Complexity management and analysis of genomic DNA

• US 6,361,947 B1
• Filed: 10/27/1999
• Issued: 03/26/2002
• Est. Priority Date: 10/27/1998
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Lockhart, David J., Dong, Shoulian
• Primary Examiner(s): Brusca, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/428,350
• Time in Patent Office: 881 Days
• Field of Search: 435/6, 536/23.1
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 2521/313 Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2563/143 Magnetism, e.g. magnetic label
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: Y10S 977/924 using nanostructure as support of dna analysis

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.

Claims

1. A method of analyzing a first nucleic acid sample comprising:

providing said first nucleic acid sample;

obtaining a second nucleic acid sample by;

(a) fragmenting said first nucleic acid sample to produce fragments, ligating adaptor sequences to said fragments, amplifying at least some of said fragments, and isolating said amplified fragments;

or

(b) fragmenting said first nucleic acid sample to produce fragments, denaturing said fragments, allowing at least some of said fragments to reanneal to form double stranded DNA sequences and removing said double stranded DNA sequences thus isolating said single stranded fragments;

or

(c) amplifying said first nucleic acid sample by arbitrarily primed PCR to produce an amplification product and isolating said amplification product;

or

(d) fragmenting said first nucleic acid sample to produce fragments, hybridizing said fragments to an oligonucleotide probe bound to a solid support, and isolating said hybridized fragments;

or

(e) fragmenting said first nucleic acid sample to produce fragments, binding said fragments to a mismatch binding protein, and isolating said bound fragments;

providing a nucleic acid array;

hybridizing said second nucleic acid sample to said array; and

analyzing a hybridization pattern resulting from said hybridization.

2. The method of claim 1 wherein said second nucleic acid sample comprises at least 0.5% of said first nucleic acid sample.

3. The method of claim 1 wherein said second nucleic acid sample comprises at least 3% of said first nucleic acid sample.

4. The method of claim 1 wherein said second nucleic acid sample comprises at least 12% of said first nucleic acid sample.

5. The method of claim 1 wherein said second nucleic acid sample comprises at least 50% of said first nucleic acid sample.

6. The method of claim 1 wherein said first nucleic acid sample is DNA.

7. The method of claim 1 wherein said first nucleic acid sample is genomic DNA.

8. The method of claim 1 wherein said first nucleic acid sample is cDNA derived from RNA or mRNA.

9. The method of claim 1 wherein steps (b), (d) and (e) further comprise the step of amplifying the isolated fragments.

10. The method of claim 9 wherein said step of amplifying is performed by a polymerase chain reaction (PCR).

11. The method of claim 1 wherein the entire method is performed in a single reaction vessel.

12. The method of claim 1 wherein said step of fragmenting the first nucleic acid sample comprises digestion with at least one restriction enzyme.

13. The method of claim 1 wherein said step of fragmenting the first nucleic acid sample comprises digestion with a type IIs endonuclease.

14. The method of claim 1 wherein said adaptor sequences comprise PCR primer template sequences.

15. The method of claim 1 wherein said adaptor sequences comprise tag sequences.

16. The method of claim 1 wherein said solid support is a magnetic bead.

17. The method of claim 1 wherein said mismatch binding protein is bound to a magnetic bead.

18. The method of claim 1 wherein said method for analyzing a first nucleic acid sample comprises determining whether the first nucleic acid sample contains sequence variations.

19. The method of claim 18 wherein said sequence variations are single nucleotide polymorphisms (SNPs).

20. The method of claim 1 wherein the nucleic acid array is designed to query DNA fragments which have been produced by the identical procedures used to obtain said second nucleic acid sample.

21. The method of claim 20 wherein the sequences contained in said second nucleic acid sample are predetermined.

22. The method of claim 20 wherein said sequences contained in said second nucleic acid sample are first determined by a computer system.

23. The method of claim 19 wherein said second nucleic acid sample is obtainable by:

binding oligonucleotide probes containing a desired SNP sequence to magnetic beads to form probe-bead complexes;

hybridizing said probe-bead complexes to said first nucleic acid sample;

exposing said first nucleic acid sample to a single strand DNA nuclease to remove single stranded DNA thereby obtaining only DNA duplexes;

ligating a double stranded adaptor sequence comprising a restriction enzyme site to said DNA duplexes;

digesting said DNA duplexes with a restriction enzyme to release the magnetic bead; and

isolating the duplexes.

24. The method of claim 23 wherein said restriction enzyme is a Class IIs endonuclease.

25. A method of screening for DNA sequence variations in an individual comprising:

providing a first nucleic acid sample from said individual;

obtaining a second nucleic acid sample by;

(a) fragmenting said first nucleic acid sample to produce fragments, ligating adaptor sequences to said fragments, amplifying at least some of said fragments, and isolating said amplified fragments;

or

(b) 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 thus isolating said single stranded fragments;

or

(c) amplifying said first nucleic acid sample by arbitrarily primed PCR to produce an amplification product and isolating said amplification product;

or

(d) fragmenting said first nucleic acid sample to produce fragments, hybridizing said fragments to an oligonucleotide probe bound to a solid support, and isolating said hybridized fragments;

or

(e) fragmenting said first nucleic acid sample to produce fragments, binding said fragments to a mismatch binding protein, and isolating said bound fragments;

providing a nucleic acid array wherein said array comprises probes designed to interrogate for DNA sequence variations;

hybridizing said second nucleic acid sample to said array;

generating a hybridization pattern resulting from said hybridization; and

determining the presence or absence of DNA sequence variations in the individual based upon an analysis of the hybridization pattern.

26. The method of claim 25 wherein said sequence variation is a single nucleotide polymorphism (SNP).

27. The method of claim 26 wherein said SNP is associated with a disease.

28. The method of claim 26 wherein said SNP is associated with the efficacy of a drug.

29. A method of screening for DNA sequence variations in a population of individuals comprising:

providing a first nucleic acid sample from each of said individuals;

providing a second nucleic acid sample by;

(a) fragmenting said first nucleic acid sample to produce fragments, ligating adaptor sequences to said fragments, amplifying at least some of said fragments, and isolating said amplified fragments;

or

(b) 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 thus isolating said single stranded fragments;

or

(c) amplifying said first nucleic acid sample by arbitrarily primed PCR to produce an amplification product and isolating said amplification product;

or

(d) fragmenting said first nucleic acid sample to produce fragments, hybridizing said fragments to an oligonucleotide probe bound to a solid support, and isolating said hybridized fragments;

or

(e) fragmenting said first nucleic acid sample to produce fragments, binding said fragments to a mismatch binding protein, and isolating said bound fragments;

providing a plurality of identical nucleic acid arrays wherein said arrays comprise probes which are designed to interrogate for DNA sequence variations;

hybridizing each of said second nucleic acid samples to one of said plurality of identical arrays; and

generating a plurality of hybridization patterns resulting from said hybridizations; and

analyzing the hybridization patterns to determine the presence or absence of sequence variation in the population of individuals.

30. The method of claim 29 wherein said sequence variation is a single nucleotide polymorphism.