Method and apparatus for aligning microbeads in order to interrogate the same

• US 7,399,643 B2
• Filed: 09/12/2003
• Issued: 07/15/2008
• Est. Priority Date: 09/12/2002
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: CyVera Corporation (Illumina Incorporated)
• Inventors: Traynor, Joseph, Li, Tuo, Putnam, Martin A., Moon, John
• Primary Examiner(s): Warden; Jill
• Assistant Examiner(s): HYUN, PAUL SANG HWA
• Application Number:
  US10/661,836
• Publication Number:
  US 20040132205A1
• Time in Patent Office: 1,768 Days
• Field of Search: 436/501, 436/527
• US Class Current: 436/521
• CPC Class Codes: B01J 2219/00459 Beads
• CPC Class Codes: B01J 2219/00463 Directed sorting
• CPC Class Codes: B01J 2219/0047 Pins
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01L 2200/0636 Focussing flows, e.g. to laminate flows
• CPC Class Codes: B01L 2200/0668 Trapping microscopic beads
• CPC Class Codes: B01L 2300/0654 Lenses; Optical fibres
• CPC Class Codes: B01L 2400/0409 centrifugal forces
• CPC Class Codes: B01L 2400/0457 passive flow or gravitation
• CPC Class Codes: B01L 2400/0487 fluid pressure, pneumatics
• CPC Class Codes: B01L 3/502761 specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules investigating characteristics of particles G01N15/00
• CPC Class Codes: B01L 3/5085 for multiple samples, e.g. microtitration plates
• CPC Class Codes: G03H 1/0272 Substrate bearing the hologram
• CPC Class Codes: G03H 2210/53 Coded object not directly interpretable, e.g. encrypted object, barcode
• CPC Class Codes: G03H 2230/10 Microhologram not registered to the substrate
• CPC Class Codes: G03H 2270/20 Shape
• CPC Class Codes: G03H 2270/24 Having particular size, e.g. microscopic
• CPC Class Codes: Y10T 436/25 : including sample preparation

Abstract

A method and apparatus are provided for aligning optical elements or microbeads, wherein each microbead has an elongated body with a code embedded therein along a longitudinal axis thereof to be read by a code reading device. The microbeads are aligned with a positioning device so the longitudinal axis of the microbeads is positioned in a fixed orientation relative to the code reading device. The microbeads are typically cylindrically shaped glass beads between 25 and 250 microns (μm) in diameter and between 100 and 500 μm long, and have a holographic code embedded in the central region of the bead, which is used to identify it from the rest of the beads in a batch of beads with many different chemical probes. A cross reference is used to determine which probe is attached to which bead, thus allowing the researcher to correlate the chemical content on each bead with the measured fluorescence signal. Because the code consists of a diffraction grating typically disposed along an axis, there is a particular alignment required between the incident readout laser beam and the readout detector in two of the three rotational axes. The third axis, rotation about the center axis of the cylinder, is azimuthally symmetric and therefore does not require alignment.

Claims

1. A method for aligning microbeads to be read by a code reading or other detection device, comprising:

providing microbeads to a positioning device, each microbead having an elongated body with a holographic code disposed thereon or therein, the code being oriented to extend along a longitudinal axis of the corresponding microbead and being defined at least in part by variation of a refractive index of the microbead, the refractive index varying in an axial direction along the longitudinal axis of the microbead; and

aligning the microbeads with the positioning device so the codes, the variation in the refractive index of the codes, and the longitudinal axis of the microbeads are in a common fixed orientation relative to the code reading or other detection device.

2. A method according to claim 1, wherein the positioning device includes a plate having a multiplicity of grooves therein, the microbeads being aligned in the grooves such that the longitudinal axis of the microbeads extends along a length of the corresponding groove.

3. A method according to claim 2, wherein the method includes agitating the plate to encourage alignment of the microbeads into the grooves.

4. A method according to claim 1, wherein the microbeads are tubularly shaped with a length extending along the longitudinal axis and with a circular diameter traversing the longitudinal axis, the length being greater than the diameter.

5. A method according to claim 1, wherein the microbeads have the holographic code embedded in a central region thereof.

6. A method according to claim 1, wherein the code is used to correlate a chemical content on each bead with a measured fluorescence signal.

7. A method according to claim 1, wherein the elongated body has opposite ends arranged along the longitudinal axis and sides located transversely with respect to the longitudinal axis, the positioning device holding each microbead in a substantially known fixed orientation and alignment in relation to an end to end pitch direction and a side to side yaw direction while permitting the microbeads to rotate in a roll direction about the longitudinal axis.

8. A method according to claim 2, wherein the plate has a series of parallel grooves having one of a square shape, a rectangular shape, v-shape and semi-circular shape.

9. A method according to claim 2, wherein the plate is an optically transparent medium including boro-silicate glass, fused silica or plastic, and the grooves are open sided.

10. A method according to claim 2, wherein the microbeads have a tubular shape with a circular cross-section and are positioned end to end in the grooves, the grooves having an open side with a depth that is dimensioned to be at least a diameter of the microbeads.

11. A method according to claim 2, wherein the microbeads have a circular dimension and either the grooves have a depth between 10 and 125 microns, the depth is dimensioned within 90% of the diameter of the microbeads, or a combination thereof.

12. A method according to claim 2, wherein the microbeads have a circular dimension and a spacing of the grooves is between 1 and 2 times the diameter of the microbeads.

13. A method according to claim 2, wherein the grooves have an open side and the microbeads, when introduced, are free to move across a side of the plate until aligning with and coming to rest in the grooves.

14. A method according to claim 2, wherein the microbeads have a tubular shape and the grooves are arranged in one of rows, concentric circles and spirals.

15. A method according to claim 2, wherein the grooves have a bottom that is flat enough to prevent the beads from rotating, by more than a few tenths of a degree, relative to the code reader device.

16. A method according to claim 1, wherein the code reader device includes a readout camera.

17. A method according to claim 2, further comprising agitating the plate using a sonic transducer, a mechanical wipe, or shaking or rocking device.

18. A method according to claim 1, wherein the method includes using an open format approach by dispensing the microbeads onto the plate using a pipette tip or syringe tip and not covering the plate.

19. A method according to claim 1, further comprising dispensing the microbeads into a cuvette-like device comprising a plate, at least three walls and a cover.

20. A method according to claim 19, wherein the step of dispensing includes injecting the microbeads near an edge of an opening into the cuvette-like device and allowing surface tension, or an induced fluid flow, to pull the microbeads into the cuvette-like device.

21. A method according to claim 19, wherein the method includes using a closed format approach by sectioning a closed region into two regions, a first region where the microbeads are free to move about in a plane, either in a groove or not, and a second region where the microbeads are trapped in a groove and can only move along an axis of the groove.

22. A method according to claim 21, wherein the method includes the step of trapping the microbeads in a groove by reducing the height of the closed region so that the microbeads can no longer come out of the groove.

23. A method according to claim 21, wherein the first region is used to pre-align the beads into a groove, facilitating the introduction of beads into the second region.

24. A method according to claim 21, wherein the method includes tilting the cuvette-like device up so gravity can be used to pull the microbeads along a groove from the first region to the second region.

25. A method according to claim 21, wherein the plate is made of silicon having walls formed by Su8 coupled thereto, or having walls formed by etching the silicon.

26. A method according to claim 1, wherein the method includes the step of identifying a chemical content on the surface of the microbead with a measured fluorescence signal.

27. A method according to claim 1, wherein the method includes passing a code reading signal through the microbead aligned on the positioning device.

28. A method according to claim 1, wherein the method further includes the step of correlating a chemical content identified on each microbead with a fluorescence signal, including one provided by an incident laser beam device.

29. A method according to claim 1, wherein the method includes the step of identifying the code in the microbead.

30. A method according to claim 2, wherein the grooves of the plate are formed using a photo lithographic process.

31. A method according to claim 2, wherein the plate includes a glass plate having Su8 thereon.

32. A method according to claim 31, wherein the glass plate is a low fluorescence glass.

33. A method according to claim 1, wherein the glass plate is a boro silicate glass.

34. A method according to claim 2, wherein the grooves on the plate are mechanically machined.

35. A method according to claim 1, wherein the grooves on the plate are formed by deep reactive ion etching.

36. A method according to claim 1, wherein the grooves on the plate are formed by injection molding.

37. A method according to claim 2, wherein the plate has a mirror coating.

38. A method according to claim 2, wherein the plate is a disk having circumferential grooves, concentric grooves, or a combination thereof.

39. A method according to claim 2, wherein the plate is a disk having radial grooves.

40. A method according to claim 2, wherein the plate is a disk having a microbead loading area located in the center of the disk.

41. A method according to claim 2, wherein the plate is a disk having one or more radial water channels extending from the center to the outer periphery thereof.

42. A method according to claim 2, wherein the method includes arranging the plate on a rotating disk.

43. A method according to claim 1, wherein the positioning device is a flow tube.

44. A method according to claim 43, wherein the step of providing includes providing the microbeads to the flow tube in a fluid.

45. A method according to claim 1, wherein the positioning device comprises a plurality of holes that receive the microbeads.

46. A method according to claim 1, wherein the microbeads have teeth or protrusions thereon.

47. A method for aligning microbeads to be read by a code reading or other detection device, comprising:

providing microbeads to a positioning device, wherein the positioning device comprises a groove plate with a side having a multiplicity of grooves therein to receive the microbeads, each microbead having an elongated body with a code disposed thereon or therein, the code being oriented to extend along a longitudinal axis of the corresponding microbead and being defined at least in part by variation of a refractive index of the microbead, the refractive index varying in an axial direction along the longitudinal axis of the microbead;

causing the microbeads to flow freely across the side of the groove plate; and

aligning the microbeads with the positioning device by moving the groove plate to cause at least a portion of the microbeads to align within the grooves so the codes, the variation in the refractive index of the codes, and the longitudinal axis of the microbeads are in a fixed orientation relative to the code reading or other detection device.

48. A method according to claim 47, wherein the holographic code comprise a numeric code formed from a series of bits arranged proximate one another along the longitudinal axis of the microbead, each of the bits being assigned one of at least two values.

49. A method according to claim 47, wherein the positioning device includes a plate having a multiplicity of grooves therein, the microbeads being aligned in the grooves such that the longitudinal axis of the microbeads extends along a length of the corresponding groove.

50. A method according to claim 47, wherein the microbeads are tubularly shaped with a length extending along the longitudinal axis and with a circular diameter traversing the longitudinal axis, the length being greater than the diameter.

51. A method according to claim 47, wherein the elongated body has opposite ends arranged along the longitudinal axis and sides located transversely with respect to the longitudinal axis, the positioning device holding each microbead in a substantially known fixed orientation and alignment in relation to an end to end pitch direction and a side to side yaw direction while permitting the microbeads to rotate in a roll direction about the longitudinal axis.

52. A method according to claim 49, wherein the plate is an optically transparent medium including boro-silicate glass, fused silica or plastic, and the grooves are open sided.

53. A method according to claim 49, wherein the microbeads have a tubular shape with a circular cross-section and are positioned end to end in the grooves, the grooves having an open side with a depth that is dimensioned to be at least a diameter of the microbeads.

54. A method according to claim 49, wherein the microbeads have a circular dimension and either the grooves have a depth between 10 and 125 microns, the depth is dimensioned within 90% of the diameter of the microbeads, or a combination thereof.

55. A method according to claim 49, wherein the microbeads have a circular dimension and a spacing of the grooves is between 1 and 2 times the diameter of the microbeads.

56. A method according to claim 49, wherein the grooves have a bottom that is flat enough to prevent the beads from rotating, by more than a few tenths of a degree, relative to the code reader device.

57. A method according to claim 47, wherein the method includes the step of identifying a chemical content on the surface of the microbead with a measured fluorescence signal.

58. A method according to claim 47, wherein the method includes passing a code reading signal through the microbead aligned on the positioning device.

59. A method according to claim 47, wherein the method further includes the step of correlating a chemical content identified on each microbead with a fluorescence signal, including one provided by an incident laser beam device.

60. A method according to claim 47, wherein the method includes the step of identifying the code in the microbead.