Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid
Reexamination Certificate
2005-06-07
2005-06-07
Fredman, Jeffrey (Department: 1634)
Chemistry: molecular biology and microbiology
Measuring or testing process involving enzymes or...
Involving nucleic acid
C435S091100, C435S091200, C435S287200, C536S023100, C536S023700, C536S024100, C536S024300
Reexamination Certificate
active
06902894
ABSTRACT:
The present invention provides a diagnostic test method for detecting a tendency to rifampin resistance caused by mutations in a rpoB gene ofM. tuberculosis, comprising the steps of (i) extracting genomic DNA from a biological sample containingM. tuberculosiscells; (ii) amplifying from the extracted genomic DNA the rpoB gene coding sequence or at least one distinct fragment thereof containing nucleotides encoding at least one test amino acid of the group consisting of amino acid numbers 511, 512, 513, 514, 515, 516, 517, 518, 522, 526, 529, 531, 533 to produce fluorescently labeled amplification product; (iii) contacting said fluorescently labeled amplification product with a first control array of oligonucleotide probes having DNA sequences specific to the wildtypeM. tuberculosisrpoB gene coding sequence, including the nucleotides encoding the at least one test amino acid, and with a second test array of oligonucleotide probes having DNA sequences specific to theM. tuberculosisrpoB gene coding sequence, including nucleotides encoding mutations in the at least one test amino acid, wherein at least 3 mutations of the rpoB gene are probed for by the second test array of oligonucleotide probes; detecting any fluorescent hybridization signal of said purified fluorescently labeled amplification product which hybridized with the first and second arrays of oligonucleotide probes; (iv) correlating said detected hybridization with a tendency to rifampin resistance; and (v) correlating the detected hybridization to a tendency to rifampcin resistance and MDR.
REFERENCES:
patent: 5643723 (1997-07-01), Persing et al.
patent: 5789173 (1998-08-01), Peck et al.
patent: 5851763 (1998-12-01), Heym et al.
patent: 6228575 (2001-05-01), Gingeras et al.
patent: 6312960 (2001-11-01), Balch et al.
patent: 6329138 (2001-12-01), De Beenhouwer et al.
patent: 6465178 (2002-10-01), Chappa et al.
Erlich et al., “PCR Technology, Principles and Applications for DNA Amplification” May 21, 1991.
Mikhailovich et al, Journal of Clinical Microb. vol. 39, No. 7, Jul. 2001 pp. 2531-2540.
Towards Fully Automated Genome-Wide Polymorphism Screening, Nature Genetics, vol. 9, Apr. 1995.
A Primer-Guided Nucleotide Incorporating Assay in the Genotyping of Apolipoprotein E, Syvanen et al., Genomics 8, 684-692 (1990).
Minisequencing: A Specific Tool for DNA Analysis and Diagnostics on Oligonucleotide Arrays, Pastinen et al.; Genome Research, 7:606-614 (1997).
Fluorescence Energy Transfer Detection as a Homogeneous DNA Diagnostic Method, Chen et al;Proc. Natl. Acad. Sci. USA, vol. 94, pp. 10756-10761, Sep. 1997.
Fluorescence Polarization in Homogeneous Nucleic Acid Analysis, Chen et al., Genome Research, 9:492-498 (1999).
Single-Well Genotyping of Diallellic Sequence Variations by a Two-Color ELISA-based Oligonucleotide Ligation Assay, Tobe et al., 3728-32,Nucleic Acids Research, 1996, vol. 24, No. 19.
Multicolor Molecular Beacons for Allele Discrimination, Tyagi et al.,Nature Biotechnology, vol. 16, Jan. 1998.
Large-Scale Identification, Mapping and Genotyping of Single-Nucleotide Polymorphisms in the Human Genome, Wang et al.,Science, vol. 280, May 15, 1998.
Dynamic Allele-Specific Hybridization, Howell et al.,1999 Nature Biotechnology, Inc., vol. 17, Jan. 17, 1999.
Evaluation of Single Nucleotide Polymorphism Typing with Invader on PCR Amplicons and its Automation, Mein et al., Genome Research, 10:330-343 (2000).
PCR—A Practical Approach, Quirke et al., Feb. 1991.
DNA Cloning, vol. 1, A Practical Approach.
DNA Sequencing with Chain-Terminating Inhibitors, Sanger et al.,Proc. Natl. Acad. Sci. USA, vol. 74, No. 12, pp 5463-67, Dec. 1977.
Using Antibodies—A Laboratory Manual, Harlow.
General Techniques of Cell Culture, Harrison et al., published 1997.
Phage Display of Peptides and Proteins—A Laboratory Manual, published 1996.
Isolation of Genomic DNA from Mycobacteria, Belisle et al., fromMethods in Molecular Biology, vol. 101, Mycobacteria Protocols.
Molecular Evidence for Heterogenity of the Multiple-Drug-Resistant Mycobacterium Tuberculosis Population in Scotland (1990 to 1997), Zang et al.,Journal of Clinical Microbiology, Apr. 1999, pp 998-1003, vol. 37, No. 4.
Simultaneous Genotyping and Species Identification Using Hydridization Pattern Recognition Analysis of Generic Mycobacterium DNC Arrays, Gingeras et al., Genome Research 1998, 8:435-448 (1998).
Bioconjugate Techniques, Hermanson.
Mutations in the rpoB Gene of Rifampin-Resistant Mycobacterium Tuberculosis Strains Isolated Mostly In Asian Countries and Their Rapid Detection by Line Probe Assay, Hirano et al.,Journal of Clinical Microbiology, Aug. 1999, p 2663-66, vol. 37, No. 8.
SBE-Tags: An Array-Based Method for Efficient Single-Nucleotide Polymorphism Genotyping, Hirschhorn et al.,PNAS, Oct. 24, 2000, vol. 97, No. 22.
Detection of a Genetic Locus Encoding Resistance to Rifamph in Mycobacterial Cultures and in Clinical Specimens, Hunt et al., Diagn Microbiol Infect Dis 1994, 18:219-27.
Characterization by Automated DNC Sequencing of Mutations in the Gene (rpoB) Encoding the RNA Polymerase B Subunit in Rifampin-Resistant Mycobacterium Tuberculosis Strains for New York City and Texas,Journal of Clinical Microbiology, Kapur et al., Apr. 1994, p 1095-98, vol. 32, No. 4.
The rpoB Gene of Mycobacterium Tuberculosis, Miller et al.,Antimicrobial Agents and Chemotherapy, Apr. 1994; p 805-11, vol. 38, No. 4.
Detection of Resistance to Isoniazid, Rifampin and Streptomycin in Clinical Isolates of Mycobacterium Tuberculosis by Molecular Methods, Nachamkin et al., Clinical Infectious Diseases, 1997, 24:894-00.
rpoB Mutations in Multidrug-Resistant Strains of Mycobacterium Tuberculosis Isolated in Italy,Journal of Clinical Microbiology, Apr. 1999, p 1197-99, vol. 37, No. 4.
Evaluation of the INNO-LIPA Rif. TB Assay, a Reserve Hydridization Assay for the Simultaneous Detection of Mycobacterium Tuberculosis Complex and Its Resistance to Rifampin, Rossau et al.,Antimicrobial Agents and Chemotherapy, Oct. 1997, p 2093-98, vol. 41, No. 10.
Mycobacterium Species Identification and Rifampin Resistance Testing with High-Density DNA Probe Arrays, Troesch et al.,Journal of Clinical Microbiology, Jan. 1999, p 49-55, vol. 37, No. 1.
Direct, Automated Detection of Rifampin-Resistant Mycobacterium Tuberculosis by Polymerase Chain Reaction and Single-Strand Conformation Polymorphism Analysis, Talenti et al.,Antimicrobial Agents and ChemotherapyOct. 1993, p 2054-58, vol. 37, No. 10.
Characterization of Rifampin Resistance in Pathogenic Mycobacteria, Williams et al.,Antimicrobial Agents and Chemotherapy, Oct. 1994, p 2380-86, vol. 38, No. 10.
Evaluation of a Polymerase Chain Reaction-Based Universal Heteroduplex Generator Assay for Direct Detection of Rifampin Susceptibility of Mycobacterium Tuberculosis from Sputum Specimens, Williams et al., Clinical Infectious Diseases, 1998, 26:446-50.
Woo Hok Sin
Yang Mengsu
Fredman Jeffrey
Genetel Pharmaceuticals Ltd.
Sakelaris Sally A
Wallenstein Wagner & Rockey Ltd.
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