Acellular Exponential Or Geometric Amplification (e.g., Pcr, Etc.) Patents (Class 435/91.2)
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Patent number: 9109264Abstract: Compositions, methods and kits for detecting viral nucleic acids. Targets that can be detected in accordance with the invention include HBV and/or HIV-1 and/or HCV nucleic acids. Particularly described are oligonucleotides that are useful as hybridization probes and amplification primers that facilitate detection of very low levels of HBV nucleic acids.Type: GrantFiled: July 6, 2010Date of Patent: August 18, 2015Assignee: Gen-Probe IncorporatedInventors: Jeffrey M. Linnen, Daniel P. Kolk, Janel M. Dockter, Damon K. Getman, Tadashi Yoshimura, Martha K. Ho-Sing-Loy, Reinhold B. Pollner, Leslie A. Stringfellow
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Patent number: 9101933Abstract: An integrated gel based microfluidic sample processing device, suitable for forensic investigations at the scene of a crime, including a substrate having a plurality of micro-channels to form at least a DNA extraction chamber in fluidic cooperation with an amplification chamber which in turn is in fluidic cooperation with a separation and detection channel. The micro-channels containing a DNA extraction material and gel based reaction reagents necessary for processing the sample. The device further having electrical contacts for coupling to an external power source and capable of inducing electro-kinetic manipulation of the gel based reagents and DNA extracted from the sample throughout the device.Type: GrantFiled: October 12, 2009Date of Patent: August 11, 2015Assignee: University of HullInventor: Stephen John Haswell
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Patent number: 9096897Abstract: The present invention features compositions and methods for quantifying detection of a target oligonucleotide in a sample in real time comprising one or more primer oligonucleotides comprising a 5? nicking enzyme recognition site and a 3?-terminal region comprising a 2?-modified nucleotide. These methods are compatible with target oligonucleotides amplified using a nicking amplification reaction.Type: GrantFiled: April 9, 2013Date of Patent: August 4, 2015Assignee: EnviroLogix Inc.Inventors: Daniel Shaffer, Stephen A. Judice
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Patent number: 9090934Abstract: The invention provides an assay method for detection and/or quantification of a plurality of nucleic acid or protein targets in a sample. In the method probes are used to associate a detectable tag sequence with each of the selected targets present in the sample. Probes or primers sufficient to identify at least 25, and preferably at least 500, different targets are used. The method involves segregating aliquots of the sample from each other and detecting the tag sequences in each aliquot.Type: GrantFiled: July 14, 2014Date of Patent: July 28, 2015Assignee: Fluidigm CorporationInventors: Michael Lucero, Marc Unger
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Patent number: 9080206Abstract: The invention generally relates to methods for detecting a target nucleic acid and a target protein in a single assay.Type: GrantFiled: August 6, 2013Date of Patent: July 14, 2015Assignee: Physicians Choice Laboratory Services, Inc.Inventors: Anthony P. Shuber, Eugene Chiu
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Patent number: 9074246Abstract: The application relates generally to methods useful for the selective amplification of one or more target nucleic acid or fragments thereof, as well as compositions and kits comprising said amplification reaction mixtures. More specifically, the application relates to a composite primer that comprises a 5? promoter portion and a 3? target-recognition portion which is complementary to the 3? end portion of a target polynucleotide sequence; and optionally, a means for identifying the 5? end portion of the target polynucleotide sequence. The amplification reaction mixture comprises at least one handle-stem-loop structure which comprises a 5? single-stranded handle comprising the promoter portion and a double-stranded stem comprising at least one pair of self-folding segments hybridized to each other, and optionally, a single-stranded loop comprising the sequence between the pair of self-folding segments.Type: GrantFiled: January 25, 2011Date of Patent: July 7, 2015Assignee: RD Biosciences, Inc.Inventor: Jingliang Ju
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Patent number: 9074248Abstract: It has been unexpectedly and surprisingly found that Helicase Dependent Amplification (HDA) primers having termini enriched for A or C at the 5?-ends, result in a much more efficient HDA reaction than those primers having G or T rich 5?-ends. Since A is a low melting base and C is a high-melting base, the melting characteristic of primer termini is not correlated with melting characteristics of amplicon termini. Optimized HDA primers, methods of making and using optimized primers, as well as methods of as well as kits for optimized HDA are disclosed.Type: GrantFiled: December 18, 2012Date of Patent: July 7, 2015Assignee: QIAGEN GMBHInventors: Christian Korfhage, Sven van Ooyen
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Patent number: 9067208Abstract: The invention relates to an apparatus for blocking nucleic acids by means of photoactivating intercalating agents, comprising: a housing (1) with an upper wall (1a) with one or more through holes (2), intended for inserting therethrough one or more test or microcentrifuge tubes (3), each of which contains a respective sample (M) including nucleic acids and photosensitive intercalating agents mixed in liquid form, and one or more LEDs (L1, L2, L3, L10, L20, L30) mounted inside the housing (1) such that they emit light, according to one or more determined directions, towards respective parts (3a, 3b and 3c) of said of tubes (3), to photoactivate the intercalating agents in order to covalently bond them to free or accessible nucleic acids.Type: GrantFiled: October 21, 2010Date of Patent: June 30, 2015Assignee: INGENIA BIOSYSTEMS, S.L..Inventors: Francesc Godony Iglesias, Jordi Morató Farreras, Didac Sánchez Solar
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Patent number: 9062336Abstract: This invention covers methods for isothermal amplification of DNA. It is based on the unexpected discovery that primers having, at some positions, adenine substituted by 2-aminopurine or diaminopurine, guanine by inosine, thymine by 2-thiothymine, and cytosine by N4-ethylcytosine (“substituted primers”) were accepted by enzymes used in the standard recombinase polymerase assay (RPA). Further unexpected was the discovery that target nucleotides are efficiently amplified in an RPA-like process (hereinafter abbreviated as simply RPA) using substituted primers. RPA-like processes were also discovered to amplify target DNA with substituted primers tagged with oligonucleotides incorporating nucleotides from an artificially expanded genetic information system (AEGIS).Type: GrantFiled: March 7, 2013Date of Patent: June 23, 2015Inventors: Steven A Benner, Nidhi Sharma
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Publication number: 20150140611Abstract: The present teachings comprise a device and method for lysing and/or purifying biological sample. The device can comprise a cartridge having a chamber containing a biological sample receiving region, a plurality of electrodes, and one or more sieving matrices. The electrodes can be configured to lyse the biological sample through the production of a pulsed electrical field. The electrodes can also be configured to heat lyse the biological sample. The electrodes can also be configured to electrophoretically move the biological sample through one or more sieving matrices. A portion of the sample can be isolated on a membrane. The portion of the sample isolated on the membrane can be amplified and detected. A portion of the sample can be isolated in a collection area present in the cartridge. The portion of the sample isolated in the collection area can be removed from the cartridge.Type: ApplicationFiled: October 20, 2014Publication date: May 21, 2015Inventors: Charles Vann, Michael Greenstein, Yuh-Min Chiang
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Publication number: 20150140567Abstract: Methods and compositions for the amplification of nucleic acids and generation of concatemers are disclosed. Amplification methods provided herein may be performed under isothermal conditions. Methods and compositions may include reagents such as nucleic acid polymerases and primers.Type: ApplicationFiled: November 18, 2014Publication date: May 21, 2015Inventors: Kamila Belhocine, Josephine Lee, Pranav Patel, Aaron Richardson, Scott Tabakman
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Patent number: 9034635Abstract: A thermocycler apparatus and method for rapidly performing the PCR process employs at least two thermoelectric modules which are in substantial spatial opposition with an interior space present between opposing modules. One or multiple sample vessels are placed in between the modules such that the vessels are subjected to temperature cycling by the modules. The sample vessels have a minimal internal dimension that is substantially perpendicular to the modules that facilitates rapid temperature cycling. In embodiments of the invention the sample vessels may be deformable between: a) a shape having a wide mouth to facilitate filling and removing of sample fluids from the vessel, and b) a shape which is thinner for conforming to the sample cavity or interior space between the thermoelectric modules of the thermocycler for more rapid heat transfer.Type: GrantFiled: February 19, 2009Date of Patent: May 19, 2015Assignee: Streck, Inc.Inventors: Joel R. Termaat, Hendrik J. Viljoen, Scott E. Whitney
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Patent number: 9034605Abstract: Modified double-stranded oligonucleotides that have terminal regions on each of their strands, that have a hybrid length of 6-50 nucleotides long, that have a melting temperature Tm of at least 32° C.Type: GrantFiled: March 11, 2010Date of Patent: May 19, 2015Assignee: Brandeis UniversityInventors: Lawrence J. Wangh, John Rice, Nicholas Rice, Yanwei Jia
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Patent number: 9034603Abstract: The present invention relates to a dried composition for hot-start PCR, more precisely a dried composition for hot-start PCR with improved stability and long-term storagability which is characteristically prepared by the steps of preparing a reaction mixture by mixing an aqueous solution containing reaction buffer, MgCl2, 4 types of dNTPs, DNA polymerase with pyrophosphate and pyrophosphatase in a reaction tube; and drying the reaction mixture prepared above, a preparation method of the same and a method for amplifying nucleic acid using the same. The dried composition for hot-start PCR is added with pyrophosphate and pyrophosphatase together before drying, so that it can have improved stability and long-term storagability as well as convenience in use, compared with the conventional compositions for hot-start PCR. Therefore, this composition can be effectively used for hot-start PCR, multiplex PCR or real-time quantitative PCR.Type: GrantFiled: October 28, 2008Date of Patent: May 19, 2015Assignee: BIONEER CORPORATIONInventors: Seong-Youl Kim, Hyun Bae Kim, Hae-Joon Park, Han Oh Park
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Patent number: 9034604Abstract: The present invention relates to a method for determining contaminations in a cell culture sample comprising the steps of: a) contacting a sample of a cell culture suspected to comprise contaminations with a composition comprising oligonucleotides under conditions which allow for amplification of polynucleotides, wherein said oligonucleotides comprise oligonucleotides of at least three different groups of oligonucleotides, and b) determining the contaminations based on the amplified polynucleotides obtained by using the oligonucleotide groups of step (a). Moreover, the invention relates to a composition comprising an oligonucleotide mixture. Further encompassed by the present invention is a composition comprising a probe oligonucleotide mixture. Finally, the present invention also relates to kits comprising said oligonucleotide mixtures.Type: GrantFiled: March 5, 2009Date of Patent: May 19, 2015Assignee: DKFZ Deutsches KrebsforschungszentrumInventors: Markus Schmitt, Michael Pawlita
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Patent number: 9034606Abstract: Methods are provided for a rapid, low cost approach to monitoring an amplification reaction. This includes monitoring the progress of isothermal or PCR amplification reactions to completion using pH-sensitive dyes that are either colored or fluorescent. Compositions are described that include a mixture of a DNA polymerase, deoxyribonucleotide triphosphate and a weak buffer of less than 1 mM Tris or equivalent or no buffer.Type: GrantFiled: March 13, 2013Date of Patent: May 19, 2015Assignee: New England Biolabs, Inc.Inventors: Nathan Tanner, Yinhua Zhang, Thomas C. Evans
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Publication number: 20150132804Abstract: The present invention relates to a device for thermal cycling of biological samples, a heat sink used in such a device and a method. The heat sink comprises a base plate designed to fit in a good thermal contact against a generally planar thermoelectric element included in the device, and a plurality of heat transfer elements projecting away from the base plate. According to the invention, the heat transfer elements of the heat sink and arranged in a non-parallel configuration with respect to each other for keeping the temperature of the base plate of the heat sink spatially uniform during thermal cycling.Type: ApplicationFiled: January 19, 2015Publication date: May 14, 2015Inventors: David Cohen, Sakari Viitamaki
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Patent number: 9029103Abstract: Provided herein is a method for sequencing a polynucleotide molecules. The method includes the steps of providing a plurality of polynucleotide molecules attached to a surface, wherein a first portion of each polynucleotide molecule is attached to a first location of the surface and a second portion of each polynucleotide molecule is attached to a second location of the surface, the relative proximity of the first and second locations being correlated with the probability that the first and second portions are paired, separating the first and second portions of the polynucleotide molecules on the surface, determining the sequences of the first and second portions of the polynucleotide molecules and comparing the relative proximities and the sequences to determine which first and second portions are paired and to determine the sequence of the target polynucleotide molecules.Type: GrantFiled: August 26, 2011Date of Patent: May 12, 2015Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Niall Anthony Gormley, Jonathan Mark Boutell
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Patent number: 9029083Abstract: The invention describes a method for isolating one or more genetic elements encoding a gene product having a desired activity, comprising the steps of: (a) compartmentalising genetic elements into microcapsules; and (b) sorting the genetic elements which express the gene product having the desired activity; wherein at least one step is under microfluidic control. The invention enables the in vitro evolution of nucleic acids and proteins by repeated mutagenesis and iterative applications of the method of the invention.Type: GrantFiled: October 10, 2005Date of Patent: May 12, 2015Assignees: Medical Research Council, President and Fellows of Harvard CollegeInventors: Andrew David Griffiths, David Weitz, Darren Link, Keunho Ahn, Jerome Bibette
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Patent number: 9023602Abstract: The present invention relates to a method for determining the presence of a cyst nematode in a sample comprising the steps of: providing a pair of bidirectional oligonucleotide primers or an oligonucleotide probe that hybridizes specifically, under stringent hybridization conditions, to a nucleic acid sequence encoding the SSU rRNA or LSU rRNA, or the complement or transcript thereof, of a sub genus-cluster of nematodes, said subgenus-cluster comprising cyst nematodes belonging to at least one species of nematode, and wherein said primers or probe do not hybridize to a nucleic acid sequence encoding the LSU rRNA, or the complement or transcript thereof, of cyst nematodes not part of said subgenus-cluster of cyst nematodes; providing a sample in which the presence of the cyst nematode is to be detected, and performing a nucleic acid detection assay on said sample using said pair of bidirectional oligonucleotide primers or said oligonucleotide probe.Type: GrantFiled: December 21, 2007Date of Patent: May 5, 2015Assignees: Wageningen Universiteit, Tree of Knowledge Patents B.V.Inventors: Johannes Helder, Gerrit Karssen, Sven Johannes Josephus van den Elsen, Martijn Hermanus Maria Holterman, Paulus Jacques Willem Mooijman, Roel Victor Staps, Renske Landeweert, Henri Hekman, Jaap Bakker
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Patent number: 9024006Abstract: A method of sample analysis is provided. In certain embodiments, the method involves: a) amplifying a product from a sample that comprises both wild type copies of a genomic locus and mutant copies of the genomic locus that have a point mutation relative to said wild type copies of the genomic locus, to produce an amplified sample, where: i. the amplifying is done using a first primer and a second primer; and ii. the first primer comprises a 3? terminal nucleotide that base pairs with the point mutation and also comprises a nucleotide sequence that is fully complementary to a sequence in the locus with the exception of a single base mismatch within 6 bases of the 3? terminal nucleotide; and b) detecting the presence of said product in said amplified sample using a flap assay that employs an invasive oligonucleotide. A kit for performing the method is also provided.Type: GrantFiled: March 14, 2014Date of Patent: May 5, 2015Assignee: Exact Sciences CorporationInventors: Hongzhi Zou, Graham P. Lidgard, Michael J. Domanico, Hatim Allawi
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Publication number: 20150118715Abstract: Methods, devices, and kits are provided for performing PCR in <20 seconds cycle, with improved efficiency and yield.Type: ApplicationFiled: May 23, 2013Publication date: April 30, 2015Applicant: University of Utah Research FoundationInventors: Carl T. Wittwer, Steven Jared Farrar
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Patent number: 9017941Abstract: A method for nucleic acid analysis including injecting a slight amount of nucleic acid sample for analysis, characterized in that most of a nucleic acid sample which is not used, excluding the slight amount of the nucleic acid sample which is used for analysis, can be obtained as a pure product which is not contaminated with a fluorescent material, and a microchip for analyzing nucleic acid which enables such method for nucleic acid analysis, are provided. The method for nucleic acid analysis may analyze at least two different nucleic acid samples in a continuous manner by sequentially injecting the at least two different nucleic acid samples.Type: GrantFiled: March 7, 2013Date of Patent: April 28, 2015Assignee: Postech Academy-Industry FoundationInventors: Jong Hoon Hahn, Byoung Joo Kwak, Han-Ok Kim
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Patent number: 9017948Abstract: The present invention generally relates to droplets and/or emulsions, such as multiple emulsions. In some cases, the droplets and/or emulsions may be used in assays, and in certain embodiments, the droplet or emulsion may be hardened to form a gel. In some aspects, a heterogeneous assay can be performed using a gel. For example, a droplet may be hardened to form a gel, where the droplet contains a cell, DNA, or other suitable species. The gel may be exposed to a reactant, and the reactant may interact with the gel and/or with the cell, DNA, etc., in some fashion. For example, the reactant may diffuse through the gel, or the hardened particle may liquefy to form a liquid state, allowing the reactant to interact with the cell. As a specific example, DNA contained within a gel particle may be subjected to PCR (polymerase chain reaction) amplification, e.g., by using PCR primers able to bind to the gel as it forms. As the DNA is amplified using PCR, some of the DNA will be bound to the gel via the PCR primer.Type: GrantFiled: February 4, 2014Date of Patent: April 28, 2015Assignee: President and Fellows of Harvard CollegeInventors: Jeremy Agresti, Liang-Yin Chu, David A. Weitz, Jin-Woong Kim, Amy Rowat, Morten Sommer, Gautam Dantas, George Church
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Patent number: 9017973Abstract: The invention provides methods and compositions, including, without limitation, algorithms, computer readable media, computer programs, apparatus, and systems for determining the identity of nucleic acids in nucleotide sequences using, for example, data obtained from sequencing by synthesis methods. The methods of the invention include correcting one or more phenomena that are encountered during nucleotide sequencing, such as using sequencing by synthesis methods. These phenomena include, without limitation, sequence lead, sequence lag, spectral crosstalk, and noise resulting from variations in illumination and/or filter responses.Type: GrantFiled: November 28, 2011Date of Patent: April 28, 2015Assignee: Intelligent BioSystems, Inc.Inventors: Steven Gordon, Jerzy Olejnik
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Patent number: 9017947Abstract: The present invention provides for soybean plant and seed comprising transformation event MON89788 and DNA molecules unique to these events. The invention also provides methods for detecting the presence of these DNA molecules in a sample.Type: GrantFiled: August 19, 2011Date of Patent: April 28, 2015Assignee: Monsanto Technology LLCInventors: Marianne Malven, Jennifer Rinehart, Nancy Taylor, Ellen Dickinson
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Patent number: 9017971Abstract: The invention provides improved methods for investigating nucleic acid sequences, wherein at least one additional probe is used which is specific for a (pseudo)gene variant of a target nucleic acid.Type: GrantFiled: November 5, 2009Date of Patent: April 28, 2015Assignee: Stichting Sanquin BloedvoorzieningInventors: Taco Willem Kuijpers, Martin de Boer
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Patent number: 9017970Abstract: The present invention relates to the discovery of RNA 5? polyphosphatase enzymes not previously described in the art, methods for discovery of said enzymes, compositions of said enzymes, methods for making said enzymes, and various methods and kits for using said enzymes for biomedical research, for human and non-human diagnostics, for production of therapeutic products, and for other applications. In particular, some embodiments provide compositions, kits and methods for employing RNA polyphosphatases for isolation, purification, production, and assay of capped RNA using a biological sample or a sample from an in vitro capping reaction wherein the sample also contains RNA that is not capped. Other embodiments provide compositions, kits and methods wherein RNA polyphosphatases comprise signal-amplifying enzymes for analyte-specific assays.Type: GrantFiled: May 4, 2009Date of Patent: April 28, 2015Assignee: CellScript, LLCInventors: Jerome J. Jendrisak, Ramesh Vaidyanathan, Ronald Meis
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Patent number: 9017972Abstract: The present invention relates to a method, in particular an in vitro method for identifying FoxP3-positive CD25+CD4+ regulatory T cells of a mammal, comprising analyzing the methylation status of at least one CpG position in the FOXP3 gene, in particular its “upstream” regulatory regions, and in particular the promoter and the TSDR region of the gene foxp3, wherein a demethylation to at least 90% of at least one CpG in the sample as analyzed is indicative for a FoxP3-positive CD25+CD4+ regulatory T cell, and the use of said DNA-methylation analysis of the gene of the transcription factor FoxP3 for a detection and quality assurance and control of regulatory T cells. Furthermore, the present invention relates to a kit for performing the above methods as well as respective uses.Type: GrantFiled: July 2, 2009Date of Patent: April 28, 2015Inventor: Ivana Türbachova
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Publication number: 20150111256Abstract: Methods and compositions for synthesizing nucleic acid sequences in an emulsion are provided.Type: ApplicationFiled: February 14, 2013Publication date: April 23, 2015Inventors: George M. Church, Richard C. Terry, Sriram Kosuri, Di Zhang
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Publication number: 20150111257Abstract: A thermal cycling apparatus having a sample interfacing wall extending from a mounting wall. The sample interfacing wall can accept and apply thermal cycles to samples. An air source can direct an air stream to cool the sample. Another source can direct heated air away from the sample.Type: ApplicationFiled: May 15, 2013Publication date: April 23, 2015Inventor: Doug Dority
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Patent number: 9012208Abstract: A self-contained apparatus for isolating nucleic acid, cell lysates and cell suspensions from unprocessed samples apparatus, to be used with an instrument, includes at least one input, and: (i) a macrofluidic component, including a chamber for receiving an unprocessed sample from a collection device and at least one filled liquid purification reagent storage reservoir; and (ii) a microfluidic component in communication with the macrofluidic component through at least one microfluidic element, the microfluidic component further comprising at least one nucleic acid purification matrix; and (iii) at least one interface port to a drive mechanism on the instrument for driving said liquid purification reagent, through the microfluidic element and the nucleic acid purification matrix, wherein the only inputs to the apparatus are through the chamber and the interface port to the drive mechanism.Type: GrantFiled: February 3, 2010Date of Patent: April 21, 2015Assignee: NetBio, Inc.Inventors: Richard F. Selden, Eugene Tan
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Patent number: 9012183Abstract: A method of preparing a DNA copy of a target polynucleotide using template switching is described. The method includes mixing a double stranded template/primer substrate made up of a DNA primer oligonucleotide associated with a complementary oligonucleotide template strand with a target polynucleotide in a reaction medium and adding a suitable amount of a non-retroviral reverse transcriptase to the reaction medium to extend the DNA primer oligonucleotide from its 3? end to provide a DNA copy polynucleotide. The DNA copy polynucleotide includes a complementary target DNA polynucleotide that is synthesized using the target polynucleotide as a template. Methods of adding nucleotides to the double stranded template/primer substrate are also described. The method can be used to facilitate detection, PCR amplification, cloning, and determination of RNA and DNA sequences.Type: GrantFiled: February 23, 2012Date of Patent: April 21, 2015Assignee: Board of Regents, The University of Texas SystemInventors: Alan M. Lambowitz, Sabine Mohr, Travis B. White, Scott Kuersten
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Patent number: 9012184Abstract: The invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides and also the use of the 5? and 3? modified library of templates in methods of solid-phase nucleic acid amplification. In particular, the invention relates to a method of preparing a 5? and 3? modified library of template polynucleotides which have common sequences at their 5? ends and at their 3? ends, wherein over-representation of “end” sequences of the primary polynucleotide molecules from when the 5? and 3? modified library is generated is greatly reduced or prevented.Type: GrantFiled: February 7, 2007Date of Patent: April 21, 2015Assignee: Illumina Cambridge LimitedInventors: Roberto Rigatti, Niall Anthony Gormley, Helen Rachel Bignell
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Patent number: 9012185Abstract: The invention provides systems, devices, and methods for heating and cooling chemical or biological samples, such as genetic materials during Polymerase Chain Reaction (“PCR”). The systems, devices, and methods comprise use of a fluid that performs repeated heating and cooling cycles, e.g., ‘thermal cycling’, on sample reactants with a phase changing fluid during evaporation and condensation. The systems, devices, and methods eliminate the need for a heating block as a means to obtain fast and uniform thermal cycling. The disclosure also describes the use of an optical system in conjunction with the thermodynamic cycler for real-time detection. Ultimately, uniformity and speed of the thermodynamic cycler provides for higher sensitivity and throughput of gene replication and detection.Type: GrantFiled: November 28, 2012Date of Patent: April 21, 2015Assignee: Pyro-E, LLCInventor: Rui Zhang
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Patent number: 9012142Abstract: A method for detecting the presence of a target nucleotide sequence in a sample of DNA is described herein in which a test sample comprising single stranded DNA is exposed to a DNA probe and a nicking endonuclease under conditions that would permit sequence-specific hybridization of the probe to a complementary target sequence. The probe comprises a sequence complementary to the target sequence to be detected and this sequence also includes a recognition sequence for the nicking endonuclease. If the sample contains the target sequence, the probe hybridizes to the target and is cleaved by the nicking endonuclease, which leaves the target intact. Observing the presence of probe cleaved by the nicking endonuclease indicates the presence of the target nucleotide sequence in the sample of DNA.Type: GrantFiled: February 15, 2006Date of Patent: April 21, 2015Assignee: Georgetown UniversityInventors: Mark Danielsen, Eugene A. Davidson, Kenneth L. Dretchen, Traci K. Pals
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Patent number: 9012149Abstract: Improved methods that increase the specificity and sensitivity of detection of small RNAs, including miRNAs, using oligonucleotide primers and nucleic acid amplification, are provided. Reaction conditions that result in preferential decrease in cDNA synthesis of RNAs other than the small RNA molecules targeted for detection during miRNA tailing and reverse transcription reactions are described. Using these reaction conditions greater sensitivity and specificity of amplification of small RNAs including miRNAs is achieved.Type: GrantFiled: January 18, 2013Date of Patent: April 21, 2015Assignee: QIAGEN Sciences LLCInventors: Daniel Y. Kim, Yexun Wang
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Patent number: 9005931Abstract: A programmable probe design of DNA micro array and detection methodology is provided. DNA probes, which are complemented with the target DNA, are designed and classified into groups according to optimum hybridization temperature. The probes are arrayed by the group and immobilized on the substrate surface of the DNA micro array. The control system, imaging system and temperature control system are programmed to cooperate with each other during the detection process. This design increases the detection capabilities of the parallel-analysis system.Type: GrantFiled: December 24, 2007Date of Patent: April 14, 2015Assignee: Honeywell International Inc.Inventors: Zhenhong Sun, Wendy Wang, Hang Liao
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Patent number: 9005933Abstract: The present invention relates to a method for amplifying a template nucleic acid, wherein the method comprises amplifying said template nucleic acid using the helicase dependent amplification (HDA) reaction in the presence of a nicking endonuclease, and wherein said template nucleic acid comprises a sequence recognized by said nicking endonuclease or a sequence recognized by said nicking endonuclease is introduced into the template nucleic acid during the HDA reaction. The invention further pertains to a kit for amplifying a nucleic acid, comprising a nicking endonuclease, a helicase and a DNA polymerase.Type: GrantFiled: August 16, 2011Date of Patent: April 14, 2015Assignee: Qiagen GmbHInventors: Christian Korfhage, Gerd Grosshauser, Thomas Rothmann, Ralf Himmelreich
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Patent number: 9005891Abstract: The invention relates to methods of depleting RNA from a nucleic acid sample. The RNA may be any RNA, including, but not limited to, rRNA, tRNA, and mRNA. The method is useful for depleting RNA from a nucleic acid sample obtained from a fixed paraffin-embedded tissue (FPET) sample. The method may also be used to prepare cDNA, in particular, a cDNA library for further analysis or manipulation.Type: GrantFiled: November 5, 2010Date of Patent: April 14, 2015Assignee: Genomic Health, Inc.Inventors: Dominick Sinicropi, John Morlan
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Patent number: 9005894Abstract: Disclosed is a method of determining KIR genotypes for one or more individuals in parallel, the method comprising: for each individual, amplifying the polymorphic exon sequences of the KIR genes, pooling the KIR amplicons, performing emulsion PCR followed by pyrosequencing in parallel to determine all the amplicon sequences present in the individual to determine which KIR alleles are present in the individual.Type: GrantFiled: September 17, 2010Date of Patent: April 14, 2015Assignees: Roche Molecular Systems, Inc., Childrens Hospital & Research Center at Oakland, Conexio Genomics Pty LtdInventors: Martha Ladner, Elizabeth Trachtenberg, Lloyd Gordon Bentley, Damian Goodridge, Henry A. Erlich
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Patent number: 9005932Abstract: A method for analysing genetic mutations, and in particular single nucleotide polymorphisms (SNPs) and/or somatic mutations, is described, as well as methods for preferentially amplifying one allelic form compared with another form. The methods use an oligonucleotide probe which hybridises to a first allele with a lower melting temperature (Tm) than that with which it hybridises to a second allele, together with amplification primers which flank the oligonucleotide probe binding site and which bind to the sample with a higher Tm than that of the probe and the first allele. An amplification reaction may be carried out at a temperature such that the probe is preferentially hybridised to the second allele, thereby amplifying the first allele. The amplified sequences may be detected using the same probe as acted as the blocking probe during amplification.Type: GrantFiled: January 6, 2012Date of Patent: April 14, 2015Assignee: Epistem LimitedInventor: Ben Cobb
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Publication number: 20150099659Abstract: Methods and reagents suitable for conducing polymerase chain reaction are described. In particular, the disclosure provides probes and primers that are suitable in dynamic flux amplification procedures. In aspects, the disclosure provides long oligonucleotide probes and primers, as well as triplex forming probes and primers, which function within the narrow Tm ranges used with dynamic flux amplification. However, embodiments are also provided wherein the probes and primers taught herein can be utilized in standard PCR.Type: ApplicationFiled: October 9, 2014Publication date: April 9, 2015Inventor: Brian Caplin
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Publication number: 20150099279Abstract: A nucleic acid amplification method includes: adsorbing a nucleic acid onto fine particles by mixing a chaotropic substance-containing adsorbent liquid and the fine particles with a nucleic acid-containing sample; washing the fine particles adsorbing the nucleic acid with a first washing liquid; eluting the nucleic acid adsorbed to the fine particles in an eluate; and performing a nucleic acid amplification reaction on the nucleic acid in the eluate. The adsorbent liquid contains an alcohol, and the first washing liquid is acidic. This method can be carried out by a nucleic acid extraction device, a nucleic acid amplification reaction cartridge, and a nucleic acid amplification reaction kit.Type: ApplicationFiled: October 8, 2014Publication date: April 9, 2015Inventors: Kiyohito YAMADA, Masato HANAMURA, Yuji SAITO
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Publication number: 20150099642Abstract: The present invention is directed to methods for capturing, amplifying and identifying one or more of a plurality of target nucleotide sequences in a sample. The present invention is further directed to a device comprising a solid support having a plurality of wells or pillars and a plurality of oligonucleotides attached to the wells or pillars. Other aspects of the invention are directed to methods of making such devices.Type: ApplicationFiled: July 23, 2012Publication date: April 9, 2015Applicants: Board of Supervisors of Louisiana State University and Agricultural and Mechanical College, CORNELL UNIVERSITYInventors: Francis A. Barany, Steven A. Soper, George Grills, Yu-wei Cheng, Jianmin Huang, Malgorzata A. Witek, Daniel San-won Park, Michael C. Murphy, Robin Lindsey McCarley, Mateusz L. Hupert
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Patent number: 8999677Abstract: Objective of the present invention is to provide a method for keeping of directional information in double-stranded DNA. We suggest to convert polynucleotide into a hybrid double-stranded DNA. One particular strand of this hybrid double-stranded DNA should be synthesized using at least one modified nucleotide. Thus, this particular strand would contain modified nucleotides along the whole length. Density of directional markers would not depend on the length of polynucleotides. Any internal fragments of the hybrid double-stranded DNA would have directional information. When it is necessary the modified strand may be easily degraded or separated from the other strand. It was found that such hybrid double-stranded DNA may be easily generated in a number of molecular biology tasks and may be used for molecular cloning, library preparation and strand separation.Type: GrantFiled: November 18, 2014Date of Patent: April 7, 2015Assignee: Max-Planck Gesellschaft zur Förderung der Wissenschaften e.V.Inventors: Aleksey Soldatov, Tatiana Borodina, Hans Lehrach
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Patent number: 8999673Abstract: Provided is a method for selectively obtaining, for a given target gene, a “joined DNA fragment” wherein just a target gene fragment is joined with desired other DNA fragments, regardless of whether a DNA fragment containing a target gene sequence has been purified. In the provided method, a double-stranded joining DNA fragment containing a sequence A and/or a sequence B is selectively joined to the ends of a target gene fragment. A mixture of a double-stranded gene fragment, the 3? end of which is protruding, and the double-stranded joining DNA fragment, which are related in a prescribed manner, undergoes at least two cycles of thermal denaturation, reassociation, and DNA synthesis, resulting in a “joined DNA fragment,” which is a double-stranded DNA fragment including at least one instance of a sequence resulting from joining sequence A, the target gene sequence, and sequence B. A “single-side joined DNA fragment” can also be obtained, by a similar method.Type: GrantFiled: September 2, 2010Date of Patent: April 7, 2015Assignee: National University Corporation University of ToyamaInventors: Nobuyuki Kurosawa, Masaharu Isobe
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Patent number: 8999648Abstract: A system (100) for classifying a biological test sample, including a database (112) populated with reference expression data. The reference expression data includes expression levels of a plurality of molecules (polynucleotides or polypeptides), including a set of marker molecules, in a plurality of reference samples. Each reference sample has a pre-assigned value for each of one or more clinically significant variables. The system includes at least one processor (110) and at least one storage medium containing program instructions for execution by said processor (110). The program instructions cause the processor to accept (122) input expression data including a test vector of expression levels of the marker molecules in the biological test sample; and pass the input expression data to one or more analysis programs (130a, 130b, 35).Type: GrantFiled: September 30, 2010Date of Patent: April 7, 2015Assignee: Signal Genetics, Inc.Inventor: Ryan Van Laar
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Patent number: 8999676Abstract: Provided are compositions comprising recombinant DNA polymerases that include amino acid substitutions, insertions, deletions, and/or exogenous features that confer modified properties upon the polymerase for enhanced single molecule sequencing. Such properties can include enhanced metal ion coordination, reduced exonuclease activity, reduced reaction rates at one or more steps of the polymerase kinetic cycle, decreased branching fraction, altered cofactor selectivity, increased yield, increased thermostability, increased accuracy, increased speed, increased readlength, and the like. Also provided are nucleic acids which encode the polymerases with the aforementioned phenotypes, as well as methods of using such polymerases to make a DNA or to sequence a DNA template.Type: GrantFiled: July 5, 2011Date of Patent: April 7, 2015Assignee: Pacific Biosciences of California, Inc.Inventors: Robin Emig, Lei Jia, Satwik Kamtekar, Erik Miller, Colleen Cutcliffe, Walter Lee
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Patent number: 8999675Abstract: Nucleic acid assays for detecting nucleic acids of Dengue virus serotypes 1-4 derived from 5? NTR.Type: GrantFiled: August 31, 2010Date of Patent: April 7, 2015Assignee: Gen-Probe IncorporatedInventors: James M. Carrick, Jeffrey M. Linnen