MULTIPLEX DECODING OF ARRAY SENSORS WITH MICROSPHERES

• US 20070231824A1
• Filed: 04/24/2007
• Published: 10/04/2007
• Est. Priority Date: 06/24/1998
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Chee, Mark, Stuelpnagel, John, Czarnik, Anthony
• Granted Patent: US 8,460,865 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00619 using hydrophilic or hydrophobic regions
• CPC Class Codes: B01J 2219/00621 by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00644 the porous medium being present in discrete locations, e.g. gel pads
• 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 2219/00677 : Ex-situ synthesis followed by deposition on the substrate
• 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: B01L 3/5085 : for multiple samples, e.g. microtitration plates
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/6816 : characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6825 : Nucleic acid detection involving sensors
• 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 2521/313 : Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2527/137 : Concentration of a component of medium
• CPC Class Codes: C12Q 2537/143 : Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2563/155 : Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/179 : the label being a nucleic acid
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 33/54313 : the carrier being characterised by its particulate form
• CPC Class Codes: Y10S 977/924 : using nanostructure as support of dna analysis

Abstract

The invention relates to compositions and methods for multiplex decoding of microsphere array sensors.

Claims

1. A method of decoding an array, said method comprising:

providing an array comprising a plurality of distinct capture probes, wherein said capture probes are randomly distributed on said array;

hybridizing a plurality of first sets of decoder probes with said capture probes, wherein each of said first sets of decoder probes comprises a different label, each different label producing a different signal;

hybridizing a plurality of second sets of decoder probes with said capture probes, wherein each of said second sets of decoder probes is different from said first sets of decoder probes, and wherein each of said second sets of decoder probes comprises a different label, each different label producing a different signal; and

detecting said different signals produced by the hybridization of said first sets of decoder probes and detecting said different signals produced by the hybridization of said second sets of decoder probes so as to generate a code indicative of the location of a capture probe, thereby decoding said array.

2. The method of claim 1, wherein said array comprises a flat planar surface.

3. The method of claim 2, wherein said flat planar surface comprises a depression comprising one or more particles.

4. The method of claim 3, wherein said capture probes are attached to said one or more particles.

5. The method of claim 4, wherein said one or more particles comprise micro spheres.

6. The method of claim 2, wherein said flat planar surface comprises at least one well having a microsphere deposited therein.

7. The method of claim 1, wherein said capture probes and said decoder probes comprise nucleic acids.

8. The method of claim 1, wherein said labels comprise fluorescent labels.

9. The method of claim 1, wherein said detecting step comprises imaging said different signals produced by the hybridization of said first sets of decoder probes and imaging said different signals produced by the hybridization of said second set of decoder probes.

10. A method of decoding an array, said method comprising:

contacting an array comprising a plurality of particle subpopulations, wherein each particle subpopulation comprises a distinct bioactive agent and wherein capture probes are randomly distributed on said array, with a first population of decoder probes, said first population comprising a plurality of different labels;

obtaining a first image of the location of said first population of decoder probes;

removing said first population of decoder probes;

contacting said array with a second population of decoder probes, said second population comprising a plurality of different labels;

obtaining a second image of the location of said second population of decoder probes; and

comparing said first image with said second image to determine the identity of the label that is present at a location in said first image and the identity of the label that is present at the same location in said second image so as to generate a code indicative of the location of a capture probe, thereby decoding said array.

11. The method of claim 10, wherein the particles comprise microspheres.

12. The method of claim 10, wherein the number of labels in said first population of decoder probes or said second population of decoder probes is less than the number of subpopulations of particles.

13. The method of claim 10, wherein said first population of decoder probes and said second population of decoder probes comprise the same population of decoder probes, said first population of decoder probes comprising different labels than said second population of decoder probes.

14. The method of claim 10, wherein at least one of said bioactive agents comprises a nucleic acid.

15. The method of claim 10, wherein said first population of decoder probes and said second population of decoder probes comprise fluorescent labels.

16. A method of decoding an array, said method comprising:

providing an array comprising a population of microspheres having capture probes attached thereto, said population of microspheres being randomly distributed on said array at discrete sites;

hybridizing a plurality of first sets of decoder probes with said capture probes, wherein each of said first sets of decoder probes comprises a different label, each different label producing a different signal;

removing said plurality of first sets of decoder probes;

hybridizing a plurality of second sets of decoder probes with said capture probes, wherein each of said second sets of decoder probes comprises a different label, each different label producing a different signal; and

detecting said different signals produced by the hybridization of said first sets of decoder probes and detecting said different signals produced by the hybridization of said second sets of decoder probes so as to generate a code indicative of the location of a capture probe, thereby decoding said array.

17. The method of claim 16, wherein said discrete sites are wells.

18. The method of claim 16, wherein said array comprises a flat planar surface.

19. The method of claim 16, wherein said capture probes and said decoder probes comprise nucleic acids.

20. A method of decoding an array so as to determine the location of at least one capture probe that has been randomly distributed on the array, said method comprising:

providing an array of capture probes, wherein at least one capture probe is randomly distributed on said array;

hybridizing a first decoder probe with said at least one capture probe at a location on the array, wherein said first decoder probe comprises a first label, said first label producing a first signal;

detecting said first signal at said location;

dehybridizing said first decoder probe;

hybridizing a second decoder probe with said at least one capture probe at said location on the array, wherein said second decoder probe comprises a second label, said second label producing a second signal;

detecting said second signal at said location; and

decoding said array by generating a code comprising the sequence of signals detected at said location, said code indicative of the capture probe present at said location.

21. The method of claim 20, wherein said array comprises a flat planar surface.

22. The method of claim 21, wherein said flat planar surface comprises a depression comprising one or more particles.

23. The method of claim 22, wherein said at least one capture probe is attached to a particle.

24. The method of claim 23, wherein said particle comprises a microsphere.

25. The method of claim 21, wherein said flat planar surface comprises at least one well having a microsphere deposited therein.

26. The method of claim 20, wherein said at least one capture probe and said decoder probe comprise nucleic acids.