Method and apparatus for identifying, classifying, or quantifyin

Details Method and apparatus for identifying, classifying, or quantifyin Method and apparatus for identifying, classifying, or quantifyin

1995-10-24

1999-02-16

Jones, W. Gary

Chemical apparatus and process disinfecting, deodorizing, preser

Analyzer, structured indicator, or manipulative laboratory...

Means for analyzing liquid or solid sample

435 6, 435 3, 435 912, 536 231, 536 243, 536 2433, 702 20, G01N 1506, G06G 758, C12Q 168, C07H 2104

Patent

active

058716971

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: 5604100 (1997-02-01), Perlin et al.
Brenner and Livak, "DNA fingerprinting by sampled sequencing", Proc. Natl. Acad. Sci., U.S.A., 86:8902-8906 (1989).
Unrau and Deugau, "Non-cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA `indexers`", Gene 145:163-169 (1994).
Adams et al., 1991, Science 252:1651-11656.
Adams et al., 1992, Nature 355:632-634.
AFLP Analysis System 1 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.
Caetano-Anolles, 1994, Plant Mol Biol 25:1011-1026.
Celis et al., 1994, Cell Biology (Academic Press, New York, NY). vol. #, pp. # not applicable.
Chevet 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. vol. # pages, not applicable.
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):11-14.
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 1 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 et 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, p. 2. vol. # not applicable.
Olson, 1993, Proc Natl Acad Sci 90:4338-4344.
Pease et al., 1994, Proc Natl Acad Sci 91:5022-5026.
Prashar 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.). vol. #, pages not applicable.
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. vol. #, pages not applicable.
Simpson, 1995, Technical Report. vol. #, pages not applicable.
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 50:193-204.
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). vol. #, pages not applicable.
Welsh et al., 1992, Nucleic Acids Res 20:4965-4970.
Woolley and Matheis, 1994, Proc Natl Acad Sci 91:11348-11352.
Zon, 1988, Pharm Res 5:539-549.
Mathieu-Daude et al., 1996, "Screening of differently amplified cDNA products from RNA arbitrarily primed PCR fingerprints using single strand conformation polymorphism (SSCP) gels", Nuc. Acids Res. 24: 1504-1507.
Matsubara and Okubo, 1995, "Recent Progress in human molecular biology and expression profiling of active genes in the body", Jpn. J. Pharmacol. 69: 181-185.
Brenner and Livak, "DNA fingerprinting by sampled sequencing", Proc. Natl. Acad. Sci., U.S.A., 86:8902-8906 (1989).
Unrau and Deugau, "Non-cloning amplification of specific DNA fragments from whole genomic DNA digests using DNA `indexers`", Gene 145:163-169 (1994).

Affiliated with

Also associated with

Rating

Method and apparatus for identifying, classifying, or quantifyin 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 quantifyin, 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 quantifyin will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-2059461