Method and apparatus for identifying classifying or quantifying

Data processing: database and file management or data structures – Database design – Data structure types

Patent

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

702 20, 435 6, 435 912, G06F 1730, C12Q 168

Patent

active

061416576

ABSTRACT:
This invention provides methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. The methods make use of information on the presence of carefully chosen target subsequences, typically of length from 4 to 8 base pairs, and preferably the length between target subsequences in a sample DNA sequence together with DNA sequence databases containing lists of sequences likely to be present in the sample to determine a sample sequence. The preferred method uses restriction endonucleases to recognize target subsequences and cut the sample sequence. Then carefully chosen recognition moieties are ligated to the cut fragments, the fragments amplified, and the experimental observation made. Polymerase chain reaction (PCR) is the preferred method of amplification. Another embodiment of the invention uses information on the presence or absence of carefully chosen target subsequences in a single sequence clone together with DNA sequence databases to determine the clone sequence. Computer implemented methods are provided to analyze the experimental results and to determine the sample sequences in question and to carefully choose target subsequences in order that experiments yield a maximum amount of information.

REFERENCES:
patent: 4555019 (1985-11-01), Spendel et al.
patent: 4987066 (1991-01-01), Epplen
patent: 5093245 (1992-03-01), Keith et al.
patent: 5171534 (1992-12-01), Smith et al.
patent: 5175082 (1992-12-01), Jeffreys
patent: 5202231 (1993-04-01), Drmanac et al.
patent: 5262311 (1993-11-01), Pardee et al.
patent: 5366877 (1994-11-01), Keith et al.
patent: 5459037 (1995-10-01), Sutcliffe et al.
patent: 5523208 (1996-06-01), Kohler et al.
patent: 5604100 (1997-02-01), Perlin
patent: 5632041 (1997-05-01), Peterson et al.
patent: 5706498 (1998-01-01), Fujimiya et al.
patent: 5733729 (1998-03-01), Lipshutz et al.
Okubo, K. "Large scale cDNA sequencing tor analysis of quantitative and qualitative aspectes of gene expression" Nature Genetics, vol. 2, pp. 173-179, Nov. 1992.
Keele, J.W. et al. A Conceptual Database Model for Genomic Research Journal or Computaional Biology, vol. 1, No. 1 pp. 65-76, 1994.
Matsubara, K. et al. "Identification of new genes by systematic analysis of cDNAs and database construction" Curent Opinion in Biotechnology, vol. 4, pp. 672-677, 1993.
Adams et al., 1991, Science 252:1651-11656.
Adams et al., 1992, Nature 355:632-634.
AFLP Analysis System I AFLP Starter Primer Kit, Instruction Manual, Life Technology.
Anon, 1995, Nature Medicine 1(2):102.
Ayala et al., 1995, BioTechniques 18(5):842-850.
Bassam et al., 1991, Anal Biochem 196:80-83.
Broude et al., 1994, Proc Natl Acad Sci 91:3072-3076.
Castano-Anolles, 1994, Plant Mol Biol 25:1011-1026.
Celis et al., 1994, Cell Biology (Academic Press, New York, NY).
Chavet et al., 1995, Nucleic Acids Res 23(16):3343-3344.
Chomczynski and Sacchi, 1987, Anal Biochem 162:156-159.
Chomczynski, 1993, BioTechniques 15(3):532-536.
CLONETECHniques, Jan. 1996.
Dorper and Winnacker, 1983, Nucleic Acids Res 11(9):2575-2584.
Drmanac et al., 1991, Int Conf Electrophor, Supercomput Hum Gen, Cantor (ed.), pp. 60-74.
Drmanac et al., 1993, Science 260:1649-1652.
Drmanac et al., 1992, Electrophoresis 13:566-573.
Egholm et al., 1993, Nature 365:566-567.
Eigen et al., 1994, Proc Natl Acad Sci 91:5740-5747.
Fischer et al., 1995, Proc Natl Acad Sci 92:5331-5335.
Gautier et al., 1987, Nucleic Acids Res 15:6625-6641.
Gubler et al., 1983, Gene 25:263-269.
Guo et al., 1994, Nucleic Acids Res 22:5456-5465.
Hedgpeth et al., 1972, Proc Natl Acad Sci 69:3448-3452.
Hoheisel, 1994, TIG 10(3):.
Holtke et al., 1992, BioTechniques 12(1):104-113.
Ito et al., 1994, FEBS Lett 351:231-236.
Ivanova and Belyavsky, 1995, Nucleic Acids Res 23:2954-2958.
Ju et al., 1995, Proc Natl Acad Sci 92:4347-4351.
Kato et al., 1994, Gene 243-250.
Kato, 1995, Nucleic Acids Res 23(18):3685-3690.
Kricka et al., 1995, Molecular Probing, Blotting and Sequencing Chapter I and Table IX (Academic Press, New York, NY.
Krol et al., 1988, BioTechniques 6:958-976.
Lamture, 1994, Nucleic Acids Res 22:2121-2125.
Langer et al., 1981, Proc Natl Acad Sci 78(11):6633-6637.
Lennon et al., 1991, Trends in Genetics 7(10):314-317.
Liang et al., 1992, Science 257:967-971.
Liang et al., 1994, Nucleic Acids Res 22(25):5763-5764.
Liang et al., 1995, Curr Opin Immunol 7:274-280.
Lisitsyn, 1993, Science 259:946-950.
Maier et al., 1994, Nucleic Acids Res 22(16):3423-3424.
Maniatis, 1982, Molecular Cloning: A Laboratory Manual (Cold Spring Harbor, NY) pp. 124-125, 286-288.
McClelland el al., 1995, TIG 11(6):242-246.
McClelland et al., 1993, Exs 67:103-115.
Meier-Ewert et al., 1993, Nature 361:375-376.
Mou et al., 1994, Biochem Biophys Res Comm 199(2):564-569.
Mutter et al., 1995, Nucleic Acids Res 23:1411-1418.
Okayama and Berg. 1982, Mol Cell Biol 2(2):161-170.
Olesen et al., 1993, BioTechniques 15(3):480-485.
OLIGO Version 4.0 for Macintosh, Reference Manual, Eqn. 1, pg. 2.
Olson, 1993, Proc Natl Acad Sci 90:4338-4344.
Pease et al., 1994, Proc Natl Acad Sci 91:5022-5026.
Prasher and Weissman, 1996, Proc Natl Acad Sci 93:659-663.
Press et al., 1986, Numerical Recipes--The Art of Scientific Computing .sctn.10.9, (Cambridge University Press, Cambridge, U.K.).
Sanger et al., 1977, Proc Natl Acad Sci 74(12):5436-5467.
Sarin et al., 1988, Proc Natl Acad Sci 85:7448-7451.
Schmidt and Mueller, 1996, Nucleic Acids Res 24(9):1789-1791.
Sedgewick, 1990, Algorithms in C. chapter 19, Addison-Wesley, Reading, MA.
Simpson, 1995, Technical Report.
Smith and Birnstiel, 1976, Nucleic Acids Res 3:2387-2399.
Soares et al., 1994, Proc Natl Acad Sci 91:9228-32.
Sokolov and Prockop, 1994, Nucleic Acids Res 22(19):4009-4015.
Song and Osborn, 1994, Plant Mol Biol 26:1065-1071.
Stein et al., 1988, Nucleic Acids Res 16:3209.
Stimson et al., 1995, Proc Natl Acad Sci 92:6379-6383.
Tatari et al., 1995, Proc Natl Acad Sci 92:8803-8807.
Titus et al., 1982, J Immunol Meth 60:193-204.
Ushijima et al., 1995, Mutation Research 334:283-292.
Velculescu et al., 1995, Science 270:484-487.
Watson et al., 1992 Recombinant DNA, Chapter 7 (W.H. Freeman, New York).
Welsh et al., 1992, Nucleic Acids Res 20:4965-4970.
Woolley and Mathies, 1994, Proc Natl Acad Sci 91:11348-11352.
Zon, 1998, Pharm Res 5:539-549.
Mathieu-Daude et al., 1996, Nuc. Acids Res, 24:1504-1507.
Matsubara and Okubo, 1995, Jpn. J. Pharmacol. 69:181-185.
Brenner and Livak, 1989, Proc. Natl Acad. Sci. 86:8902-8906.
Unrau and Deugau, 1994, Gene 145:163-169.

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 and apparatus for identifying classifying or quantifying 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 and apparatus for identifying classifying or quantifying , we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and apparatus for identifying classifying or quantifying will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-2064750

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