Combinatorial decoding of random nucleic acid arrays

• US 7,563,576 B2
• Filed: 01/22/2007
• Issued: 07/21/2009
• Est. Priority Date: 05/20/1999
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Chee, Mark S., Walt, David R.
• Primary Examiner(s): Kim; Young J
• Application Number:
  US11/625,708
• Publication Number:
  US 20080009000A1
• Time in Patent Office: 911 Days
• Field of Search: None
• US Class Current: 435/6.11
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/179 incorporating arbitrary or random nucleotide sequences
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/161 Vesicles, e.g. liposome
• CPC Class Codes: C12Q 2563/185 Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C40B 20/04 Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

The invention provides methods and compositions for combinatorially decoding arrays.

Claims

1. A method of determining the location of a decoding sequence on an array, said method comprising the steps of:

a) providing an array substrate comprising individual sites, wherein a first and second subpopulation of identifier nucleic acids are distributed among said individual sites, said first and second subpopulation of identifier nucleic acids comprising the same primer sequence and a different decoding sequence adjacent to said primer sequence;

b) providing a set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence and a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said different decoding sequences, wherein said set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide; and

c) adding to said array substrate a subset of said set of combinatorial decoding probes and detecting the presence of said label, thereby determining the location of said decoding sequence on said array.

2. The method of claim 1, wherein said first and second subpopulations of identifier nucleic acids are attached to microspheres.

3. The method of claim 2, wherein said microspheres are randomly distributed among said individual sites.

4. The method of claim 1, wherein said identifier nucleic acids comprise genomic DNA.

5. The method of claim 1, wherein said identifier nucleic acids are prepared by an amplification technique.

6. The method of claim 1, wherein said set of combinatorial decoding probes comprises four subsets.

7. The method of claim 1, wherein said variable region comprises a universal base.

8. The method of claim 1, wherein at each variable region nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding probe of said set of combinatorial decoding probes.

9. The method of claim 1, wherein said decoding nucleotide is immediately adjacent to said priming sequence.

10. The method of claim 1, wherein said decoding nucleotide is an internal nucleotide of said variable region.

11. The method of claim 1, wherein said variable region comprises at least one nucleotide between said priming sequence and said decoding nucleotide.

12. The method of claim 1, wherein said variable region comprises at least one nucleotide 5′

and at least one nucleotide 3′

of said decoding nucleotide.

13. The method of claim 1, further comprising the steps of:

d) removing said decoding probes from said array substrate; and

e) repeating steps (b)-(d) in sufficient iterations to determine the sequence of said decoding sequences.

14. The method of claim 1, wherein said individual sites comprise discrete sites.

15. A method of determining the location of a decoding sequence on an array, said method comprising the steps of:

a) providing an array surface comprising individual sites and a population of microspheres comprising at least a first and a second subpopulation distributed among said individual sites, wherein each subpopulation comprises identifier nucleic acids comprising;

1) the same primer sequence; and

2) a different decoding sequence adjacent to said primer sequence;

b) providing a first set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence, a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said decoding sequences, wherein said first set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide; and

c) adding to said array substrate a subset of said first set of combinatorial decoding probes and detecting the presence of said label, thereby determining the location of said decoding sequence on said array.

16. The method of claim 15 further comprising the steps of:

d) removing said decoding probes from said array substrate;

e) providing a second set of combinatorial decoding probes comprising a priming sequence complementary to said primer sequence, a variable region adjacent to said priming sequence, wherein said variable region comprises at least one decoding nucleotide that will basepair with a nucleotide of at least one of said decoding sequences at a position that is different from the position that will basepair with said decoding nucleotide of said first set of combinatorial decoding probes, wherein said second set of combinatorial decoding probes comprises subsets, each subset having a different decoding nucleotide at the same position and a label unique to each different decoding nucleotide; and

f) adding to said array substrate a subset of said second set of combinatorial decoding probes and detecting the presence of said label.

17. The method of claim 16, wherein said first set of combinatorial decoding probes comprises four subsets.

18. The method of claim 17, wherein said second set of combinatorial decoding probes comprises four subsets.

19. The method of claim 15, wherein said population of microspheres is randomly distributed among said individual sites.

20. The method of claim 15, wherein said identifier nucleic acids comprise genomic DNA.

21. The method of claim 15, wherein said identifier nucleic acids are prepared by an amplification technique.

22. The method of claim 15, wherein said variable region comprises a universal base.

23. The method of claim 15, wherein at each variable region nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding probe of said set of combinatorial decoding probes.

24. The method of claim 15, wherein said decoding nucleotide is immediately adjacent to said priming sequence.

25. The method of claim 15, wherein said decoding nucleotide is an internal nucleotide of said variable region.

26. The method of claim 15, wherein said variable region comprises at least one nucleotide between said priming sequence and said decoding nucleotide.

27. The method of claim 15, wherein said variable region comprises at least one nucleotide 5′

and at least one nucleotide 3′

of said decoding nucleotide.

28. The method of claim 15, wherein said individual sites comprise discrete sites.

29. A method of determining the location of a decoding sequence on an array, said method comprising the steps of:

a) providing an array substrate comprising individual sites, wherein a first and second subpopulation of identifier nucleic acids are distributed among said individual sites, said first and second subpopulation of identifier nucleic acids comprising the same primer sequence and a different decoding sequence adjacent to said primer sequence;

b) adding to the array a first combinatorial decoding probe and a second combinatorial decoding probe, each combinatorial decoding probe comprising a priming sequence complementary to said primer sequence and a variable region adjacent to said priming sequence, each variable region comprising a decoding nucleotide that will basepair with a nucleotide of at least one of said different decoding sequences, wherein said first combinatorial decoding probe and said second combinatorial decoding probe have a different decoding nucleotide at the same position and a label unique to the different decoding nucleotide; and

c) determining the location of said decoding sequence on said array by detecting the presence of said label.

30. The method of claim 29, wherein said first and second subpopulations of identifier nucleic acids are attached to microspheres.

31. The method of claim 29, wherein said individual sites comprise discrete sites.