Hybrid random bead/chip based microarray

• US 20040263923A1
• Filed: 01/22/2004
• Published: 12/30/2004
• Est. Priority Date: 01/22/2003
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kersey, Alan D., Li, Tuo, Putnam, Martin A., Moon, John
• Granted Patent: US 7,164,533 B2
• Time in Patent Office: Days
• US Class Current: 359/2
• CPC Class Codes: G01N 21/4788 Diffraction for sizing particles G01N15/0205
• CPC Class Codes: G01N 21/6428 Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" in vivo A61B5/00; immunoassay G01N33/53
• CPC Class Codes: G01N 21/645 Specially adapted constructive features of fluorimeters
• CPC Class Codes: G01N 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/7743 the reagent-coated grating coupling light in or out of the waveguide
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/54313 the carrier being characterised by its particulate form
• CPC Class Codes: G01N 33/54366 Apparatus specially adapted for solid-phase testing
• CPC Class Codes: G01N 33/54386 Analytical elements
• CPC Class Codes: G01N 33/552 Glass or silica
• CPC Class Codes: G03H 1/0005 Adaptation of holography to specific applications holographic optical element G02B5/32; holographic scanner G02B26/106; recognition using holographic mask G06V10/88; holographic memories G11B7/0065, G11C13/042
• CPC Class Codes: G03H 1/02 Details of features involved during the holographic process; Replication of holograms without interference recording
• CPC Class Codes: G03H 1/0236 Form or shape of the hologram when not registered to the substrate, e.g. trimming the hologram to alphanumerical shape substrates bearing a hologram G03H1/0272
• CPC Class Codes: G03H 1/26 Processes or apparatus specially adapted to produce multiple sub- holograms or to obtain images from them, e.g. multicolour technique
• CPC Class Codes: G03H 2001/0033 in hologrammetry for measuring or analysing
• CPC Class Codes: G03H 2001/0044 holographic fringes deformations; holographic sensors
• CPC Class Codes: G03H 2210/53 Coded object not directly interpretable, e.g. encrypted object, barcode
• CPC Class Codes: G03H 2210/63 Environment affecting the recording, e.g. underwater G03H2001/0432 takes precedence
• CPC Class Codes: G03H 2230/10 Microhologram not registered to the substrate
• CPC Class Codes: G03H 2250/12 Special arrangement of layers
• CPC Class Codes: G06K 19/04 : characterised by the shape
• CPC Class Codes: G06K 19/06009 : with optically detectable marking G06K19/063, G06K19/08 take precedence

Abstract

A hybrid random bead/chip based microarray includes a plurality of loose optical identification elements (or beads) comprising a substrate having at least one identifiable code disposed thereon. The are randomly placed on a substrate, e.g., tray, plate, slide, or “chip” in an identifiable position (or location) on the slide (not necessarily immobily fixed). For example, the beads are randomly distributed (but oriented) in one dimension along grooves in the slide. Then, each bead code is read and its location determined, i.e., the bead code and location are mapped to its location on the chip. The beads on the chip may then be read/examined (and re-read if desired) by a conventional chip reader. The beads may be functionalized with a desired probe and/or reacted with a desired analyte when in the loose state and/or when on the chip. After reading the chip, the beads may be removed from the chip for further or alternative processing.

Claims

1. An optical identification element attached to a chemical, comprising:

an optical substrate;

at least a portion of said substrate having at least one diffraction grating disposed therein, said grating having at least one refractive index pitch superimposed at a common location;

the grating providing an output optical signal when illuminated by an incident light signal;

said optical output signal being indicative of a code in said substrate; and

the chemical being attached to said substrate.

2. The apparatus of claim 1 wherein said substrate is made of a glass material.

3. The apparatus of claim 1 wherein said code comprises a plurality of bits.

4. The apparatus of claim 1 wherein the number of pitches is indicative of the number of said bits in said code.

5. The apparatus of claim 1 wherein said substrate has a length that is less than about 500 microns.

6. The apparatus of claim 1 wherein said substrate has a cylindrical shape.

7. The apparatus of claim 1 wherein said grating is a blazed grating.

8. The apparatus of claim 1 wherein said code comprises a plurality of bits, each bit having a plurality of states.

9. The apparatus of claim 1 wherein said substrate has a reflective coating disposed thereon.

10. The apparatus of claim 1 wherein said substrate is has a magnetic or electric charge polarization.

11. The apparatus of claim 1 wherein said substrate has a grating region where said grating and a non-grating region where said grating is not located;

and wherein said substrate has a plurality of grating regions.

12. The apparatus of claim 1 wherein said substrate has geometry having holes therein.

13. The apparatus of claim 1 wherein said substrate is has a geometry having protruding sections.

14. The apparatus of claim 1 wherein at least a portion of said substrate is has an end cross sectional geometry selected from the group:

circular, square, rectangular, elliptical, clam-shell, D-shaped, and polygon

15. The apparatus of claim 1 wherein at least a portion of said substrate is has a side view geometry selected from the group:

circular, square, rectangular, elliptical, clam-shell, D-shaped, and polygon.

16. The apparatus of claim 1 wherein at least a portion of said substrate is has a 3-D shape selected from the group:

sphere, a cube, a pyramid.

17. The apparatus of claim 1 wherein said code comprises at least a predetermined number of bits, said number being:

3, 5, 7, 9, 10, 12, 14, 16, 18, 20, 24, 28, 30, 40, 50, or 100.

18. A microparticle attached to a chemical comprising:

an optical substrate;

at least a portion of said substrate having at least one diffraction grating disposed therein, said grating having at least one refractive index pitch superimposed at a common location;

the grating providing an output optical signal when illuminated by an incident light signal;

said optical output signal being indicative of a code in said substrate; and

the chemical being attached to said substrate.

19. A method of performing a multiplexed experiment, comprising:

obtaining an optical substrate at least a portion of which having a diffraction grating with one or more refractive index pitches superimposed at a common location;

attaching a chemical to said substrate;

illuminating said substrate with incident light, said substrate providing an output light signal; and

reading said output light signal and detecting a code therefrom.