Complexity management and analysis of genomic data
First Claim
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1. A method of analyzing a first nucleic sample comprising:
- providing said first nucleic acid sample;
reproducibly reducing the complexity of said first nucleic acid sample to produce a second nucleic acid sample which may comprise a plurality of non-identical sequences whereby said second nucleic acid sample is obtainable by;
fragmenting said first nucleic acid sample to produce fragments and ligating adaptor sequences to said fragments;
fragmenting said first nucleic acid sample to produce fragments, denaturing said fragments, allowing some of said fragments to reanneal to form double stranded DNA sequences and removing said double stranded DNA sequences. amplification by arbitrarily primed PCR;
hybridizing said first nucleic acid sample to an oligonucleotide probe bound to a solid support;
hybridizing said first nucleic acid sequence to a mismatch binding protein;
providing a nucleic acid array;
hybridizing said second nucleic acid sample to said array; and
analyzing a hybridization pattern resulting from said hybridization.
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Abstract
The present invention provides for novel methods of sample preparation and analysis involving reproducibly reducing the complexity of a nucleic sample. The invention further provides for analysis of the above sample by hybridization to an array which may be specifically designed to interrogate the desired fragments for particular characteristics, such as, for example, the presence or absence of a polymorphism. The invention further provides for novel methods of using a computer system to model enzymatic reactions in order to determine experimental conditions before conducting actual experiments.
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Citations
38 Claims
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1. A method of analyzing a first nucleic sample comprising:
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providing said first nucleic acid sample;
reproducibly reducing the complexity of said first nucleic acid sample to produce a second nucleic acid sample which may comprise a plurality of non-identical sequences whereby said second nucleic acid sample is obtainable by;
fragmenting said first nucleic acid sample to produce fragments and ligating adaptor sequences to said fragments;
fragmenting said first nucleic acid sample to produce fragments, denaturing said fragments, allowing some of said fragments to reanneal to form double stranded DNA sequences and removing said double stranded DNA sequences. amplification by arbitrarily primed PCR;
hybridizing said first nucleic acid sample to an oligonucleotide probe bound to a solid support;
hybridizing said first nucleic acid sequence to a mismatch binding protein;
providing a nucleic acid array;
hybridizing said second nucleic acid sample to said array; and
analyzing a hybridization pattern resulting from said hybridization. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29)
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26. The method of claim wherein said step of predetermining the sequences contained in said second nucleic acid sample is conducted in a computer system.
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30. A method of screening for DNA sequence variations in an individual comprising:
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providing said first nucleic acid sample from said individual;
providing a second nucleic acid sample by reproducibly reducing the complexity of said first nucleic acid sample to produce a second nucleic acid sample which may comprise a plurality of non-identical sequences whereby said second nucleic acid sample is obtainable by;
fragmenting said first nucleic acid sample to produce fragments and ligating adaptor sequences to said fragments;
fragmenting said first nucleic acid sample to produce fragments, denaturing said fragments, allowing some of said fragments to reanneal to form double stranded DNA sequences and removing said double stranded DNA sequences. amplification by arbitrarily primed PCR;
hybridizing said first nucleic acid sample to an oligonucleotide probe bound to a solid support;
hybridizing said first nucleic acid sequence to a mismatch binding protein;
providing a nucleic acid array;
hybridizing said second nucleic acid sample to said array; and
analyzing a hybridization pattern resulting from said hybridization. - View Dependent Claims (31, 32, 33, 35, 36)
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34. A method of screening for DNA sequence variations in a population of individuals comprising:
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providing said a first nucleic acid sample from each of said individuals;
providing a second nucleic acid sample by reproducibly reducing the complexity of said first nucleic acid sample to produce a second nucleic acid sample which may comprise a plurality of non-identical sequences whereby said second nucleic acid sample is obtainable by;
fragmenting said first nucleic acid sample to produce fragments and ligating adaptor sequences to said fragments;
fragmenting said first nucleic acid sample to produce fragments, denaturing said fragments, allowing some of said fragments to reanneal to form double stranded DNA sequences and removing said double stranded DNA sequences. amplification by arbitrarily primed PCR;
hybridizing said first nucleic acid sample to an oligonucleotide probe bound to a solid support;
hybridizing said first nucleic acid sequence to a mismatch binding protein;
providing a nucleic acid array;
hybridizing said second nucleic acid sample to said array; and
analyzing a hybridization pattern resulting from said hybridization.
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37. In a computer system, a method of designing an array comprising:
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modeling specific enzymatic reactions between a known nucleic acid sequence and an enzyme;
obtaining the results of said modeled enzymatic reactions;
obtaining probe sequences based upon said results; and
designing an array to contain said probe sequences.
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38. A method of analyzing a plurality of nucleic acid samples, comprising:
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treating a first nucleic acid sample according to a defined procedure that produces a first population of fragments, the collective sequences of the fragments comprising a subset of the collective sequences present in the first nucleic acid sample, determining abundance or composition of a subset of the population of the first population of fragments;
treating a second nucleic acid sample according to the defined procedure to produce a second population of fragments containing corresponding fragments to the fragments in the first population;
determining abundance or composition of a subset of fragments in the second population having sequences corresponding to the subset of fragments in the first population.
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Specification