Patents Examined by Suryaprabha Chunduru
  • Method for linking sequences of interest
    Patent number: 7749697
    Abstract: Multiplex overlap-extension RT-PCR provides an efficient method of linking two or more nucleotide sequences encoding for domains or subunits of a heteromeric protein, in a single reaction. Especially, the linkage of variable region encoding sequences from e.g. immunoglobulins, T cell receptors or B cell receptors is eased with the method of the present invention. This allows for a more efficient way of generating libraries of variable region encoding sequences. The capability to perform the multiplex overlap-extension RT-PCR using template derived from an isolated single cell enables the generation of cognate pair libraries in a high-throughput format.
    Type: Grant
    Filed: September 17, 2004
    Date of Patent: July 6, 2010
    Assignee: Symphogen A/S
    Inventors: Martin B. Oleksiewicz, Lars S. Nielsen, Peter S. Andersen, Margit H. Hansen
  • Method for rapid detection and identification of bioagents
    Patent number: 7741036
    Abstract: Method for detecting and identifying unknown bioagents, including bacteria, viruses and the like, by a combination of nucleic acid amplification and molecular weight determination using primers which hybridize to conserved sequence regions of nucleic acids derived from a bioagent and which bracket variable sequence regions that uniquely identify the bioagent. The result is a “base composition signature” (BCS) which is then matched against a database of base composition signatures, by which the bioagent is identified.
    Type: Grant
    Filed: January 13, 2006
    Date of Patent: June 22, 2010
    Assignee: Ibis Biosciences, Inc.
    Inventors: David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven Hofstadler, John McNeil
  • ELF3 gene compositions and methods
    Patent number: 7718783
    Abstract: ELF3 gene compositions associated with cancer are provided, including ELF3 mRNA intron retention, a novel ELF3 5? untranslated region, and a novel Alu, Alukwd. Methods and kits using primers or probes to detect the presence of these ELF3 gene compositions are also provided. Methods for determining whether a cell comprises a virus are also provided.
    Type: Grant
    Filed: November 21, 2003
    Date of Patent: May 18, 2010
    Inventors: Mark H. Kaplan, Michael H. Dosik, Xue-Ping Wang
  • DNA markers for management of cancer
    Patent number: 7718364
    Abstract: A method is provided for assessing allelic losses and hypermethylation of genes in CpG tumor promotor region on specific chromosomal regions in cancer patients, including melanoma, neuroblastoma breast, colorectal, and prostate cancer patients. The method relies on the evidence that free DNA and hypermethylation of genes in CpG tumor promotor region may be identified in the bone marrow, serum, plasma, and tumor tissue samples of cancer patients. Methods of melanoma, neuroblastoma, colorectal cancer, breast cancer and prostate cancer detection, staging, and prognosis are also provided.
    Type: Grant
    Filed: March 25, 2004
    Date of Patent: May 18, 2010
    Assignees: John Wayne Cancer Institute
    Inventors: Dave S. B. Hoon, Bret Taback
  • Process for obtaining recombined nucleotide sequences in vitro, libraries of sequences and sequences thus obtained
    Patent number: 7718786
    Abstract: Ligation-mediated method of recombining polynucleotides in vitro. Polynucleotides from a library are fragmented and the fragments are hybridized to an assembly template. The hybridized fragments are iteratively re-hybridized and ligated until the ends of the hybridized fragments are adjacent to the ends of other hybridized fragments on the assembly template. A final ligation produces recombined polynucleotides.
    Type: Grant
    Filed: June 3, 2005
    Date of Patent: May 18, 2010
    Assignee: Proteus SA
    Inventors: Daniel Dupret, Jean-Michel Masson, Fabrice Lefevre
  • Compositions and methods for terminating a sequencing reaction at a specific location in a target DNA template
    Patent number: 7700287
    Abstract: Compositions and methods for sequencing a template polynucleotide comprising a sequence of interest are provided herein. The compositions and methods employ at least one blocking probe that is designed to bind in a sequence-specific manner to a blocking sequence such that primer extension beyond the site where the blocking probe binds is reduced or prevented.
    Type: Grant
    Filed: January 27, 2006
    Date of Patent: April 20, 2010
    Assignee: Life Technologies Corporation
    Inventors: Shiaw-Min Chen, John W. Brandis
  • Assay for bcr/abl gene rearrangement
    Patent number: 7700279
    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 18, 2003
    Date of Patent: April 20, 2010
    Assignee: Quest Diagnostics Investments Incorporated
    Inventors: Richard W. Tseng, Michael K. Samoszuk
  • Method for amplifying genomic DNA
    Patent number: 7678543
    Abstract: A method for amplifying genomic DNA is provided. The method comprises the steps of: (1) incubating a cell-containing agarose solution at a pH of 9 to 12 and a temperature of 45 to 80° C. to produce a genomic DNA-dispersed agarose solution wherein 0.002 to 1 copies/5 microliter of single-stranded genomic DNA is dispersed; (2) solidifying the genomic DNA-dispersed agarose solution to produce a genomic DNA-dispersed agarose gel and neutralizing a pH of the gel; and (3) adding a DNA polymerase with strand displacement activity, primer and dNTP to the genomic DNA-dispersed agarose gel and incubating the gel at a temperature of 0 to 60° C. to amplify the genomic DNA.
    Type: Grant
    Filed: June 16, 2008
    Date of Patent: March 16, 2010
    Assignee: National Institute of Radiological Sciences
    Inventors: Takashi Imai, Mayumi Iwakawa, Yuichi Michikawa
  • Methods for rapid forensic analysis of mitochondrial DNA and characterization of mitochondrial DNA heteroplasmy
    Patent number: 7666588
    Abstract: The present invention provides methods for rapid forensic analysis of mitochondrial DNA and methods for characterizing heteroplasmy of mitochondrial DNA, which can be used to assess the progression of mitochondrial diseases.
    Type: Grant
    Filed: September 12, 2003
    Date of Patent: February 23, 2010
    Assignee: Ibis Biosciences, Inc.
    Inventors: David J. Ecker, Richard H. Griffey, Rangarajan Sampath, Steven A. Hofstadler, John McNeil, Stanley T. Crooke, Lawrence B. Blyn, Thomas A. Hall, Yun Jiang, James C. Hannis, Neil White, Vivek Samant, Mark W. Eshoo, Jared J. Drader
  • Detection and distinguishing infections bursal disease virus (IBDV) strains by molecular biology method
    Patent number: 7659066
    Abstract: The present invention relates to a novel method to detect and differentiate different strains of infectious bursal disease virus (IBDV) in a chicken and other bird sample. RNA was obtained from said samples by using a pair of primer (Primer FVVC & RVVC) in a reverse transcriptase-polymerase chain reaction. Two different primer combinations (Primer IF & IVIR) and (Primer IF & RCLA) and real-time polymerase chain reaction conditions were designed and optimized for rapid differentiation of very virulent and vaccine strains of IBDV based on detection of signatory threshold cycle (Ct) and melting temperature (Tm) values.
    Type: Grant
    Filed: November 7, 2005
    Date of Patent: February 9, 2010
    Assignee: Universiti Putra Malaysa
    Inventors: Abdul Rahman Omar, Mohd Hair-Bejo, Ideris Aini, Hairul Aini Hamzah
  • Methods for genetic analysis of DNA to detect sequence variances
    Patent number: 7659054
    Abstract: The presently claimed invention concerns a method for biasing the amplification of the DNA molecules in a sample such that a nucleic acid molecule having a specific nucleotide at a selected position (e.g., a polymorphic site) is preferentially amplified relative to an otherwise identical nucleic acid molecule not having the specific nucleotide at the selected position. The method entails amplification of target nucleic acid molecules using a pair of primers one of which causes the incorporation into the amplification product of a sequence that interferes with amplification of nucleic acid molecules not having the specific nucleotide at the selected position. The method is useful for preferentially amplifying at least a portion of one allele of a gene relative to another, different allele of the gene in a sample containing both alleles of the gene.
    Type: Grant
    Filed: October 25, 2000
    Date of Patent: February 9, 2010
    Assignee: Nuvelo, Inc.
    Inventors: Jeffrey Olson, Vincent P. Stanton, Jr.
  • Method and apparatus for detecting a mutation in a nucleic acid fragment in a sample
    Patent number: 7659056
    Abstract: A method and apparatus for the detection of polymorphisms in a nucleic acid sample (e.g. blood, sperm, saliva, cells, . . . ). To enhance the efficiency and the reliability of the known methods (e.g. DGGE, SSCP and TGGE) the amplification process (e.g. PCR) preceding the actual detection step is performed in or on the polyacrylamide gel. Multiple gradients (of chemical denaturants, thermal denaturants and of porosity of the gel matrix) are used for the separation of DNA fragments, by zone electrophoresis on gel slabs or by capillary electrophoresis.
    Type: Grant
    Filed: October 23, 2000
    Date of Patent: February 9, 2010
    Assignee: Ingeny Holding B.V.
    Inventor: Gerrit Johannis De Vos
  • Methods for using riboprimers for strand displacement replication of target sequences
    Patent number: 7659072
    Abstract: Methods, compositions and kits for amplifying a target sequence by strand displacement replication using strand-displacing primers. The method uses primers that have only ribonucleotides or purine ribonucleotides and at least one 2?-substituted pyrimidine-2?-deoxyribonucleotide.
    Type: Grant
    Filed: August 5, 2008
    Date of Patent: February 9, 2010
    Assignee: Epicentre Technologies Corporation
    Inventors: Gary A. Dahl, Jerome J. Jendrisak, Agnes J. Radek
  • System for monitoring the location of transgenes
    Patent number: 7645865
    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: May 1, 2003
    Date of Patent: January 12, 2010
    Assignee: Mayo Foundation for Medical Education and Research
    Inventors: Stephen James Russell, John Morris
  • Detection of nucleic acids by type-specific hybrid capture method
    Patent number: 7645571
    Abstract: Target-specific hybrid capture (TSHC) provides a nucleic acid detection method that is not only rapid and sensitive, but is also highly specific and capable of discriminating highly homologous nucleic acid target sequences. The method produces DNA/RNA hybrids which can be detected by a variety of methods.
    Type: Grant
    Filed: June 15, 2001
    Date of Patent: January 12, 2010
    Assignee: Qiagen Gaithersburg, Inc.
    Inventors: James Anthony, Attila Lorincz, Inna Williams, John Troy, Yanlin Tang
  • Cleavage of RNA at redundant sites
    Patent number: 7645578
    Abstract: The invention relates to methods for treating samples of RNA. In an embodiment the method includes contacting the sample of RNA with a set of oligodeoxynucleotides to provide a DNA/RNA duplex. The method includes contacting the DNA/RNA duplex with an enzyme having a DNA:RNA nuclease activity to provide a digested RNA sample. Kits in accordance with the invention are also described.
    Type: Grant
    Filed: October 31, 2006
    Date of Patent: January 12, 2010
    Assignee: Agilent Technologies, Inc.
    Inventor: Hui Wang
  • Compositions and methods for cDNA synthesis
    Patent number: 7638612
    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: September 3, 2003
    Date of Patent: December 29, 2009
    Assignee: Quanta Biosciences, Inc.
    Inventors: Ayoub Rashtchian, David M. Schuster
  • Association of TSPYL polymorphisms with SIDDT syndrome
    Patent number: 7632640
    Abstract: The identification of a novel mutation in the testis specific Y-like gene and association of the mutation with SIDDT syndrome are disclosed. Methods for diagnosing SIDDT syndrome are disclosed. Methods for identifying compounds for use in the diagnosis and treatment of disorders associated with mutation in the TSPYL gene are also disclosed. The invention therefore provides nucleic acid sequences, genes, polypeptides, antibodies, vectors containing the gene, host cells transformed with vectors containing the gene, animal models for the disease, methods for expressing the polypeptide, genetic screening methods and kits, diagnostic methods and kits.
    Type: Grant
    Filed: December 8, 2004
    Date of Patent: December 15, 2009
    Assignee: The Clinic for Special Children
    Inventors: Erik G. Puffenberger, Dietrich A. Stephan
  • Purification of a triple helix formation with an immobilized oligonucleotide
    Patent number: 7622566
    Abstract: A method for double-stranded DNA purification, by which a solution containing DNA in a mixture with other components is passed over a support on which is covalently coupled an oligonucleotide capable of hybridizing with a specific sequence present on the DNA to form a triple helix.
    Type: Grant
    Filed: October 20, 2005
    Date of Patent: November 24, 2009
    Assignee: Centelion
    Inventors: Joël Crouzet, Daniel Scherman, Pierre Wils
  • Detection of extracellular tumor-associated nucleic acid in blood plasma or serum using nucleic acid amplification assays
    Patent number: RE41327
    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, and to methods of detecting and monitoring extracellular mutant oncogenes or tumor-associated 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 mutated nucleic acid of the neoplasm in plasma or serum fractions.
    Type: Grant
    Filed: July 11, 2008
    Date of Patent: May 11, 2010
    Assignee: The Penn State Research Foundation
    Inventors: Christopher Gocke, Michael Kopreski