Combinatorial decoding of random nucleic acid arrays

• US 7,166,431 B2
• Filed: 08/21/2003
• Issued: 01/23/2007
• Est. Priority Date: 05/20/1999
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Chee, Mark S., Walt, David R.
• Primary Examiner(s): Kim; Young J.
• Application Number:
  US10/648,848
• Publication Number:
  US 20050266407A1
• Time in Patent Office: 1,251 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 composition, said method comprising:

a) providing an array composition comprising;

i) a substrate with a surface comprising discrete sites; and

ii) a population of microspheres comprising at least a first and a second subpopulation distributed on said discrete sites, wherein each subpopulation comprises identifier nucleic acid sequences comprising;

1) the same primer sequence; and

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

wherein said microspheres are distributed on said surface; and

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

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

2. The method according to claim 1, further comprising:

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

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

3. The method of claim 2, wherein said population of microspheres is randomly distributed on said discrete sites.

4. The method of claim 2, wherein said identifier nucleic acid sequence comprises genomic DNA.

5. The method of claim 2, wherein said identifier nucleic acid sequence is prepared by an amplification technique.

6. The method of claim 2, wherein said first set of combinatorial decoding probes comprises four subsets.

7. The method of claim 2, wherein nucleotides in said variable sequence comprise universal bases.

8. The method of claim 2, wherein at each variable sequence nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding sequence of said first set of decoding sequences.

9. The method of claim 2, wherein said decoding nucleotide is an internal nucleotide of said variable sequence.

10. The method of claim 2, wherein said decoding nucleotide is a terminal nucleotide of said variable sequence.

11. The method of claim 2, wherein at each variable sequence nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding sequence of said second set of decoding sequences.

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

a) providing at least a first and a second subpopulation of identifier nucleic acid sequences distributed on said surface, said identifier nucleic acid sequences comprising the same primer sequence and 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 sequence and at least one decoding nucleotide included in said variable sequence that will basepair with at least one nucleotide of at least one of said decoding sequences, wherein said first set comprises different subsets of combinatorial decoding probes, each subset having the same decoding nucleotide; and

c) adding to said array composition a subset of said first set of combinatorial decoding probes and determining the location of said decoding sequence on said array composition.

13. The method according to claim 12, further comprising:

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

e) adding to said array composition a subset of said second set of combinatorial decoding probes.

14. The method of claim 13, wherein said identifier nucleic acid sequence comprises genomic DNA.

15. The method of claim 13, wherein said identifier nucleic acid sequence is prepared by an amplification technique.

16. The method of claim 13, wherein said first set of combinatorial decoding probes comprises four subsets.

17. The method of claim 13, wherein nucleotides in said variable sequence comprise universal bases.

18. The method of claim 13, wherein at each variable sequence nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding sequence of said first set of decoding sequences.

19. The method of claim 13, wherein said decoding nucleotide is an internal nucleotide of said variable sequence.

20. The method of claim 13, wherein said decoding nucleotide is a terminal nucleotide of said variable sequence.

21. The method of claim 13, wherein at each variable sequence nucleotide position, all possible naturally occurring nucleotides are represented in at least one decoding sequence of said second set of decoding sequences.