Patents Examined by Suryaprabha Chunduru
  • Compositions and methods for cDNA synthesis
    Patent number: 8420324
    Abstract: Methods for making cDNA molecules, for amplification of RNA by PCR and for preparation of cDNA libraries are provided. Kits for making cDNA molecules also are provided. Compositions are also provided comprising mixtures of reagents, including reverse transcriptases, buffers, cofactors and other components, suitable for immediate use in conversion of RNA into cDNA and RT PCR without dilution or addition of further components. These compositions are useful, alone or in the form of kits, for cDNA synthesis or nucleic acid amplification (e.g., by the Polymerase Chain Reaction) or for any procedure utilizing reverse transcriptases in a variety of research, medical, diagnostic, forensic and agricultural applications.
    Type: Grant
    Filed: December 8, 2009
    Date of Patent: April 16, 2013
    Assignee: Quanta Biosciences
    Inventors: Ayoub Rashtchian, David Schuster
  • Method of detecting H5 or H7 avian influenza virus
    Patent number: 8389221
    Abstract: The present invention provides oligonucleotide primers specifically hybridizing to an arbitrary nucleotide sequence designed from the nucleotide sequence of hemagglutinin of an H5 or H7 avian influenza virus, a nucleic acid amplification method using the primers, a method for diagnosis of infection with an H5 or H7 avian influenza virus by detection of nucleic acid amplification, and a kit for influenza diagnosis.
    Type: Grant
    Filed: September 14, 2011
    Date of Patent: March 5, 2013
    Assignees: Japan as represented by Director-General of National Institute of Infectious Diseases, Eiken Kagaku Kabushiki Kaisha
    Inventors: Harumi Minekawa, Toshihiro Yonekawa, Takato Odagiri
  • Assay for BCR/ABL gene rearrangement
    Patent number: 8367814
    Abstract: The present invention provides a simple high-throughput assay for detecting bcr/abl translocations. The method includes qualitative PCR methods for identifying the particular amplified translocation (e1a2 or b2a3/b3a2) and real time PCR for quantifying an amount of bcr/abl transcript (e1a2, b2a3 and b3a2). Quantitative measurement of bcr/abl transcript in accordance with the methods of the invention is useful for monitoring response to therapy.
    Type: Grant
    Filed: December 9, 2009
    Date of Patent: February 5, 2013
    Assignee: Quest Diagnostics Investments Incorporated
    Inventors: Richard W. Tseng, Michael K. Samoszuk
  • High throughput nucleic acid sequencing by expansion
    Patent number: 8324360
    Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.
    Type: Grant
    Filed: March 30, 2011
    Date of Patent: December 4, 2012
    Assignee: Stratos Genomics, Inc.
    Inventors: Mark Stamatios Kokoris, Robert N. McRuer
  • Method for determining the amount of template nucleic acid present in a sample
    Patent number: 8309308
    Abstract: A method for determining the amount of template nucleic acid present in a sample comprising the steps of: i) bringing into association with the sample all the components necessary for nucleic acid amplification, and all the components necessary for a bioluminescence assay for nucleic acid amplification and subsequently: ii) performing the nucleic acid amplification reaction; iii) monitoring the intensity of light output from the bioluminescence assay; and iv) determining the amount of template nucleic acid present in the sample.
    Type: Grant
    Filed: July 29, 2005
    Date of Patent: November 13, 2012
    Assignee: Lumora Limited
    Inventors: Laurence Carlo Tisi, James Augustus Henry Murray, Olga Gandelman, Victoria Louise Church
  • Method for determining azole resistance in
    Patent number: 8021846
    Abstract: There is disclosed a method for determining azole resistance in Candida glabrata. A biological sample containing Candida glabrata is obtained and a normalized mRNA level of CDR1 gene is determined using qRT-PCR. Using a microbroth dilution assay conducted at azole concentrations of about 2-8 ?g/mL, a susceptible isolate of Candida glabrata is obtained. A qRT-PCR assay is employed on the susceptible isolate and an average mRNA level of CDR1 is obtained. A fold-change value for CDR1 is obtained by comparing the CDR1 mRNA level of the biological sample with that of the average mRNA level. A ?2-fold change value is indicative of an azole resistance in Candida glabrata. The present method provides a qRT-PCR assay for azole resistance that has a sensitivity of ?90% and a specificity of ?90%.
    Type: Grant
    Filed: March 12, 2009
    Date of Patent: September 20, 2011
    Assignee: Medical Diagnostic Laboratories, LLC
    Inventors: Scott E. Gygax, John-Paul Vermitsky, Sean G. Chadwick, Matthew J. Self, Eli Mordechai, Martin E. Adelson
  • Reversible di-nucleotide terminator sequencing
    Patent number: 8017338
    Abstract: The present teachings provide methods, compositions, and kits for synthesizing and sequencing nucleic acids. In some embodiments, reversible di-nucleotide compounds are employed along with cleaving reactions that remove a label and a blocking moiety. Improved sequencing efficiency is achieved by the rapid polymerase-mediated incorporation of reversible di-nucleotide compounds. In some embodiments, the di-nucleotides do not contain conventional nucleotide triphosphates, but rather employ amino acid phosphoramidate nucleotides (AAPNs).
    Type: Grant
    Filed: November 20, 2008
    Date of Patent: September 13, 2011
    Assignee: Life Technologies Corporation
    Inventor: Gerald Zon
  • Genomic library construction
    Patent number: 7985546
    Abstract: Compositions and methods for amplifying nucleic acid sequences from a single cell are provided. Compositions and methods for constructing a genomic library from a single cell are also provided.
    Type: Grant
    Filed: November 5, 2008
    Date of Patent: July 26, 2011
    Assignee: President and Fellows of Harvard College
    Inventors: George M. Church, Kun Zhang
  • System for monitoring the location of transgenes
    Patent number: 7982022
    Abstract: A novel strategy for monitoring the location of a transgene in a mammal is disclosed. A sodium iodide symporter is genetically fused to either the N-terminus or C-terminus of the product of a transgene through a linker peptide which bears the recognition sequence of a host cell protease. Expression of the transgene confers the activity of the sodium iodide symporter (NIS) to a host cell which expresses the transgene. Subsequent administration of labeled iodine results in transport of the labeled iodine into the cell bearing the NIS, which can then be localized and measured using standard imaging techniques. The system is particularly useful for monitoring the location of therapeutic transgenes and tissue-specific distribution of the therapeutic gene product.
    Type: Grant
    Filed: December 15, 2009
    Date of Patent: July 19, 2011
    Assignee: Mayo Foundation for Medical Education and Research
    Inventors: Stephen J. Russell, John Morris
  • Method for amplification of nucleotide sequence
    Patent number: 7977055
    Abstract: To provide a method for selectively amplifying a target nucleic acid and a method for detecting a nucleic acid by the method, which are useful as a method for synthesizing the nucleic acid. A method for amplifying a nucleic acid sequence (EVA (Endonuclease V-dependent Amplification) method) which selectively amplifies a target nucleic acid in a sample, by the use of an oligonucleotide primer containing a base which can be recognized by an endonuclease V, the endonuclease V and a DNA polymerase having a strand displacement activity, and a method for detecting a nucleic acid by the method.
    Type: Grant
    Filed: June 20, 2007
    Date of Patent: July 12, 2011
    Assignee: Nishikawa Rubber Co., Ltd.
    Inventors: Katsunori Nakashima, Isao Ohiso
  • Method for rapid purification of nucleic acids for subsequent analysis by mass spectrometry by solution capture
    Patent number: 7964343
    Abstract: The present invention provides a method for rapid solution capture purification of nucleic acids for subsequent analysis by electrospray mass spectrometry which is efficient and cost-effective relative to existing methods. The present invention also provides kits useful for practicing rapid solution capture of nucleic acids so that purified samples are in condition for analysis by electrospray mass spectrometry.
    Type: Grant
    Filed: May 12, 2004
    Date of Patent: June 21, 2011
    Assignee: Ibis Biosciences, Inc.
    Inventors: Steven A. Hofstadler, Lendell L. Cummins
  • Assays based on detection of photobleaching reaction products from dye catalytic complex
    Patent number: 7964355
    Abstract: The present invention relates to the methods for assaying an analyte comprising a nucleic acid analog binding substrate in a sample, comprising reacting a catalytic complex comprising a nucleic acid analog, a nucleic acid analog specific binding substrate and a light reactive dye with a light stimulus, and detecting the presence or absence or amount of a reaction product of the catalytic complex and light stimulus. The present invention also relates to a method of assaying a nucleic acid analyte in a sample using an analyte-specific reporter complex. The present invention also relates to a method of assaying an analyte in a sample using a reporter molecule.
    Type: Grant
    Filed: February 17, 2009
    Date of Patent: June 21, 2011
    Assignee: Investigen, Inc.
    Inventors: Maiomiao Wang, Rachel Anne Holmes-Davis, Rick Blidner, Zbigniew Rafinski, Beata Anna Jedrzejewska, Jerzy Paczkowski, Brian David Warner, Heather Koshinsky
  • Labels for electronic detection of individual molecules and methods for their detection
    Patent number: 7964347
    Abstract: The invention provides labels for electronic detection of individual molecules. The labels are comprised of elements with different electrical properties that affect the electric current flowing through a nanoelectrode. The labels are of polymeric or filamentous structure where the elements are arranged linearly along their length. The arrangement of the elements is predetermined and combinatorial, so that a high diversity of labels can be generated in a manner that resembles barcoding on a nanoscale level. Methods for the synthesis of said barcode labels and for the binding of the barcode labels to individual molecules, their movement past a nanoelectrode, and their detection are also provided.
    Type: Grant
    Filed: June 12, 2007
    Date of Patent: June 21, 2011
    Inventor: Krassen Dimitrov
  • Reaction buffer composition for nucleic acid replication with packed DNA polymerases
    Patent number: 7939645
    Abstract: The invention relates to compositions, methods, and kits for nucleic acid replication, including polymerase chain reaction (PCR) and mutagenesis reactions. A buffer composition is provided which allows higher concentrations of DNA polymerase to be used, resulting in greater yield of amplified product and faster reaction kinetics.
    Type: Grant
    Filed: January 8, 2007
    Date of Patent: May 10, 2011
    Assignee: Agilent Technologies, Inc
    Inventor: Michael Borns
  • High throughput nucleic acid sequencing by expansion
    Patent number: 7939259
    Abstract: Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected.
    Type: Grant
    Filed: June 19, 2008
    Date of Patent: May 10, 2011
    Assignee: Stratos Genomics, Inc.
    Inventors: Mark Stamatios Kokoris, Robert N. McRuer
  • RNA detection assays
    Patent number: 7935800
    Abstract: The present invention provides novel cleavage agents and polymerases for the cleavage and modification of nucleic acid. The cleavage agents and polymerases find use, for example, for the detection and characterization of nucleic acid sequences and variations in nucleic acid sequences. In some embodiments, the 5? nuclease activity of a variety of enzymes is used to cleave a target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.
    Type: Grant
    Filed: December 19, 2006
    Date of Patent: May 3, 2011
    Assignee: Third Wave Technologies, Inc.
    Inventors: Hatim T. Allawi, Brad T. Argue, Christian Tor Bartholomay, LuAnne Chehak, Michelle L. Curtis, Peggy S. Eis, Jeff G. Hall, Hon S. Ip, Lin Ji, Michael W. Kaiser, Robert W. Kwiatkowski, Andrew A. Lukowiak, Victor Lyamichev, Natalie E. Lyamicheva, WuPo Ma, Bruce P. Neri, Sarah M. Olson, Marilyn C. Olson-Munoz, James J. Schaefer, Zbigniev Skrzypczynski, Tsetska Y Takova, Lisa C. Thompson, Kevin L. Vedvik
  • Detection of extracellular tumor-associated nucleic acid in blood plasma or serum using nucleic acid amplification assay
    Patent number: 7935484
    Abstract: This invention relates to detection of specific extracellular nucleic acid in human or animal blood plasma or serum associated with disease. Specifically, the invention relates to detection of nucleic acid derived from mutant oncogenes or other tumor-associated DNA including non-mutated hypermethylated DNA, and to methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated DNA including non-mutated hypermethylated DNA found in blood plasma or serum. In particular, the invention relates to the detection, identification, or monitoring of the existence, progression or clinical status of neoplasia in humans or other animals that contain a mutation that is associated with the neoplasm through detection of the non-mutated hypermethylated nucleic acid of the neoplasm in plasma or serum fractions.
    Type: Grant
    Filed: April 2, 2007
    Date of Patent: May 3, 2011
    Assignee: The Penn State Research Foundation
    Inventors: Christopher D. Gocke, Michael S. Kopreski
  • Methods for detection and quantification of analytes in complex mixtures
    Patent number: 7919237
    Abstract: The invention provides a diverse population of uniquely labeled probes, containing about thirty or more target specific nucleic acid probes each attached to a unique label bound to a nucleic acid. Also provided are methods of using and producing these populations of uniquely labeled nucleic acid probes.
    Type: Grant
    Filed: July 3, 2002
    Date of Patent: April 5, 2011
    Assignee: Nanostring Technologies, Inc.
    Inventors: Krassen Dimitrov, Dwayne Dunaway
  • Methods and compositions for use in analyte detection using proximity probes
    Patent number: 7914987
    Abstract: Methods and compositions for detecting an analyte in a sample are provided. In practicing the subject methods, a sample is combined with at least a pair of proximity probes that each include an analyte binding domain and a nucleic acid domain. The resultant mixture is then contacted with a pair of asymmetric nucleic acid connectors. Proximity dependent connector mediated interaction between the nucleic acid domains of the proximity probes is then detected to determine the presence of the analyte in the sample. Also provided are kits and systems for practicing the subject methods.
    Type: Grant
    Filed: June 14, 2005
    Date of Patent: March 29, 2011
    Assignee: The Board of Trustees of the Leland Stanford Junior University
    Inventors: Simon Fredriksson, Ronald W. Davis
  • Detection of microsatellite instability and its use in diagnosis of tumors
    Patent number: 7902343
    Abstract: Methods and kits are disclosed for use in the analysis of microsatellite instability in genomic DNA. Methods and kits are also disclosed which can be used to detect microsatellite instability DNA present in biological materials, such as tumors. The methods and kits of the present invention can be used to detect or diagnose diseases associated with microsatellite instability, such as certain types of cancer.
    Type: Grant
    Filed: April 25, 2008
    Date of Patent: March 8, 2011
    Assignee: Promega Corporation
    Inventors: Jeffery W. Bacher, Laura Flanagan, Nadine Nassif