Method for detecting a biological entity in a sample

Chemistry: molecular biology and microbiology – Measuring or testing process involving enzymes or... – Involving nucleic acid

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C536S023100, C435S091100, C435S091200

Reexamination Certificate

active

07070935

ABSTRACT:
The invention relates to the detection of a biological entity in a sample. More particularly, the invention relates to detection of specific pathogens from a possible presence of hundreds to thousands of distinct biological species. The invention provides new assays that can detect the presence of one or more biological entity in a sample out of a possible number of hundreds to thousands of distinct biological species. The method according to the invention for detecting a biological entity in a sample comprises randomly amplifying nucleic acids in the sample to produce labeled nucleic acids; hybridizing the labeled nucleic acids to an array of predetermined nucleic acids; and detecting the labeled nucleic acids that have hybridized to the array.

REFERENCES:
patent: 5043272 (1991-08-01), Hartley
patent: 5106727 (1992-04-01), Hartley et al.
patent: 5632957 (1997-05-01), Heller et al.
patent: 5773210 (1998-06-01), Crowl et al.
patent: 5800992 (1998-09-01), Fodor et al.
patent: 5821060 (1998-10-01), Arlinghaus et al.
patent: 5837832 (1998-11-01), Chee et al.
patent: 5858659 (1999-01-01), Sapolsky et al.
patent: 5858661 (1999-01-01), Shiloh
patent: 5861242 (1999-01-01), Chee et al.
patent: 5871928 (1999-02-01), Fodor et al.
patent: 5925522 (1999-07-01), Wong et al.
patent: 5925525 (1999-07-01), Fodor et al.
patent: 5929208 (1999-07-01), Heller et al.
patent: 5994058 (1999-11-01), Senapathy
patent: 6013440 (2000-01-01), Lipshutz et al.
patent: 6027880 (2000-02-01), Cronin et al.
patent: 6156502 (2000-12-01), Beattie
patent: 0 950 720 (1999-10-01), None
patent: WO 96/41893 (1996-12-01), None
patent: WO 97/22720 (1997-06-01), None
patent: WO99/22023 (1999-05-01), None
patent: WO 02/061659 (2002-08-01), None
Peng et al, “Multiple PCR analyses on trace amounts of DNA extracted from fresh and paraffin wax embedded tissues after random hexamer primer PCR amplification”, J. Clin. Pathol. (1994) 47:605-608.
See http://www.psrast.org/soilfertfact.htm (accessed Jun. 7, 2005).
Written Opinion for Application No. PCT/US01/04104, dated May 30, 2003 (mailing date).
Iyer, L., et al., “Adaptations of the Helix-Grip Fold for Ligand Binding and Catalysis in the START Domain Superfamily,”Proteins: Structure, Function, and Genetics,vol. 43, pp. 134-144 (2001).
Kitazoe, Y., et al., “A New Theory of Phylogeny Inference Through Construction of Multidimensional Vector Space,”Mol. Biol. Evol.,vol. 18, No. 5, pp. 812-828 (2001).
Geourjon, C., et al., “Identification of Related Proteins With Weak Sequence Identity Using Secondary Structure Information,”Protein Science,vol. 10, pp. 788-797 (2001).
Anantharaman, V., et al., “Regulatory Potential, Phyletic Distribution and Evolution of Ancient, Intracellular Small-Molecule-Binding Domains,”J. Mol. Biol.,vol. 307, pp. 1271-1292 (2001).
Liberles, D., et al., “The Adaptive Evolution Database (TAED),”Genome Biology,vol. 2, No. 4, pp. preprint/0003.1-0003.18, 2001.
Tatusov, R., et al., “The COG Database: New Developments in Phylogenetic Classification of Proteins From Complete Genomes,”Nucleic Acids Research,vol. 29, No. 1, pp. 22-28 (2001).
Anantharaman, V., et al., “TRAM, a Predicted RNA-Binding Domain, Common to tRNA Uracil Methylation and Adenine Thiolation Enzymes,”FEMS Microbiology Letters,vol. 197, pp. 215-221 (2001)
Liu, Q., et al., “DNA Computing on Surfaces,”Nature,vol. 403, pp. 175-179, Jan. 13, 2000.
Woese, Carl R., “Interpreting the Universal Phylogenetic Tree,”Proc. Natl. Acad. Sci.,vol. 97, No. 15, pp. 8392-8396, Jul. 18, 2000.
Aravind, L., et al., “The a/β Fold Uracil DNA Glycosylases: A Common Origin With Diverse Fates,”Genome Biology,vol. 1, No. 4, pp. research0007.1-0007.8 (2000).
Natale, D., et al., “Towards Understanding the First Genome Sequence of a Crenarchaeon by Genome Annotation Using Clusters of Orthologous Groups of Proteins (COGs),”Genome Biology,vol. 1, No. 5, pp. research0009.1-0009.19 (2000).
Grech, A., et al., “Complete Structural Characterisation of the Mammalian andDrosophilaTRAF Genes: Implications for TRAF Evolution and the Role of RING Finger Splice Variants,”Molecular Immunology,vol. 37, pp. 721-734 (2000).
Adleman, Leonard, M., “Computing With DNA,”Scientific American,vol. 279, pp. 54-61, Aug., 1998.
Hacia, J. G., et al., “Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High-Density Oligonucleotide Arrays,”Genome Research,vol. 8, pp. 1245-1258 (1998).
Ramsay, G., “DNA Chips: State-of-the-Art,”Nature Biotechnology,vol. 16, pp. 40-44 (1998).
Adleman, Leonard, M., “Molecular Computation of Solutions to Combinatorial Problems,”Science,vol. 266, pp. 1021-1024, Nov. 11, 1994.
Atschul, Stephen, et al., “Basic Local Alignment Search Tool,”J. Mol. Biol.,vol. 215, pp. 403-410 (1990).
International Search Report for Application No. PCT/US01/04104 dated May 6, 2002 (mailing date).
Guschin, Dmitry Y., et al., “Oligonucleotide Microchips as Genosensors for Determinative and Environmental Studies in Microbiology”,Applied and Environmental Microbiology,vol. 63, No. 6, pp. 2397-2402, Jun. 1997.
Kahl Gunter, Dictionary of Gene Technology, VCH Publishers, Inc., New York, NY (USA), Jun. 1995.
Boehringer Mannheim, 1998 Biochemical Catalog, GmbH printed in Germany, Jan. 1998.
Bej et al., Multiplex PCR amplification and immobilized capture probes for detection of bacterial pathogens and indicators in water;Molecular and Cellular Probes,vol. 4, pp. 353-365; Dec. 1990.
Hacia, J.G. et al. (1998) “Evolutionary Sequence Comparisons Using High-Density Oligonucleotide Arrays”;Nature Genetics;18:155-158.
Hacia, J.G. et al. (1998) “Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High Density Oligonucleotide Arrays”;Genome Research,8:1245-1258.
Head, S.R. et al. (1999); “Solid-Phase Sequence Scanning for Drug Resistance Detection in Tuberculosis”;Molecular and Cellular Probes; 13:81-87.
Tetenius et al., “Degenerate oligonucleotide primed PCR: General amplification of target DNA by a single degenerate primer”,Genomics(1992) 13:718-725.
Sayada et al., “Genomic fingerprinting of Yersinia enterocolitica species by degenerate oligonucleotide primed polymerase chain reaction”,Electrophoresis(1994) 15:562-565.
Muller et al., “Defining ancestral karyotype of all primates by multidirectional chromosome painting between tree shrews, lemurs and humans”,Chromosoma(1999) 108:393-400.
Castellino, A.m. (1997) “When the Chips are Down”,Genome Research7:943-946.
Grattard, F et al. (1994) “Arbitrarily Primed PCR, Ribotyping, and Plasmid Pattern Analysis Applied to Investigation of a Nosocomial Outbreak Due toEnterobacter cloacoein a Neonatal Intensive Care Unit”;Journal of Clinical Microbioloty32(3):596-602.
Hacia, J.G. et al. (1996) “Detection of Heterozygous Mutations of BRCA1 Using High Density Oligonucleotide Arrays and Two-Colour Fluorescence Analysis”;Nature Genetics14:441-447.
Ramsay, G. (1998) “DNA Chips: State-of-the-Art”;Nature Biotechnology16:40-44.
Schena, S. (1996) “Genome Analysis with Gene Expression Microarrays”;BioEssays18(5):427-431.
Struelens, M.D., M.J. et al. (1998) Comparative and Library Epidemiological Typing Systems: Outbreak Investigations Versus Surveillance Systems:, From the Fifth International Conference on the Prevention of Infection;Infection Control and Hospital Epidemiology19(8):565-569.
Tang, K. et al. (1999) “Chip-Based Genotyping by Mass Spectrometry (DNA Chip/Single Nucleotide Polymorphism)”;Proc. Natl. Acad. Sci USA96L19916-10020.
Wallraff, G. et al. (1997) “DNA Sequencing on a Chip (This Method, Which Combined Semiconductor Manufacturing Technology with Molecular Biology, Has Been Used to Build DNA and RNA Arrays at Densities as High as 106sites/cm2

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Method for detecting a biological entity in a sample does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Method for detecting a biological entity in a sample, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method for detecting a biological entity in a sample will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-3600075

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.