Multiplex decoding of array sensors with microspheres

• US 7,226,734 B2
• Filed: 06/28/2002
• Issued: 06/05/2007
• Est. Priority Date: 06/24/1998
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Czarnik, Anthony W., Chee, Mark S., Stuelpnagel, John R.
• Primary Examiner(s): Borin; Michael
• Assistant Examiner(s): Lin; Jerry
• Application Number:
  US10/187,321
• Publication Number:
  US 20030157504A1
• Time in Patent Office: 1,803 Days
• Field of Search: 435/6, 435/7.1, 435/7, 422/68.1, 702/19
• US Class Current: 435/6.11
• 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 so as to determine the location of a capture probe that has been randomly distributed on the array, said method comprising the steps of:

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

b) performing a hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal;

c) detecting the signal produced by the hybridization step at a location on said array;

d) performing a dehybridization step;

e) performing an additional hybridization step in which said capture probes are hybridized with a plurality of sets of decoder probes, wherein each of said sets of decoder probes is different from said sets of decoder probes used in the previous hybridization step, and wherein each of said sets of decoder probes comprises a different label, each different label producing a different signal;

f) detecting the signal produced by the additional hybridization step at said location;

g) repeating steps d-f for a number of stages sufficient to generate a code comprising the sequence of signals detected at said location, said code indicative of the capture probe present at said location; and

h) decoding said array with said code.

2. The method of claim 1, wherein said array comprises glass or plastic.

3. The method of claim 1, wherein said array comprises a fiber optic bundle.

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

5. The method of claim 4, wherein said flat planar surface comprises a depression comprising one or more particles.

6. The method of claim 5, wherein said capture probes are attached to said one or more particles.

7. The method of claim 6, wherein said one or more particles comprise microspheres.

8. The method of claim 6, wherein said one or more particles comprise beads.

9. The method of claim 4, wherein said flat planar surface comprises at least one well having a microsphere deposited therein.

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

11. The method of claim 10, wherein said nucleic acids comprise DNA.

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