Detection of nucleic acid reactions on bead arrays

• US 9,441,267 B2
• Filed: 07/02/2014
• Issued: 09/13/2016
• Est. Priority Date: 04/20/1999
• Status: Expired due to Fees

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Gunderson, Kevin, Stuelpnagel, John R., Chee, Mark S., Fan, Jian-Bing
• Primary Examiner(s): FORMAN, BETTY J
• Application Number:
  US14/322,529
• Publication Number:
  US 20140315729A1
• Time in Patent Office: 804 Days
• Field of Search: 435/6.1
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/137 Ligase Chain Reaction [LCR]
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2563/149 Particles, e.g. beads

Abstract

The present invention is directed to methods and compositions for the use of micro sphere arrays to detect and quantify a number of nucleic acid reactions. The invention finds use in genotyping, i.e. the determination of the sequence of nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs). Similarly, the invention finds use in the detection and quantification of a nucleic acid target using a variety of amplification techniques, including both signal amplification and target amplification. The methods and compositions of the invention can be used in nucleic acid sequencing reactions as well. All applications can include the use of adapter sequences to allow for universal arrays.

Claims

1. A method of detecting a plurality of target deoxyribonucleic acids, comprising:

a) providing a plurality of target deoxyribonucleic acids;

b) hybridizing a plurality of first primers to first portions of each of said plurality of target deoxyribonucleic acids, wherein each of said first primers comprises an adapter sequence exogenous to sequences of said target deoxyribonucleic acids, wherein said plurality of first primers are different from each other;

c) hybridizing a plurality of second primers to second portions of each of said plurality of target deoxyribonucleic acids, wherein said plurality of second primers are different from each other;

d) extending said first or said second primers, and then ligating said first and second primers together to form a plurality of modified primers comprising said adapter sequences;

e) hybridizing said adapter sequences of said modified primers to an array of capture probes attached to a solid support, thereby forming hybridized capture probes;

f) modifying said hybridized capture probes by polymerase extension to form modified capture probes, and

g) detecting said modified capture probes, thereby detecting said plurality of target deoxyribonucleic acids,

wherein unextended first or second primers are removed from said modified primers prior to (e).

2. The method of claim 1, further comprising a wash step prior to said hybridizing said adapter sequences of said modified primers to an array.

3. The method of claim 1, wherein the unextended first or second primers are removed by affinity chromatography.

4. The method of claim 1, further comprising amplifying said plurality of modified primers.

5. The method of claim 4, wherein said amplifying comprises hybridizing said plurality of modified primers with a plurality of amplifier probes complementary to said plurality of first and second primers and amplifying said modified primers.

6. The method of claim 5, wherein said amplifying comprises a polymerase chain reaction.

7. The method of claim 1, further comprising identifying a nucleotide at a detection position for each of said target deoxyribonucleic acids, wherein a primer of said plurality of first primers or said plurality of second primers is complementary to said detection position.

8. The method of claim 1, wherein said array comprises a population of beads comprising said capture probes.

9. The method of claim 8, wherein said beads are associated with individual sites of said solid support.

10. The method of claim 9, wherein each of said sites is configured to have a single associated bead.

11. The method of claim 9, wherein said solid support comprises a fiber optic bundle.

12. The method of claim 1, wherein said array is selected from the group consisting of a spotted array, a photolithographic array, and a printed array.

13. The method of claim 1, wherein detecting said modified capture probes comprises detecting a label attached to said modified capture probes.

14. The method of claim 13, wherein detecting said modified capture probes comprises detecting a fluorescent label.

15. The method of claim 1, wherein said capture probes are covalently attached to said solid support.

16. The method of claim 1, further comprising a wash step prior to said modifying said hybridized capture probes by polymerase extension.

17. The method of claim 1, wherein said target deoxyribonucleic acids comprise loci having a single nucleotide polymorphism (SNP) allele.

18. The method of claim 17, wherein said plurality of said first primers comprise allele specific primers and said plurality of second primers comprise locus specific primers.

19. The method of claim 18, wherein the terminal base of said allele specific primers correspond to said SNP allele.

20. The method of claim 18, further comprising a plurality of second allele specific primers, wherein said plurality of allele specific primers comprises a match for said SNP and said plurality of second allele specific primers comprises a mismatch for said SNP at said detection position.

21. The method of claim 18, wherein step (d) comprises extending said allele specific primer to add a base to basepair with said SNP.

22. The method of claim 18, wherein said detecting indicates a SNP clinically related to a phenotypic variant.

23. The method of claim 18, wherein said detecting determines the genotype of a target deoxyribonucleic acid that is an indicator of a disease.

24. The method of claim 1, wherein said detecting further comprises determining the amount of a target deoxyribonucleic acid present in said plurality of deoxyribonucleic acids.

25. The method of claim 1, wherein said detecting comprises determining the presence of a target deoxyribonucleic acids that is an indicator of a disease.

26. The method of claim 1, wherein said first and second primers are separated by one or more bases when hybridized to a target deoxyribonucleic acids.