Multiplexed detection of analytes

• US 6,890,741 B2
• Filed: 07/24/2001
• Issued: 05/10/2005
• Est. Priority Date: 02/07/2000
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Fan, Jian-Bing, Chee, Mark S., Stuelpnagel, John R.
• Primary Examiner(s): Whisenant, Ethan
• Assistant Examiner(s): LU, FRANK WEI MIN
• Application Number:
  US09/915,231
• Publication Number:
  US 20020132241A1
• Time in Patent Office: 1,386 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/91.5, 435/91.51, 435/183, 436/94, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/25.32
• US Class Current: 435/91.2
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/173 incorporating a polynucleotide run, e.g. polyAs, polyTs
• CPC Class Codes: C12Q 2531/125 Rolling circle
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2563/131 the label being a member of a cognate binding pair, i.e. extends to antibodies, haptens, avidin
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/519 characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

The present invention is directed to sensitive and accurate multiplexed assays for target analyte detection.

Claims

1. A method of detecting at least first and second target molecules in a sample comprising:

a) contacting said first and second target molecule with a composition comprising;

i) an amplification enzyme; and

ii) first and second target probes, said first and second target probes comprising;

(a) a first and a second bioactive agent, respectively, wherein said first and second bioactive agents specifically bind to said first and second target molecules, respectively;

(b) a first and a second adapter sequence, respectively, wherein said first adapter sequence identifies said first target molecule and said second adapter sequence identifies said second target molecule; and

(c) at least a first and a second upstream universal priming sequences;

b) amplifying said first and second adapter sequences using said first and second universal priming sequences, wherein no ligation is performed, to form first and second amplicons, respectively;

c) detecting said first and second amplicons, respectively, to indicate the presence of said first and second target molecules in said sample.

2. The method according to claim 1, wherein said first and second target molecules are selected from the group consisting of proteins and nucleic acids.

3. The method according to claim 2, wherein said first and second target molecules are nucleic acids.

4. The method according to claim 3, wherein said first and second bioactive agents are first and second target specific domains that are substantially complementary to at least one domain of said first and second target nucleic acids, respectively.

5. The method according to claim 4, wherein said first and second target nucleic acids further comprise a first and second detection position, respectively, and said first and second target specific domains comprise a nucleotide at a readout position that is perfectly complementary to the nucleotide at said first and second detection positions.

6. The method according to claim 4, wherein said first and second upstream universal priming sequences are RNA Polymerase primers and said enzyme is a RNA Polymerase.

7. The method according to claim 6, wherein said RNA Polymerase primers are T7 primers.

8. The method according to claim 4, further comprising contacting said first and second upstream universal priming sequences with first and second chimeric RNA/DNA primers, prior to said amplifying.

9. The method according to claim 4, wherein said first and second target probes further comprise first and second downstream universal priming sequences, wherein said first and second upstream universal priming sequences and said first and second downstream universal priming sequences flank said first and second adapter sequences, respectively.

10. The method according to claim 9 further comprising contacting said first and second upstream universal priming sequences and said first and second downstream universal priming sequences with first and second universal primers, wherein said amplification is by PCR.

11. The method according to claim 2, wherein said first and second target molecules are proteins.

12. The method according to claim 11, wherein at least said first bioactive agent is an antibody.

13. The method according to claim 11, wherein at least said first bioactive agent is a ligand.

14. The method according to claim 11, wherein at least said first bioactive agent is an aptamer.

15. The method according to claim 11, wherein said first and second upstream universal priming sequences are RNA Polymerase primers and said enzyme is a RNA Polymerase.

16. The method according to claim 15, wherein said first and second upstream universal priming sequences are T7 RNA Polymerase primers.

17. The method according to claim 11, further comprising contacting said first and second upstream universal priming sequences with first and second chimeric RNA/DNA primers, respectively, prior to said amplifying.

18. The method according to claim 11, wherein said first and second target probes further comprise first and second downstream universal priming sequences, wherein said first and second upstream universal priming sequences and said first and second downstream universal priming sequences flank said first and second adapter sequences, respectively.

19. The method according to claim 1, wherein said composition further comprises nucleotides.

20. The method according to claim 19, wherein at least said one of nucleotides are labeled nucleotides.

21. The method according to claim 1, wherein said detecting comprises:

a) contacting said first and second amplicons with at least one substrate comprising first and second capture probes, wherein said first capture probes are complementary to said first adapters and said second capture probes are complementary to said second adapters; and

b) detecting said first and second amplicons on said at least one substrate.

22. The method according to claim 21, wherein said substrate comprises an array, said array comprising at least first and second capture probes immobilized on said substrate.

23. The method according to claim 22, wherein said array is an ordered array.

24. The method according to claim 21, wherein said substrate comprises at least a first and a second population of microspheres, wherein said first capture probes are immobilized on said first population of microspheres and said second capture probes are immobilized on said second population of microspheres.

25. The method according to claim 24, wherein said first and second amplicons are detected in a liquid array.

26. The method according to claim 25, wherein said first and second amplicons are detected by FACS.

27. The method according to claim 24, wherein said microspheres are randomly distributed on a second substrate comprising discrete sites.

28. The method according to claim 24, wherein said microspheres are applied to a mass spectrometer and the mass of said adapter sequence is determined to identify the presence of said first and second target molecules.

29. A method for multiplex detection of a plurality of target molecules in a sample, said method comprising;

a) contacting said plurality of target molecules with a composition comprising

a plurality of target probes, each comprising;

i) a bioactive agent, wherein each bioactive agent binds to a unique target molecule;

ii) an adapter sequence that identifies said unique target molecule that binds the bioactive agent; and

iii) at least one upstream universal priming sequence;

b) removing unbound target probes, leaving bound target probes;

c) contacting said bound target probes with an amplification enzyme;

d) amplifying said adapter sequences of said bound target probes using said at least one universal priming sequence, wherein no ligation is performed, to form a plurality of amplicons;

e) detecting said plurality of amplicons, to indicate the presence of said target molecules in said sample.

30. The method according to claim 29, wherein said target molecules are selected from the group consisting of proteins and nucleic acids.

31. The method according to claim 30, wherein said target molecules are proteins.

32. The method according to claim 30, wherein said target molecules are nucleic acids.

33. The method according to claim 29 or 30, wherein said plurality of target molecules comprises at least 500 target molecules.

34. The method according to claim 29 or 30, wherein said plurality of target molecules comprises at least 1000 target molecules.