System and method for detecting a biological entity in a...

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

C435S091200, C536S024320, C536S024330

Reexamination Certificate

active

07455966

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: 5298392 (1994-03-01), Atlas 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: 6087104 (2000-07-01), Yamada et al.
patent: 6156502 (2000-12-01), Beattie
patent: 7070935 (2006-07-01), Schaudies et al.
patent: 2004/0096879 (2004-05-01), Schaudies et al.
patent: 0 950 720 (1999-10-01), None
patent: WO 96/41893 (1996-12-01), None
patent: WO 9722720 (1997-06-01), None
patent: WO 9918241 (1999-04-01), None
patent: WO 99/22023 (1999-05-01), None
patent: WO 02/061659 (2002-08-01), None
Bej et al. Multiplex PCR amplification and immobilized capture probes for detection of bacterial pathogens and indicators in water. Mol. Cell. Probes, vol. 4, pp. 353-365, 1990.
Peng et al. Multiple PCR analyses on trace amounts of DNA extracted from fresh and paraffin wax embedded tissues after random primer PCR amplification. J. Clin.Pathol., vol. 47, pp. 605-608, 1994.
Seto et al. Overlapping redundant seplets identical with regulatory elements of HIV and SV40. Nucleic Acids Res., vol. 17, No. 7, pp. 2783-2800, 1989.
Nelson et al. The limits of random fingerprinting. Genomics, vol. 40, p. 1-12, 1997.
Nelson et al. The limits of random fingerprinting. Genomics, vol. 40, p. 1-12, 1997.
Paulson et al. Loss of heterozygosity analysis using whole genome amplification, cell sorting, and fluorescence-based PCR. Genome research, vol. 9, pp. 482-491, 1999.
Nelson et al. The limits of random fingerprinting. Genomics, vol. 40, p. 1-12, 1997.
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, 8 pp., 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., “Strategies for Mutational Analysis of the Large Multiexon ATM Gene Using High Density Oligonucleotide Arrays,”Genome Research, vol. 8, pp. 1245-1258, 1998.
Telenius, et al., “Degenerate oligonucleotide primed PCR: General amplification of target DNA by a single degenerate primer,”Genomics, vol. 13, pp. 718-725, 1992.
Sayada, et al., “Genomic fingerprinting of Yersinia enterocolitica species by degenerate oligonucleotide primed polymerase chain reaction,”Electrophoresis, vol. 15, pp. 562-565, 1994.
Muller et al., “Defining ancestral karyotype of all primates by multidirectional chromosome painting between tree shrews, lemurs and humans,”Chromosoma, vol. 108, pp. 393-400, 1999.
Ramsay, G., “DNA Chips: State-of-the Art,”Nature Biotechnology, vol. 16, pp. 40-44, 1998.
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).
Kitazoc, 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-Molccule-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.
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).
Head, S. R., et al., “Solid-Phase Sequence Scanning for Drug Resistance Detection in Tuberculosis,”Molecular and Cellular Probes, vol. 13, pp. 81-87 (1999).
Tang, K., et al., “Chip-Based Genotyping by Mass Spectrometry (DNA Chip/Single Nucleotide Polymorphism),”Proc. Natl. Acad. Sci. USA, vol. 96, pp. 10016-10020 (1999).
Adleman, Leonard, M., “Computing With DNA,”Scientific American, vol. 279, pp. 54-61, Aug. 1998.
Hacia, J. G. et al., “Evolutionary Sequence Comparisons Using High-Density Oligonucleotide Arrays,”Nature Genetics, vol. 18, pp. 155-158 (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).
Struelens, M.D., M. J., et al., “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 Epidemiology, vol. 19, No. 8, pp. 565-569 (1998).
Castellino, A. M., “When the Chips are Down,”

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

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

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

Rate now

     

Profile ID: LFUS-PAI-O-4047500

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