Patents Examined by Mark Staples
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Patent number: 8361727Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.Type: GrantFiled: May 24, 2011Date of Patent: January 29, 2013Assignee: Lasergen, Inc.Inventors: Weidong Wu, Vladislav A. Litosh, Brian P. Stupi, Michael L. Metzker
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Patent number: 8211643Abstract: The application provides methods of prognosing and classifying lung cancer patients into poor survival groups or good survival groups and for determining the benefit of adjuvant chemotherapy by way of a multigene signature. The application also includes kits and computer products for use in the methods of the application.Type: GrantFiled: May 14, 2009Date of Patent: July 3, 2012Assignee: University Health NetworkInventors: Ming-Sound Tsao, Frances A. Shepherd, Igor Jurisica, Sandy D. Der, Chang-Qi Zhu, Dan Strumpf, Lesley Seymour, Keyue Ding
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Patent number: 8198029Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a non-cleavable terminating group. The non-cleavable-fluorescent group is designed to terminate DNA synthesis so that DNA oligomers can be sequenced efficiently in a parallel format. These reagents and methods will lead to more accurate identification of polymorphisms and other valuable genetic information.Type: GrantFiled: January 7, 2011Date of Patent: June 12, 2012Assignee: Lasergen, IncInventors: Weidong Wu, Vladislav A. Litosh, Brian P. Stupi, Michael L. Metzker
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Patent number: 8182991Abstract: The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to improved cleavage means for the detection and characterization of nucleic acid sequences. Structure-specific nucleases derived from a variety of thermostable organisms are provided. These structure-specific nucleases are used to cleave target-dependent cleavage structures, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: GrantFiled: October 6, 2000Date of Patent: May 22, 2012Assignee: Third Wave Technologies, Inc.Inventors: Michael W. Kaiser, Victor I. Lyamichev, Natasha Lyamicheva
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Patent number: 8178659Abstract: To identify conserved and variable regions of the 16 S rRNA, an instant evolution experiment was performed on the entire 16 S rRNA. Analysis of these mutants identified regions that are required for function. These conserved sequences may be used as targets for pharmaceuticals that are taxonomically specific and which are refractory to the development of drug resistance.Type: GrantFiled: May 11, 2006Date of Patent: May 15, 2012Assignee: Wayne State UniversityInventor: Philip R. Cunningham
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Patent number: 8168777Abstract: Methods for treating nucleic acid including: (a) providing an alkali environment to a nucleic acid sample; (b) reacting the nucleic acid sample with a bisulphite reagent and incubating the reaction so as to form a treated nucleic acid sample where methylated nucleotides in the nucleic acid sample remain unchanged while unmethylated nucleotides are converted to another form; (c) removing unwanted reagents or diluents from the treated nucleic acid sample; and (d) carrying out de-sulphonation of the precipitated treated nucleic acid at a temperature from 70° C. to 95° C. by adjusting the precipitated treated nucleic acid to a pH of between 10 and less than 12.5 to remove sulphonate groups present on the treated nucleic acid and obtain a nucleic acid sample substantially free of sulphonate groups.Type: GrantFiled: March 27, 2009Date of Patent: May 1, 2012Assignee: Human Genetic Signatures Pty. Ltd.Inventors: Douglas Spencer Millar, Cassandra Jean Vockler, Neralie Ann Coulston
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Patent number: 8129149Abstract: A rapid and sensitive method to measure endonuclease activity comprising reacting a substrate suspected of having endonuclease activity with a synthetic nucleotide to induce endonuclease cleavage of the synthetic nucleotide followed by measurement of activity by carrying out a polymerase chain reaction (PCR). When no polymerase chain reaction takes place when carrying out the method it is indicative of no endonuclease activity in the substrate. Synthetic oligonucleotides, primers, and probes useful for carrying out the method are disclosed.Type: GrantFiled: November 12, 2008Date of Patent: March 6, 2012Assignee: The United States of America as represented by the Secretary of the ArmyInventors: Russell M. Dorsey, Robert W. Dorsey
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Patent number: 8114979Abstract: The invention provides novel anthraquinone compositions that are useful as broad-spectrum quenchers of fluorescence and provides methods for making and using them. The anthraquinone quenchers can be conjugated to a variety of biologically relevant compounds, including lipids, nucleic acids, polypeptides, and more specifically antigens, steroids, vitamins, drugs, haptens, metabolites, toxins, environmental pollutants, amino acids, peptides, proteins, nucleotides, oligonucleotides, polynucleotides, carbohydrates, and their analogs. The invention also provides kits comprising, in one or more containers, at least one anthraquinone quencher dye composition of the present invention, and instructions for using that composition.Type: GrantFiled: August 10, 2010Date of Patent: February 14, 2012Assignee: Integrated DNA Technologies, Inc.Inventors: Andrei Laikhter, Mark Aaron Behlke, Yawfui Yong, Scott Rose, Lingyan Huang
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Patent number: 8106175Abstract: This invention pertains to methods for cloning microRNA (miRNA) and other small ribonucleic acid (RNA) species from relevant cell sources.Type: GrantFiled: July 8, 2010Date of Patent: January 31, 2012Assignee: Integrated DNA Technologies, Inc.Inventors: Eric J. Devor, Lingyan Huang, Mark A. Behlke
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Patent number: 8088582Abstract: The present invention provides compositions, kits and methods for rapid identification and quantification of fungi by molecular mass and base composition analysis.Type: GrantFiled: April 6, 2007Date of Patent: January 3, 2012Assignee: Ibis Biosciences, Inc.Inventors: Rangarajan Sampath, Thomas A. Hall, David J. Ecker
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Patent number: 8067175Abstract: Polymerase chain reaction primers and methods directed to detecting the EGFR mutant C?T at the position corresponding to base 2369 of EGFR cDNA. The invention provides a PCR primer that hybridizes under suitable PCR conditions to a polynucleotide sequence 5? in each respective strand to a mutation of an EGFR gene that encodes a substitution of threonine by methionine at position 790 of the EGFR polypeptide. The invention also provides a PCR primer hybridizes to a sequence that includes a mutant T at the position corresponding to base 2369 of EGFR cDNA but not to a second EGFR polynucleotide containing a wild type C. The invention provides several methods and kits for detecting a mutant epidermal growth factor receptor (EGFR) gene in a sample comprising probing the sample with a means for selectively detecting a nucleotide sequence comprising a mutant T at the position corresponding to base 2369 of EGFR cDNA, and identifying that the base at said position is T.Type: GrantFiled: February 13, 2006Date of Patent: November 29, 2011Assignee: Memorial Sloan-Kettering Cancer CenterInventors: Harold Varmus, Katerina Politi, William Pao, Vincent Miller
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Patent number: 8012683Abstract: Methods for identifying a subject at risk for developing AMD are disclosed, as are kits which can be used to practice the methods. The methods include identifying specific protective or risk polymorphisms or genotypes from the subject's genetic material, including polymorphisms in the BF, C2 and/or CFH genes. Microarrays and kits for use in these methods are also provided.Type: GrantFiled: February 13, 2007Date of Patent: September 6, 2011Assignees: University of Iowa Research Foundation, The Trustees of Columbia University in the City of New York, United States of America, as represented by the Secretary of the Department of Health and Human ServicesInventors: Rando L. Allikmets, Gregory S. Hageman, Michael C. Dean, Albert M. Gold
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Patent number: 7993880Abstract: The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.Type: GrantFiled: February 19, 2010Date of Patent: August 9, 2011Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Thomas D. Willis, Paul Hardenbol, Maneesh Jain, Viktor Stolc, Mostafa Ronaghi, Ronald W. Davis
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Patent number: 7989169Abstract: The invention is related to a method for amplifying a methylated target nucleic acid in a sample while avoiding amplification of a non-methylated target nucleic acid by inactivating it. This is accomplished by a restriction enzyme digest after bisulfite treatment of the target nucleic acid. The invention is further related to the use of a restriction enzyme to avoid amplification of a non-methylated target nucleic acid while amplifying a methylated target nucleic acid in a sample and kits for performing the methods according to the invention.Type: GrantFiled: September 2, 2005Date of Patent: August 2, 2011Assignee: Roche Molecular Systems, Inc.Inventors: Frank Bergmann, Christine Markert-Hahn
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Patent number: 7972820Abstract: Methods for isothermal amplification of nucleic acids by the means of a solid support are disclosed. These methods are useful for applications needing high throughput, in particular nucleic acid sequencing.Type: GrantFiled: May 5, 2010Date of Patent: July 5, 2011Assignees: Illumina Cambridge Limited, Illumina, Inc.Inventor: Pascal Mayer
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Patent number: 7964352Abstract: Provided are novel nucleotides, nucleoside, and their derivatives described herein, that can be used in DNA sequencing technology and other types of DNA analysis. In one embodiment, the nucleotide or nucleoside with an unprotected 3?-OH group is derivatized at the nucleobase to include a fluorescent dye attached via a linker to a photocleavable terminating group. The photocleavable-fluorescent group is designed to terminate DNA synthesis as well as be cleaved so that DNA oligomers can be sequenced efficiently in a parallel format. The design of such rapidly cleavable fluorescent groups on nucleotides and nucleosides can enhance the speed and accuracy of sequencing of large oligomers of DNA in parallel, to allow rapid whole genome sequencing, and the identification of polymorphisms and other valuable genetic information, as well as allowing further manipulation and analysis of nucleic acid molecules in their native state following cleavage of the fluorescent group.Type: GrantFiled: November 11, 2008Date of Patent: June 21, 2011Assignee: LaserGen, Inc.Inventors: Weidong Wu, Vladislav A. Litosh, Brian P. Stupi, Michael L. Metzker
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Patent number: 7951533Abstract: Novel technologies are provided to determine the structure of and produce a functional substance that has a high affinity to a target. Candidates for a substance having an affinity to a target (functional substance) are synthesized; a functional substance that has an affinity to the target is selected from among the functional substance candidates; a specific substituent group is eliminated from the selected functional substance; the functional substance from which the specific substituent group has been eliminated is amplified; the structure of the amplified functional substance is determined; and the functional substance is produced, based on the structure.Type: GrantFiled: October 31, 2005Date of Patent: May 31, 2011Assignee: Fujitsu LimitedInventors: Tsuyoshi Fujihara, Shozo Fujita
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Patent number: 7951564Abstract: A method for evaluating microsatellite instability associated with a tumour, which entails the steps of amplifying microsatellite loci in a biological sample containing genomic DNA from the tumour and determining sizes of DNA amplification products, wherein at least one microsatellite locus selected from the group consisting of NR 21, NR 22, NR 24 and NR 27, is amplified.Type: GrantFiled: March 30, 2009Date of Patent: May 31, 2011Assignee: Institut National de la Sante et de la RechercheInventors: Richard Hamelin, Nirosha Suraweera
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Patent number: 7939258Abstract: The invention provides methods for amplification of polynucleotide sequences using primers containing single-stranded RNA. The methods employ use of an enzyme capable of cleaving single-stranded RNA, such as RNase I, to degrade a first RNA-containing primer prior to addition of a second RNA-containing primer. The invention also provides compositions and kits for practicing the amplification methods, as well as methods which use the amplification products.Type: GrantFiled: September 7, 2006Date of Patent: May 10, 2011Assignee: Nugen Technologies, Inc.Inventors: Nurith Kurn, Shenglong Wang
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Patent number: 7939339Abstract: The invention relates to an arrangement for fluorescence amplification including a substrate, a fluorescence amplifier coating applied to the substrate, and a thin fluorescencable material which lies on the coating and emits light with the emission wavelength ?E when it is exposed to excitation light of an excitation wavelength ?A. The fluorescence amplifier coating includes an interference layer system of high-index and low-index dielectric layers, which reflects at least the excitation light. What is crucial for the design of the coating is that the fluorescencable material applied to the coating is arranged on the surface of the coating in the region of the maximum of the electric field amplitude of the standing wave with the excitation wavelength ?A, which is formed during exposure to the excitation light.Type: GrantFiled: March 17, 2005Date of Patent: May 10, 2011Assignee: Schott AGInventors: Niko Schultz, Samuel D. Conzone, Otmar Becker, Dan Haines, Edgar Pawlowski, Volker Scheumann