Patents Examined by Heather G. Calamita
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Patent number: 7550258Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.Type: GrantFiled: April 14, 2006Date of Patent: June 23, 2009Assignees: Metabolon, Inc., Cornell Research Foundation, Inc.Inventors: Rima Kaddurah-Daouk, Bruce Kristal
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Patent number: 7550260Abstract: The small molecule profiles of cells are compared to identify small molecules which are modulated in altered states. Cellular small molecule libraries, methods of identifying tissue sources, methods for treating genetic and non-genetic diseases, and methods for predicting the efficacy of drugs are also discussed.Type: GrantFiled: March 27, 2007Date of Patent: June 23, 2009Assignees: Metabolon, Inc., Cornell Research Foundation, Inc.Inventors: Rima Kaddurah-Daouk, Bruce S. Kristal
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Patent number: 7541147Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid, if present in the sample, by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.Type: GrantFiled: October 12, 2006Date of Patent: June 2, 2009Assignee: EraGen Biosciences, Inc.Inventors: David J. Marshall, James R. Prudent, Christopher B. Sherrill, Gideon Shapiro, Simona Jurczyk, Jerod L. Ptacin
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Patent number: 7531309Abstract: The present invention relates to molecular diagnostics. In particular, the present invention relates to PCR based diagnostics for the typing of Group B streptococci.Type: GrantFiled: December 6, 2005Date of Patent: May 12, 2009Assignee: Michigan State UniversityInventors: Dele Davies, David W. Lacher, Thomas S. Whittam, Shannon Manning
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Patent number: 7531307Abstract: It is an object of the present invention to provide a solution to problems associated with the use of microarray technology for the analysis DNA. The present invention provides compositions and methods for the use of simple and compound representations of DNA in microarray technology. The present invention is also directed to methods for the production of High Complexity Representations (HCRs) of the DNA from cells.Type: GrantFiled: March 30, 2005Date of Patent: May 12, 2009Assignee: Cold Spring Harbor LaboratoryInventors: Michael Wigler, Robert Lucito
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Patent number: 7527928Abstract: The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on a solid support and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5? nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: GrantFiled: December 4, 2002Date of Patent: May 5, 2009Assignee: Third Wave Technologies, Inc.Inventors: Bruce P. Neri, Jeff G. Hall, Victor Lyamichev, Lloyd M. Smith
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Patent number: 7521185Abstract: Primers and probes derived from SARS-CoV nucleic acid that facilitate detection and/or quantification of the replicase gene are disclosed. The disclosed sequences may be used in a variety of amplification and non-amplification formats for detection of SARS-CoV infection.Type: GrantFiled: September 13, 2004Date of Patent: April 21, 2009Assignee: Becton, Dickinson and CompanyInventors: Jianrong Lou, James A. Price, Jr., Daretta A. Yursis, David M. Wolfe, Lisa M. Keller, Tobin J. Hellyer
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Patent number: 7517651Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid, if present in the sample, by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; and correlating a signal of the label with the presence of the target nucleic acid in the sample. The invention also provides corresponding kits for use in detecting target nucleic acids in a sample.Type: GrantFiled: July 14, 2006Date of Patent: April 14, 2009Assignee: EraGen Biosciences, Inc.Inventors: David J. Marshall, James R. Prudent, Christopher B. Sherrill, Gideon Shapiro, Simon Jurczyk, Jerod L. Ptacin
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Patent number: 7510836Abstract: The present invention relates to an alpha-arteether resistance domain (ADR) of Sequence ID No.1 and a method of identifying ADR in alpha-arteether resistant pathogens and lastly, it relates to set three pairs of primers of sequence ID Nos. 3 to 8.Type: GrantFiled: March 26, 2004Date of Patent: March 31, 2009Assignee: Council of Scientific & Industrial ResearchInventors: Suman Preet Singh Khanuja, Suchi Srivastava, Ajit Kumar Shasany, Tiruppadiripuliyur Ranganathan Santha Kumar, Mahendra Pandurang Darokar, Preeti Chand, Sushil Kumar
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Patent number: 7504220Abstract: The present invention relates to reverse transcription of RNA, and in particular to reverse transcription by thermostable DNA polymerases. Thermoactinomyces vulgaris and Bacillus stearothermophilus possess reverse transcriptase activity in the presence of magnesium or manganese ions. Methods, compositions, and kits for reverse transcription and RT-PCR are also provided.Type: GrantFiled: June 27, 2006Date of Patent: March 17, 2009Assignee: Promega CorporationInventors: Trent Gu, Fen Huang, James Robert Hartnett
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Patent number: 7495093Abstract: The present invention concerns oligonucleotides containing one or more modified nucleotides which increase the binding affinity of the oligonucleotides to target nucleic acids having a complementary nucleotide base sequence. These modified oligonucleotides hybridize to the target sequence at a faster rate than unmodified oligonucleotides having an identical nucleotide base sequence. Such modified oligonucleotides include oligonucleotides containing at least one 2?-O-methylribofuranosyl moiety joined to a nitrogenous base. Oligonucleotides can be modified in accordance with the present invention to preferentially bind RNA targets. The present invention also concerns methods of using these modified oligonucleotides and kits containing the same.Type: GrantFiled: October 26, 2007Date of Patent: February 24, 2009Assignee: Gen-Probe IncorporatedInventors: Michael M. Becker, Mehrdad R. Majlessi
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Patent number: 7465542Abstract: Methods are provided for determining whether a patient treated with an anti-proliferative agent is susceptible to toxicity. In practicing the subject methods, an expression profile for the transcriptional response to a therapy is obtained from the patient and compared to a reference profile to determine whether the patient is susceptible to toxicity. In addition, reagents and kits thereof that find use in practicing the subject methods are provided.Type: GrantFiled: October 14, 2003Date of Patent: December 16, 2008Assignee: The Board of Trustees of the Leland Stanford Junior UniversityInventors: Gilbert Chu, Virginia G. Tusher, Jean Tang, Kerri Elyse Rieger, Wan-Jen Hong, Robert Tibshirani
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Patent number: 7465539Abstract: A formulation of thermostable or other DNA polymerases comprising (a) at least one thermostable or other DNA polymerase which lacks 3?-exonuclease activity, and (b) at least one thermostable DNA polymerase exhibiting 3?-exonuclease activity, wherein the ratio of (a) to (b) is greater than 1 to 1. Also provided is an improved method for enzymatic extension of DNA strands, especially while, but not limited to, amplifying nucleic acid sequences by polymerase chain reaction wherein the above formulation is made and used to catalyze primer extension, are also provided.Type: GrantFiled: June 7, 1995Date of Patent: December 16, 2008Assignee: Takara Bio, Inc.Inventor: Wayne M. Barnes
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Patent number: 7462450Abstract: Methods, apparatus, and computer program products to form arrays of polymers each having a pattern of features on a surface of a flexible elongated web, comprising. In a method polymers or their precursor units are applied at an application station to the surface. Multiple features are covered at a reagent station with a continuous volume of reagent which chemically reacts with precursors or the web. The flexible elongated web is driven in a lengthwise direction through the application station. This sequence may be repeated as needed to form the arrays along the web. Also provided is a method preparing a surface of a flexible elongated web to receive a biopolymer array.Type: GrantFiled: January 5, 2005Date of Patent: December 9, 2008Assignee: Agilent Technologies, Inc.Inventors: Steven M. Lefkowitz, Michel G. M. Perbost, Roy H. Kanemoto, Carol T. Schembri
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Patent number: 7459311Abstract: The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether Ppi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an ?-thio triphosphate analogue of said nucleotide is used, and the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.Type: GrantFiled: September 7, 2001Date of Patent: December 2, 2008Assignee: Biotage ABInventors: Pål Nyren, Mostafa Ronaghi, Annika Tallsjö
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Patent number: 7442507Abstract: The present invention relates to a method for detecting the presence of circulating mutant BRAF DNA, which may be present in circulating melanoma cells or as DNA shed from tumor cells. Methods, compositions and kits which employ one or more sets of BRAF mutant specific primer pairs for detection of circulating mutant BRAF DNA are presented. Also provided are methods for diagnosing and/or determining stage/progression of a melanoma in a mammal based on detection of a BRAF mutant nucleic acid sequence. Such methods are also well suited to monitoring disease activity in patients with active disease or those in remission.Type: GrantFiled: January 24, 2006Date of Patent: October 28, 2008Assignees: New York University School of Medicine, Memorial Sloan-Kettering Cancer CenterInventors: David Polsky, Iman Osman, Paul B. Chapman
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Patent number: 7432048Abstract: The present invention relates to compositions and methods for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. The present invention relates to methods for forming a nucleic acid cleavage structure on a solid support and cleaving the nucleic acid cleavage structure in a site-specific manner. For example, in some embodiments, a 5? nuclease activity from any of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.Type: GrantFiled: December 8, 2000Date of Patent: October 7, 2008Assignee: Third Wave Technologies, Inc.Inventors: Bruce P. Neri, Jeff G. Hall, Victor Lyamichev, Lloyd M. Smith
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Patent number: 7422850Abstract: Assays using non-natural bases are described. In one embodiment, the method involves contacting a sample suspected of containing the target nucleic acid with a polymerase and first and second primers; amplifying the target nucleic acid, if present in the sample, by PCR using the first and second primers to generate an amplification product having a double-stranded region and a single-stranded region that comprises the non-natural base; contacting the sample with a reporter comprising a label and a non-natural base that is complementary to the non-natural base of the single-stranded region; annealing at least a portion of the reporter to the single-stranded region of the amplification product; cleaving, after annealing, at least a portion of the reporter to release at least one reporter fragment; and correlating the release of the at least one reporter fragment with the presence of the target nucleic acid in the sample.Type: GrantFiled: May 18, 2001Date of Patent: September 9, 2008Assignee: Eragen Biosciences, Inc.Inventors: David J. Marshall, James R. Prudent, Christopher B. Sherrill, Gideon Shapiro, Jennifer K. Grenier, Craig S. Richmond, Simona Jurczyk, Jerod L. Ptacin
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Patent number: 7422911Abstract: Flexible array substrates having a flexible support, a flexible base, a reflective layer, and a transparent layer, in that order, are taught. Methods of forming the flexible array substrates, devices incorporating flexible array substrates, and arrays having probes arranged on a surface of the flexible array substrate are also taught.Type: GrantFiled: October 31, 2002Date of Patent: September 9, 2008Assignee: Agilent Technologies, Inc.Inventor: Carol T. Schembri
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Patent number: 7410760Abstract: The present invention provides methods and compositions for confirming the integrity of primers and other components of amplification reactions, including multiplex amplification reactions.Type: GrantFiled: November 24, 2003Date of Patent: August 12, 2008Assignee: CepheidInventor: David D. Swenson