Patents Assigned to Applied Biosystems, LLC.
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Patent number: 9492820Abstract: A filling apparatus for filling a microplate. The microplate can comprise a plurality of wells each sized to receive an assay. A substrate can comprise a first surface and an opposing second surface, a first assay input port for receiving the assay disposed on the first surface, a plurality of staging capillaries extending through the substrate, and a first plurality of microfluidic channels fluidly coupling the first assay input port with at least one of the plurality of staging capillaries. Each of the plurality of staging capillaries can comprise an inlet and an outlet and be sized to receive the assay.Type: GrantFiled: April 2, 2015Date of Patent: November 15, 2016Assignee: Applied Biosystems, LLCInventors: Mark T. Reed, Albert L. Carrillo, Ian A. Harding
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Patent number: 9481909Abstract: 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: GrantFiled: June 19, 2015Date of Patent: November 1, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventors: Jaiprakash Shewale, Manohar Furtado, Pius Brzoska, Maura Barbisin, Rixun Fang, Michael Malicdem, Cristin O'Shea
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Patent number: 9481907Abstract: 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: GrantFiled: June 12, 2014Date of Patent: November 1, 2016Assignee: Applied Biosystems, LLCInventors: John C. Gerdes, Elaine Best, Jeffrey M. Marmaro
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Patent number: 9482652Abstract: 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: GrantFiled: September 10, 2013Date of Patent: November 1, 2016Assignee: Applied Biosystems, LLCInventors: Bruce E. DeSimas, Leslie A. Dow
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Patent number: 9468927Abstract: 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: GrantFiled: April 8, 2013Date of Patent: October 18, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventors: Alexander Dromaretsky, Thomas C. Au
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Patent number: 9464315Abstract: 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: GrantFiled: March 25, 2013Date of Patent: October 11, 2016Assignee: Applied Biosystems, LLCInventors: Gary Latham, Xingwang Fang, Richard Conrad, Jon Kemppainen, Robert Setterquist, Brittan Pasloske
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Patent number: 9464320Abstract: 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: GrantFiled: April 27, 2012Date of Patent: October 11, 2016Assignee: Applied Biosystems, LLCInventors: 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
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Patent number: 9457351Abstract: 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: GrantFiled: March 12, 2014Date of Patent: October 4, 2016Assignee: Applied Biosystems, LLCInventors: Lim Hi Tan, Jew Kwee Ngui, Hon Siu Shin, Ui Leng Soh, Yang Hooi Kee, Hock Lai Khoo, Mark T. Reed, Wolfgang Heimberg
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Patent number: 9448103Abstract: 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: GrantFiled: October 9, 2015Date of Patent: September 20, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventor: Steven J. Boege
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Patent number: 9434982Abstract: 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: GrantFiled: July 2, 2015Date of Patent: September 6, 2016Assignee: Applied Biosystems LLCInventors: Muhammad A. Sharaf, Timothy Woudenberg, Khairuzzaman Bashar Mullah
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Patent number: 9422603Abstract: 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: GrantFiled: February 20, 2015Date of Patent: August 23, 2016Assignee: Applied Biosystems, LLCInventors: Kai Qin Lao, Neil A. Straus
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Patent number: 9416406Abstract: 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: GrantFiled: December 15, 2014Date of Patent: August 16, 2016Assignee: Applied Biosystems, LLCInventor: R. Scott Kuersten
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Patent number: 9416412Abstract: 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: GrantFiled: March 12, 2015Date of Patent: August 16, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventors: James Rozzelle, Elena Bolchakova
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Patent number: 9410889Abstract: 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: GrantFiled: June 9, 2006Date of Patent: August 9, 2016Assignee: Applied Biosystem, LLCInventors: Eric S. Nordman, Mark F. Oldham, Timothy Woudenberg
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Patent number: 9404155Abstract: 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: GrantFiled: April 11, 2013Date of Patent: August 2, 2016Assignee: Applied Biosystems, LLCInventor: Scott Bortner
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Patent number: 9394557Abstract: 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: GrantFiled: December 20, 2013Date of Patent: July 19, 2016Assignee: Applied Biosystems, LLCInventor: Will Bloch
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Patent number: 9382522Abstract: 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: GrantFiled: August 19, 2009Date of Patent: July 5, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventors: Elena V. Bolchakova, James E. Rozzelle
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Patent number: 9347963Abstract: 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: GrantFiled: April 21, 2011Date of Patent: May 24, 2016Assignee: Applied Biosystems, LLCInventors: Jessica E. Barzilai, Donald R. Sandell
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Patent number: 9309560Abstract: Methods for producing a paired tag from a nucleic acid sequence are provided in which the paired tag comprises the 5? end tag and 3? end tag of the nucleic acid sequence. In one embodiment, the nucleic acid sequence comprises two restriction endonuclease recognition sites specific for a restriction endonuclease that cleaves the nucleic acid sequence distally to the restriction endonuclease recognition sites. In another embodiment, the nucleic acid sequence further comprises restriction endonuclease recognition sites specific for a rare cutting restriction endonuclease. Methods of using paired tags are also provided. In one embodiment, paired tags are used to characterize a nucleic acid sequence. In a particular embodiment, the nucleic acid sequence is a genome. In one embodiment, the characterization of a nucleic acid sequence is karyotyping. Alternatively, in another embodiment, the characterization of a nucleic acid sequence is mapping of the sequence.Type: GrantFiled: May 19, 2009Date of Patent: April 12, 2016Assignee: Applied Biosystems, LLCInventors: Douglas R. Smith, Joel A. Malek, Kevin J. McKernan
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Patent number: 9310301Abstract: 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: GrantFiled: May 10, 2012Date of Patent: April 12, 2016Assignee: APPLIED BIOSYSTEMS, LLCInventors: Donald Sandell, Eugene Young, Steven Boege