Patents Examined by David Thomas
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Patent number: 9145589Abstract: 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. A plurality of smaller flow cells is employed, each with a relatively small area to be imaged, in order to provide greater flexibility and efficiency.Type: GrantFiled: August 19, 2014Date of Patent: September 29, 2015Assignee: Intelligent Biosystems, Inc.Inventors: Steven Gordon, Thomas Hagerott, Edmund Golaski, Jerzy Olejnik
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Patent number: 9146248Abstract: A method for operating a nucleic acid sequencing instrument with movable flow cells. The method includes providing a flow cell having a flow path with an inlet port and an outlet port and filling the flow path, from the inlet port to the outlet port, with a first liquid reagent. The method also includes providing a station block having an inlet passage and an outlet passage, mounting the flow cell on the station block with the inlet port in fluid communication with the inlet passage and the outlet port in fluid communication with the outlet passage, introducing a gaseous bubble into the inlet port, conveying a second liquid reagent from the inlet passage into the inlet port to move the gaseous bubble through the flow path and into the outlet passage and fill the flow passage with the second liquid reagent, and removing the flow cell from the station block.Type: GrantFiled: March 14, 2013Date of Patent: September 29, 2015Assignee: Intelligent Bio-Systems, Inc.Inventors: Thomas Hagerott, Edmund W. Golaski
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Patent number: 9145585Abstract: The present disclosure provides nucleic acid probes, as well as kits that include such probes. Methods for producing and using (for example in chromosomal in situ hybridization) the probes are also provided. Such probes in some examples are used to detect chromosomal abnormalities or the presence of a pathogen.Type: GrantFiled: August 5, 2014Date of Patent: September 29, 2015Assignee: Ventana Medical Systems, Inc.Inventor: Michael Farrell
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Patent number: 9139871Abstract: A method for amplifying nucleic acid from a higher eukaryotic, such as mammalian or plant, nucleic acid source, the method comprising (a) contacting a sampling device with the source of higher eukaryotic, such as mammalian or plant, nucleic acid such that following said contacting, higher eukaryotic such as mammalian or plant nucleic acid-containing material is adhered to at least part of the sampling device, wherein the sampling device, or part thereof to which the nucleic acid-containing material is adhered, is made of a suitable polymeric material; (b) introducing the sampling device or part thereof to which the nucleic acid-containing material is adhered into a reaction vessel which contains a reaction mixture for carrying out a nucleic acid amplification reaction, without any prior treatment of the nucleic acid-containing material; and (c) performing a nucleic acid amplification reaction.Type: GrantFiled: June 17, 2011Date of Patent: September 22, 2015Assignee: LGC LimitedInventors: Paul Gerald Debenham, John David Moore
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Patent number: 9139860Abstract: The present invention relates to a self-amplifying folded oligonucleotide structure for sensitive oligonucleotide sensing without polymerase chain reaction (PCR). A self-amplifying folded oligonucleotide structure comprise a target sensing sequence having stem loop structure, a signaling molecule and signal modifying molecule labeled two stems wherein the two stems include oligonucleotide sequence that is complementary to a target sensing sequence of another self-amplifying folded oligonucleotide structure.Type: GrantFiled: April 11, 2011Date of Patent: September 22, 2015Assignee: Korea University Research and Business FoundationInventor: Hong Gu Chun
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Patent number: 9133466Abstract: The invention relates to efficient, high-throughput methods, systems, and DNA constructs for identification and isolation of transcription termination sequences. The invention relates further to specific terminator sequences identified by said methods isolated from rice.Type: GrantFiled: May 15, 2013Date of Patent: September 15, 2015Assignee: BASF Plant Science GmbHInventors: Hee-Sook Song, Michael Kock, Jeffrey A. Brown, Linda Patricia Loyall, Liqun Xing, Hongmei Jia, John McMillan, Lesley Ireland
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Patent number: 9127316Abstract: This application discloses SNPs capable of predicting increased or decreased risk of developing late onset Alzheimer's disease.Type: GrantFiled: March 11, 2011Date of Patent: September 8, 2015Assignee: THE TRANSLATIONAL GENOMICS RESEARCH INSTITUTEInventors: Matt Huentelman, Eric M. Reiman
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Patent number: 9121053Abstract: Use of low-temperature nucleic acid amplification and binary probes to detect sequences and single nucleotide polymorphisms.Type: GrantFiled: July 8, 2011Date of Patent: September 1, 2015Assignees: University of Central Florida Research Foundation, Inc., Scheme Lab, Ltda.Inventors: Dmitry Kolpashchikov, John Katz
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Patent number: 9115394Abstract: The present invention provides methods and reagents for use in the amplification of nucleic acids. Amplification carried out using oligonucleotides containing modified nucleotides can result in less non-specific amplification compared to amplification carried out using unmodified oligonucleotides.Type: GrantFiled: December 11, 2012Date of Patent: August 25, 2015Assignee: ROCHE MOLECULAR SYSTEMS, INC.Inventors: Veeraiah Bodepudi, Nancy Schoenbrunner, Stephen Will
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Patent number: 9108177Abstract: A multi-port liquid bridge (1) adds aqueous phase droplets (10) in an enveloping oil phase carrier liquid (11) to a draft channel (4, 6). A chamber (3) links four ports, and it is permanently full of oil (11) when in use. Oil phase is fed in a draft flow from an inlet port (4) and exits through a draft exit port (6) and a compensating flow port (7). The oil carrier and the sample droplets (3) (“aqueous phase”) flow through the inlet port (5) with an equivalent fluid flow subtracted through the compensating port (7). The ports of the bridge (1) are formed by the ends of capillaries held in position in plastics housings. The phases are density matched to create an environment where gravitational forces are negligible. This results in droplets (10) adopting spherical forms when suspended from capillary tube tips. Furthermore, the equality of mass flow is equal to the equality of volume flow.Type: GrantFiled: October 18, 2013Date of Patent: August 18, 2015Assignee: Stokes Bio LimitedInventors: Mark Davies, Tara Dalton, Julie Garvey, Kieran Curran, Damian Curtin
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Patent number: 9096907Abstract: Described herein are method, compositions and kits for prognosis of prostate cancer. The methods include determining the ratio of PCA3 and of a prostate-specific marker expression in a urine sample and correlating the value of the PCA3/prostate-specific marker ratio with the aggressiveness and mortality risk of prostate cancer in the subject. The method for prognosing prostate cancer in a sample of a patient includes assessing the amount of a prostate cancer specific PCA3 mRNA and the amount of prostate-specific marker in the sample; determining a ratio value of this amount of prostate cancer specific PCA3 mRNA over the amount of prostate-specific marker; comparing the ratio value to at least one predetermined cut-off value, wherein a ratio value above the predetermined cut-off value is indicative of a higher risk of mortality of prostate cancer as compared to a ratio value below the predetermined cut-off value.Type: GrantFiled: June 10, 2013Date of Patent: August 4, 2015Assignee: Stichting Katholieke Universiteit, The University Medical Centre NijmegenInventors: Daphne Hessels, Gerald Verhaegh, Jack A. Schalken, J. Alfred Witjes
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Patent number: 9080204Abstract: Disclosed are oligonucleotide amplification primers and detection probes specific for the amplification and detection of pathogenic organisms, including for example, specific Influenza A H1N1 viral isolates. Also disclosed is a biological organism identification kit including the disclosed nucleic acid probes and primers, as well as thermal cycling reagents that is both portable and durable, and may also be self-contained for remote, or in-field analysis and identification of particular influenza isolates from a variety of biological specimen types.Type: GrantFiled: December 30, 2011Date of Patent: July 14, 2015Assignee: Longhorn Vaccines and Diagnostics, LLCInventors: Gerald W. Fischer, Luke T. Daum
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Patent number: 9068222Abstract: The present invention is directed to methods, reagents, kits, and compositions for identifying and quantifying target polynucleotide sequences. A linker probe comprising a 3? target specific portion, a loop, and a stem is hybridized to a target polynucleotide and extended to form a reaction product that includes a reverse primer portion and the stem nucleotides. A detector probe, a specific forward primer, and a reverse primer can be employed in an amplification reaction wherein the detector probe can detect the amplified target polynucleotide based on the stem nucleotides introduced by the linker probe. In some embodiments a plurality of short miRNAs are queried with a plurality of linker probes, wherein the linker probes all comprise a universal reverse primer portion a different 3? target specific portion and different stems. The plurality of queried miRNAs can then be decoded in a plurality of amplification reactions.Type: GrantFiled: August 18, 2009Date of Patent: June 30, 2015Assignee: APPLIED BIOSYSTEMS, LLCInventors: Caifu Chen, Dana Ridzon, Zhaohui Zhou, Kai Qin Lao, Neil A. Straus
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Patent number: 9068210Abstract: 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: June 30, 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: 9062303Abstract: The present invention provides methods for the rapid and efficient isolation of small RNA from a biological sample. In particular, small RNA is separated and isolated from large RNA, DNA, proteins, and other macromolecules in the biological sample.Type: GrantFiled: June 22, 2010Date of Patent: June 23, 2015Assignee: SIGMA-ALDRICH CO. LLCInventors: Fuqiang Chen, Carol Kreader
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Patent number: 9040243Abstract: The present invention relates to a method, kit and use of various nucleic acid sequences for deleting and/or quantifying one or more nucleic acids of a genome in a sample. Wherein the nucleic acid is amplified and the locus that is amplified is a multi copy locus within the genome, the multicopy locus has copies on at least two different chromosomes and the amplification product is detected and/or quantified.Type: GrantFiled: September 22, 2011Date of Patent: May 26, 2015Assignee: QIAGEN GMBHInventors: Andy Wende, Francesca Dipasquale, Sabine Werner, Sascha Strauss
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Patent number: 9029085Abstract: 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: March 7, 2008Date of Patent: May 12, 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: 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: 9024002Abstract: Described are compositions, methods and kits for detection and/or differential detection of serovars of Salmonella enterica subsp. enterica serovar such as S. Heidelberg and S. Hadar in samples. Some embodiments relate to multiplex amplification based molecular assays.Type: GrantFiled: March 7, 2013Date of Patent: May 5, 2015Assignee: Life Technologies CorporationInventors: Craig Cummings, Olga Petrauskene, Lily Wong, Allison De Los Reyes
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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