READING AND WRITING CODES USING OPTICAL DEVICES

• US 20180341798A1
• Filed: 03/11/2016
• Published: 11/29/2018
• Est. Priority Date: 03/13/2015
• Status: Active Grant

• Current Assignee: Illumina Incorporated
• Original Assignee: Illumina Incorporated
• Inventors: Blair, Dustin, Udpa, Nitin, Tran, Linh, Scheidler, Nicholas
• Granted Patent: US 10,460,140 B2
• Time in Patent Office: Days
• CPC Class Codes: G06K 19/06159 the marking being relief type, e.g. three-dimensional bar codes engraved in a support
• CPC Class Codes: G06K 7/1413 1D bar codes
• CPC Class Codes: G06K 7/1417 2D bar codes

Abstract

A method for tracking an item that includes the steps of (a) providing an item having a solid polymer material; (b) irradiating the item to create a spatial pattern of optical modifications in the polymer material, wherein the spatial pattern of optical modifications includes a code that indicates information; and (c) detecting the pattern of optical modifications, thereby determining the information.

Claims

1. A method for tracking an item, comprising

(a) providing an item comprising a solid polymer material;

(b) irradiating the item to create a spatial pattern of optical modifications in the polymer material, wherein the spatial pattern of optical modifications comprises a code that indicates information; and

(c) detecting the pattern of optical modifications, thereby determining the information.

2. The method of claim 1, wherein the polymer material comprises a polyimide material.

3. The method of claim 1, wherein the polymer material comprises amine moieties.

4. The method of claim 1, wherein the polymer material comprises a silicon-based polymer.

5. The method of any one of claims 1 to 4, further comprising a step of carrying out a manipulation of the item, wherein the spatial pattern of optical modifications comprises a code that indicates at least one characteristic of the manipulation.

6. The method of claim 5, wherein the manipulation is carried out before step (b).

7. The method of claim 5, wherein the manipulation is carried out after step (b).

8. The method of claim 1, wherein the information that is determined comprises the at least one characteristic of the manipulation.

9. The method of claim 8, wherein the manipulation is selected from the group consisting of manufacturing the item, assessing quality of the item, using the item in a diagnostic assay, transiently modifying the item, and permanently modifying the item.

10. The method of claim 8, wherein the at least one characteristic is selected from the group consisting of the occurrence of the manipulation, the duration of the manipulation, a quality assessment of the manipulation, a number of times the manipulation is carried out or repeated, a location on the item where the manipulation occurred, and the identity of a modification of the item resulting from the manipulation.

11. The method of claim 5, further comprising selecting a second manipulation for the item based on the code that is determined.

12. The method of any one of the preceding claims, further comprising halting or pausing a process carried out on the item based on the code that is determined.

13. The method of any one of the preceding claims, further comprising communicating information relating to the code to a user or to a computer.

14. The method of any one of the preceding claims, wherein the optical modifications comprise increased absorption of light of one or more wavelengths, increased luminescence emission at one or more wavelengths, decreased absorption of light of one or more wavelengths, decreased luminescence emission at one or more wavelengths, a shift in wavelength of maximum light absorption and a shift in wavelength of maximum luminescence emission.

15. The method of claim 14, wherein the shift is a bathochromic shift.

16. The method of claim 14, wherein the shift is a hypsochromic shift.

17. The method of any one of the preceding claims, wherein the irradiating does not etch the surface of the solid polymer material.

18. The method of any one of the preceding claims, wherein the irradiating comprises impinging 250 kW/cm² of radiation on the polymer material

19. The method of any one of the preceding claims, wherein the wavelength of the irradiating comprises 355 nm.

20. The method of any one of the preceding claims, wherein the irradiating occurs for at least 1 msec.

21. The method of any one of the preceding claims, wherein spatial pattern is substantially devoid of metal.

22. The method of any one of the preceding claims, wherein the item is a flow cell.

23. The method of any one of the preceding claims, further comprising a step of performing one or more steps of an assay of biological materials in the flow cell, wherein the spatial pattern of optical modifications comprises a code that indicates at least one characteristic of the one or more steps.

24. The method of claim 22, wherein the assay comprises a sequencing by synthesis protocol.

25. The method of claim 24, wherein the at least one characteristic is selected from the group consisting of occurrence of the one or more steps, a number of the steps carried out, a number of cycles carried out to repeat the one or more steps, the location on the flow cell where the one or more steps occurred, and a quality assessment of the one or more steps.

26. The method of claim 24, further comprising selecting to carry out a further cycle of the sequencing by synthesis protocol based on the code that is determined.

27. The method of claim 24, further comprising halting or pausing the sequencing by synthesis protocol based on the code that is determined.

28. The method of claim 24, further comprising communicating information relating to the sequencing by synthesis protocol to a user or to a computer.

29. The method of any one of the preceding claims, wherein the steps are automatically performed by an apparatus comprising an optical excitation source and an optical emission detector.

30. The method of claim 29, wherein the apparatus is operably connected to a computer processing unit that is programmed to determine the code.

31. The method of claim 30, wherein the apparatus further comprises a fluidic system that is configured to fluidically communicate with the item and the computer processing unit is programmed to alter the fluidic communication based on the code that is determined.

32. The method of any one of the preceding claims, wherein the spatial pattern comprises a linear barcode or matrix barcode.

33. The method of any one of the preceding claims, wherein the spatial pattern comprises features that are separated by 100 microns or less.

34. The method of claim 33, wherein the detecting of the pattern of optical modifications resolves features that are separated by 100 microns or less.

35. The method of any one of the preceding claims, wherein the detecting of the pattern of optical modifications comprises luminescence detection.

36. The method of claim 35, wherein the luminescence detection comprises exciting the spatial pattern of optical modifications at less than 660 nm.

37. The method of claim 35 or 36, wherein the luminescence detection comprises detecting emission from the spatial pattern of optical modifications at greater than 600 nm.

38. A flow cell comprising

(a) a transparent top window;

(b) a transparent bottom window;

(c) at least one channel between the transparent top window and the transparent bottom window; and

(d) a spacer material between the transparent top window and the transparent bottom window, wherein a surface of the spacer material that faces the top window or the bottom window comprises a solid polymer material, wherein the solid polymer material comprises a spatial pattern of luminescent features that form a code carrying information indicating at least one manipulation carried out on the flow cell.

39. The flow cell of claim 38, wherein the polymer material comprises polyimide.

40. The flow cell of claim 38, wherein the polymer material comprises amine moieties.

41. The flow cell of claim 38, wherein the polymer material comprises a silicon-based polymer.

42. The flow cell of any one of claims claim 38 to 41, wherein the spatial pattern is substantially devoid of metal.

43. The flow cell of any one of claims claim 38 to 42, wherein the spatial pattern comprises a linear barcode or matrix barcode.

44. The flow cell of any one of claims 38 to 43, wherein the spatial pattern comprises features that are separated by 100 microns or less.

45. The flow cell of any one of claims 38 to 44, wherein the spacer material separates the at least one channel from a second channel that is located between the transparent top window and the transparent bottom window.

46. An apparatus comprising

(i) the flow cell of any one of claims 38 through 45;

(ii) a laser excitation source having a power output that is sufficient to modify the spatial pattern of luminescent features in the polymer material to change the code;

(iii) a detector configured to resolve the spatial pattern of luminescent features; and

(iv) a computer processing unit programmed to recognize the code and to identify at least one characteristic of the at least one manipulation based on the code.

47. The apparatus of claim 46, wherein the computer processing unit is programmed to identify a manipulation selected from the group consisting of manufacturing the item, assessing quality of the item, using the item in a diagnostic assay, transiently modifying the item, and permanently modifying the item.

48. The apparatus of claim 46 or 47, wherein the at least one characteristic is selected from the group consisting of the occurrence of the manipulation, the duration of the manipulation, a quality assessment of the manipulation, a number of times the manipulation is carried out or repeated, a location on the item where the manipulation occurred, and the identity of a modification of the item resulting from the manipulation.

49. The apparatus of any one of claims 46 to 47, wherein the computer processing unit is further programmed to initiate, continue, pause or discontinue a sequencing by synthesis protocol carried out in the flow cell.

50. The apparatus of claim 49, wherein the at least one characteristic is selected from the group consisting of the occurrence of one or more cycles of the sequencing by synthesis protocol, the number of the cycles of the sequencing by synthesis protocol carried out, the location on the flow cell where one or more cycles of the sequencing by synthesis protocol occurred, and a quality assessment of one or more cycles of the sequencing by synthesis protocol.

51. The apparatus of any one of claims 46 to 50, wherein the computer processing unit is further programmed to communicate information relating to the code to a user or to another computer processing unit.

52. The apparatus of any one of claims 46 to 51, wherein the modification of the spatial pattern of luminescent features comprises increased absorption of light of one or more wavelengths, increased luminescence emission at one or more wavelengths, decreased absorption of light of one or more wavelengths, decreased luminescence emission at one or more wavelengths, a shift in wavelength of maximum light absorption and a shift in wavelength of maximum luminescence emission.

53. The apparatus of claim 52, wherein the shift is a bathochromic shift.

54. The apparatus of claim 52, wherein the shift is a hypsochromic shift.

55. The apparatus of any one of claims 46 to 54, wherein the power output of the laser comprises at least 1 Watt of laser power at 355 nm wavelength

56. The apparatus of any one of claims 46 to 55, wherein the detector is configured to resolve features that are separated by 100 microns or less.