Methods of identifying an analyte and nucleic acid analysis

• US 7,843,567 B2
• Filed: 12/22/2009
• Issued: 11/30/2010
• 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:
  US12/644,255
• Publication Number:
  US 20100099574A1
• Time in Patent Office: 343 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 an analyte. The method includes providing a plurality of microparticles. The microparticles have optically detectable codes extending along bodies of the corresponding microparticle. The microparticles have the chemical probes attached thereto. Each of the chemical probes is associated with a corresponding one of the codes. The method also includes selectively binding target analytes to the chemical probes on the microparticles to produce labeled microparticles and distributing the labeled microparticles to random locations of a substrate. The method also includes determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array. The method further includes detecting the label on the labeled microparticles in the random array and label positions of the labels in the random array. The method also includes using the code positions and the label positions to analyze the target analyte.

Claims

1. A method of identifying an analyte, the method comprising:

providing a plurality of microparticles, the microparticles having elongated bodies with optically detectable codes extending along the bodies of the corresponding microparticles, the microparticles having chemical probes attached thereto, each of the chemical probes being associated with a corresponding one of the codes;

selectively binding target analytes to the chemical probes on the microparticles to produce labeled microparticles;

distributing the labeled microparticles to random locations of a substrate, thereby providing a random array of labeled microparticles;

determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array;

detecting labels on the labeled microparticles in the random array and label positions of the labels in the random array; and

using the code positions and the label positions to analyze the target analytes.

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

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

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

5. The method of claim 1, wherein the code determining and label detecting operations are conducted in an automated manner.

6. The method of claim 1, wherein the labels are fluorescent labels and the label detecting operation includes capturing at least one image of fluorescent optical output emanating from the microparticles on the substrate.

7. The method of claim 1, wherein the code determining operation includes capturing at least one image of an optical output indicative of the codes for the microparticles.

8. The method of claim 7, wherein the optical output includes one of light reflected by the codes and light transmitted through the codes.

9. The method of claim 1, wherein the distributing the labeled microparticles onto the substrate includes flowing the microparticles onto the substrate within a solution, the microparticles falling onto the substrate in a random distribution.

10. The method of claim 9, wherein the code determining operation includes illuminating the microparticles on the substrate while submerged within the solution.

11. The method of claim 10, wherein the microparticles comprise a material having a refractive index and the solution has a refractive index, the material of the microparticles and the solution being substantially index-matched.

12. The method of claim 1, wherein the code determining operation includes illuminating the particles with an incident light, the incident light being substantially perpendicular to a plane of the substrate.

13. The method of claim 1, wherein the substrate is a two-dimensional substrate, the microparticles being arranged co-planar with each other.

14. The method of claim 1, wherein the substrate includes a plurality of grooves, the method further comprising orienting the elongated bodies of the microparticles within the grooves, the microparticles being randomly distributed within the grooves.

15. The method of claim 1, wherein the microparticles are rectangular and have a substantially square cross-sectional shape.

16. The method of claim 1, wherein the microparticles have an inner region and an outer region that surrounds the inner region, the inner region extending along a longitudinal axis of the microparticles and being located at a center of the microparticles, the code being within the inner region.

17. The method of claim 1, wherein the code is completely surrounded by a transparent material and extends along a longitudinal axis of the microparticle such that the code is determinable from any direction about the longitudinal axis.

18. The method of claim 1, wherein the code comprises a grating having a periodic or aperiodic variation in at least one of a refractive index and an optical absorption of at least a portion of the microparticle.

19. The method of claim 1, wherein the code is one of written, impressed, embedded, imprinted, etched, grown, and deposited within the microparticle.

44. The method of claim 1, further comprising determining the labels and determining the label positions.

45. The method of claim 1, wherein the code determining and label detecting operations comprise:

(a) the determining the codes for the labeled microparticles in the random array;

(b) the determining the code positions of the codes in the random array;

(c) the detecting labels on the labeled microparticles in the random array; and

(d) the detecting label positions of the labels in the random array;

and wherein the operations of (a)-(d) occur in any order or simultaneously.

46. The method of claim 1, wherein the label detecting operation includes capturing at least one image of the labeled microparticles in the random positions on the substrate.

47. The method of claim 1 further comprising capturing at least one image of the labeled microparticles in the random positions on the substrate, wherein the at least one image is utilized during at least one of the code determining and label detecting operations.

48. The method of claim 1, wherein the target analytes include one type of target analyte.

49. The method of claim 1, wherein the target analytes include at least first and second types of target analytes, the first and second types of target analytes having different chemical structures, the labels including at least first and second labels, the first and second labels being different and being associated with the first and second types of target analytes, respectively.

20. A method of nucleic acid analysis, the method comprising:

providing a plurality of microparticles, the microparticles having elongated bodies with optically detectable codes extending along the bodies of the corresponding microparticles, the microparticles having nucleic acid probes attached thereto, each of the nucleic acid probes being associated with a corresponding one of the codes;

hybridizing target nucleic acids to complementary nucleic acid probes on the microparticles to produce labeled microparticles;

distributing the labeled microparticles to random locations of a substrate, thereby providing a random array of labeled microparticles;

determining the codes for the labeled microparticles in the random array and code positions of the codes in the random array;

detecting labels on the labeled microparticles in the random array and label positions of the labels in the random array; and

using the code positions and the label positions to analyze the target nucleic acids.

21. The method of claim 20, wherein the method comprises determining a genotype.

22. The method of claim 20, wherein the method comprises gene expression analysis.

23. The method of claim 20, wherein the code determining and label detecting operations are conducted in an automated manner.

24. The method of claim 20, wherein the labels are fluorescent labels and the label detecting operation includes capturing at least one image of fluorescent optical output emanating from the microparticles on the substrate.

25. The method of claim 20, wherein the code determining operation includes capturing at least one image of an optical output indicative of the codes for the microparticles.

26. The method of claim 25, wherein the optical output includes one of light reflected by the codes and light transmitted through the codes.

27. The method of claim 20, wherein the distributing the labeled microparticles onto the substrate includes flowing the microparticles onto the substrate within a solution, the microparticles falling onto the substrate in a random distribution.

28. The method of claim 20, wherein the code determining operation includes illuminating the microparticles on the substrate while submerged within a solution.

29. The method of claim 28, wherein the microparticles comprise a material having a refractive index and the solution has a refractive index, the material of the microparticles and the solution being substantially index-matched.

30. The method of claim 20, wherein the code determining operation includes illuminating the particles with an incident light, the incident light being substantially perpendicular to a plane of the substrate.

31. The method of claim 20, wherein the substrate is a two-dimensional substrate, the microparticles being arranged co-planar with each other.

32. The method of claim 20, wherein the substrate includes a plurality of grooves, the method further comprising orienting the elongated bodies of the microparticles within the grooves, the microparticles being randomly distributed within the grooves.

33. The method of claim 20, wherein the microparticles are rectangular and have a substantially square cross-sectional shape.

34. The method of claim 20, wherein the microparticles have an inner region and an outer region that surrounds the inner region, the inner region extending along a longitudinal axis of the microparticles and being located at a center of the microparticles, the code being within the inner region.

35. The method of claim 20, wherein the code is completely surrounded by a transparent material and extends along a longitudinal axis of the microparticle such that the code is determinable from any direction about the longitudinal axis.

36. The method of claim 20, wherein the code comprises a grating having a periodic or aperiodic variation in at least one of a refractive index and an optical absorption of at least a portion of the microparticle.

37. The method of claim 20, wherein the code is one of written, impressed, embedded, imprinted, etched, grown, and deposited within the microparticle.

38. The method of claim 20, further comprising determining the labels and determining the label positions.

39. The method of claim 20, wherein the code determining and label detecting operations comprise:

(a) the determining the codes for the labeled microparticles in the random array;

(b) the determining the code positions of the codes in the random array;

(c) the detecting labels on the labeled microparticles in the random array; and

(d) the detecting label positions of the labels in the random array;

and wherein the operations of (a)-(d) occur in any order or simultaneously.

40. The method of claim 20, wherein the label detecting operation includes capturing at least one image of the labeled microparticles in the random positions on the substrate.

41. The method of claim 20 further comprising capturing at least one image of the labeled microparticles in the random positions on the substrate, wherein the at least one image is utilized during at least one of the code determining and label detecting operations.

42. The method of claim 20, wherein the target nucleic acids include nucleic acids of a common sequence.

43. The method of claim 20, wherein the target nucleic acids include at least first and second types of target nucleic acids, the first and second types of target nucleic acids having different nucleic acid sequences, the labels including at least first and second labels, the first and second labels being different and being associated with the first and second types of target nucleic acids, respectively.