Methods of identifying analytes and using encoded particles

• US 8,049,893 B2
• Filed: 11/08/2010
• Issued: 11/01/2011
• Est. Priority Date: 01/22/2003
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Kersey, Alan D., Li, Tuo, Putnam, Martin A., Moon, John A.
• Primary Examiner(s): Geisel; Kara E
• Application Number:
  US12/941,568
• Publication Number:
  US 20110058172A1
• Time in Patent Office: 358 Days
• Field of Search: 356/317, 356/417
• US Class Current: 356/417
• 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 method of identifying analytes that react with probes on encoded particles. The method includes providing a support substrate that has a plurality of the particles randomly distributed on the support substrate. The particles have elongated bodies with codes that extend along the corresponding bodies. The codes identify probes that are attached to the corresponding bodies, wherein at least some of the probes include fluorescent labels from reactions with the analytes. The method also includes detecting fluorescent signals that are emitted from the fluorescent labels. The fluorescent signals emit from random spatial locations along the support substrate. The method also includes detecting the codes of the particles at the random spatial locations along the support substrate and analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles.

Claims

1. A method of identifying analytes that react with probes on encoded particles, comprising:

(a) providing a support substrate having a plurality of the particles randomly distributed on the support substrate,

wherein the particles have elongated bodies with codes that extend along the corresponding bodies,

wherein the codes identify probes that are attached to the corresponding bodies, and

wherein at least some of the probes comprise fluorescent labels from reactions with the analytes;

(b) detecting fluorescent signals that are emitted from the fluorescent labels, the fluorescent signals emitting from random spatial locations along the support substrate;

(c) detecting the codes of the particles at the random spatial locations along the support substrate, wherein the particles are submerged within a solution on the support substrate, wherein the particles have a material with a refractive index and the solution has a refractive index, the material of the particles and the solution being substantially index-matched; and

(d) analyzing the codes and the fluorescent signals to identify the analytes that react with the probes on the particles.

2. The method of claim 1, wherein the probes and the analytes comprise nucleic acids.

3. The method of claim 2, wherein the reactions comprise nucleic acid hybridization reactions.

4. The method of claim 2, wherein the method comprises determining a genotype.

5. The method of claim 2, wherein the method comprises gene expression analysis.

6. The method of claim 1, wherein (c) further comprises obtaining position information identifying where the particles are located on the support substrate.

7. The method of claim 6, wherein the obtaining operation includes obtaining the position information from a computer.

8. The method of claim 6 further comprising determining the codes and positions of the codes to provide the position information of the particles.

9. The method of claim 8, wherein the codes are determined based on light that is reflected by the codes or light that is transmitted through the codes.

10. The method of claim 6, wherein the analyzing operation includes combining the position information for the particles and the spatial locations for the fluorescent signals.

11. The method of claim 1 further comprising providing data relating to the analytes to a display, printout, storage medium, or database.

12. The method of claim 1, wherein the detecting and analyzing operations are conducted in an automated manner using a computer.

13. The method of claim 1 further comprising exciting the labels with light while the particles are on the support substrate.

14. The method of claim 1, wherein the detecting the fluorescent signals operation includes capturing at least one image of the fluorescent signals that are emitted from the particles on the support substrate.

15. The method of claim 1, wherein the detecting the fluorescent signals operation includes detecting the fluorescent signals while the particles are submerged within a solution.

16. The method of claim 1, wherein the support substrate includes a plurality of grooves, the particles being randomly distributed within the grooves.

17. The method of claim 1, wherein the code extends along a longitudinal axis of the particle and is completely surrounded by a transparent material about the longitudinal axis such that the code can be determined from any direction about the longitudinal axis, the probes being attached to an outer surface of the transparent material.

18. The method of claim 1, wherein the fluorescent labels are attached to the analytes and the analytes are bound to the probes.

19. The method of claim 1, wherein the bodies of the particles are rectangular and have a square-cross-sectional shape.

20. The method of claim 1, wherein lengths of the bodies range from 1 to 1000 microns.