012
    Assignee: Applied Biosystems, LLC
    Inventor: Stephen J. Gunstream
  • Method for detecting the presence of a single target nucleic acid in a sample
    Patent number: 8257925
    Abstract: A miniaturized assembly is provided whereby a fluid sample can be divided into a plurality of sample portions in retaining wells and the sample fluid can be displaced from open ends of the wells while simultaneously being sealed in the wells. A method of dividing a fluid sample using the assembly is also provided.
    Type: Grant
    Filed: May 16, 2011
    Date of Patent: September 4, 2012
    Assignees: Applied Biosystems, LLC, The United States of America, as represented Department of Health and Human Services
    Inventors: James F. Brown, Jonathan E. Silver