Self-encoding sensor with microspheres

• US 7,754,498 B2
• Filed: 01/21/2005
• Issued: 07/13/2010
• Est. Priority Date: 10/06/1997
• Status: Expired due to Fees

• Current Assignee: Tufts University
• Original Assignee: Trustees of Tufts College
• Inventors: Walt, David R., Dickinson, Todd A.
• Primary Examiner(s): GABEL, GAILENE
• Application Number:
  US11/040,504
• Publication Number:
  US 20050196317A1
• Time in Patent Office: 1,999 Days
• Field of Search: 435/6, 435/7.1, 435/7.92, 435/91, 435/287.2, 435/288.4, 436/19, 436/164, 436/171, 436/172, 436/518, 436/523, 422/55, 422/68.1, 422/82.05, 422/82.06, 422/82.07, 422/82.08, 422/91
• US Class Current: 436/523
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/0045 using optical fibres
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00524 in the shape of fiber bundles
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: C12Q 1/682 Signal amplification
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C40B 60/14 for creating libraries
• 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 21/6452 Individual samples arranged in a regular 2D-array, e.g. multiwell plates
• CPC Class Codes: G01N 21/7703 using reagent-clad optical fibres or optical waveguides using measurement of total internal reflection or attenuated total reflection G01N21/552; optical fibres or waveguides per se G02B
• CPC Class Codes: G01N 2201/0846 Fibre interface with sample, e.g. for spatial resolution
• CPC Class Codes: G01N 33/0031 comprising two or more sensors, e.g. a sensor array
• CPC Class Codes: G01N 33/54313 the carrier being characterised by its particulate form
• CPC Class Codes: Y10T 436/101666 Particle count or volume standard or control [e.g., platelet count standards, etc.]
• CPC Class Codes: Y10T 436/109163 Inorganic standards or controls

Abstract

A microsphere-based analytic chemistry system is disclosed in which self-encoding microspheres having distinct characteristic optical response signatures to specific target analytes may be mixed together while the ability is retained to identify the sensor type and location of each sensor in a random dispersion of large numbers of such sensors in a sensor array using an optically interrogatable encoding scheme. An optical fiber bundle sensor is also disclosed in which individual microsphere sensors are disposed in microwells at a distal end of the fiber bundle and are optically coupled to discrete fibers or groups of fibers within the bundle. The identities of the individual sensors in the array are self-encoded by exposing the array to a reference analyte while illuminating the array with excitation light energy. A single sensor array may carry thousands of discrete sensing elements whose combined signal provides for substantial improvements in sensor detection limits, response times and signal-to-noise ratios.

Claims

1. A method of detecting a plurality of analytes, said method comprising:

(a) providing an array comprising a population of sensor elements at a density of at least 20,000 sensor elements per 1 mm², said population of sensor elements comprising different subpopulations of redundant sensor elements;

(b) contacting said array with a sample comprising a plurality of analytes under conditions wherein said analytes bind to said sensor elements, thereby producing signals at separate sensor elements;

(c) detecting the signals at the separate sensor elements in said subpopulations of redundant sensor elements; and

(d) combining the signals detected at the separate redundant sensor elements so as to produce an amplified signal indicative of said analytes.

2. The method of claim 1, wherein said combining comprises summing said signals detected at separate redundant sensor elements.

3. The method of claim 1 further comprising performing a statistical analysis on the signals detected at the separate redundant sensor elements, thereby determining statistical validity of said signals.

4. The method of claim 3, wherein the step of performing a statistical analysis comprises generating a confidence interval.

5. The method of claim 3 further comprising determining outlier signals and excluding said outlier signals from said statistical analysis.

6. The method of claim 1 further comprising obtaining at least a first control signal and adjusting the baseline of said signals detected at the separate redundant sensor elements against said first control signal.

7. The method of claim 1, wherein said subpopulations of sensor elements have at least five-fold sensor redundancy.

8. The method of claim 1, wherein said subpopulations of sensor elements have at least ten-fold sensor redundancy.

9. The method of claim 1, wherein the redundant sensor elements comprise nucleic acids.

10. The method of claim 1, wherein step (b) comprises immersing the surface of said array with a sample comprising a plurality of analytes.

11. The method of claim 1, wherein said analytes comprise nucleic acids.

12. A method of amplifying a response signal produced by a sensor array for a target analyte, said method comprising:

(a) providing an array comprising a population of sensor elements at a density of at least 20,000 sensor elements per 1 mm², said population of sensor elements comprising different subpopulations of redundant sensor elements;

(b) contacting said array with a sample comprising a target analyte under conditions wherein said target analyte binds to said redundant sensor elements in at least one subpopulation of redundant sensor elements, thereby producing signals at separate redundant sensor elements;

(c) detecting the signals from the separate redundant sensor elements in at least one subpopulation of redundant sensor elements; and

(d) summing the signals obtained from the separate redundant sensor elements, thereby amplifying the response signal produced.

13. The method of claim 12 further comprising obtaining at least a first control signal and adjusting the baseline of said signals detected at the separate redundant sensor elements against said first control signal.

14. The method of claim 12, wherein said subpopulations of sensor elements have at least five-fold sensor redundancy.

15. The method of claim 12, wherein the redundant sensor elements comprise nucleic acids.

16. The method of claim 12, wherein step (b) comprises immersing the surface of said array with a sample comprising a target analyte.

17. The method of claim 12 further comprising performing a statistical analysis on the signals detected at the separate redundant sensor elements, thereby determining statistical validity of said signals.

18. The method of claim 17, wherein the step of performing a statistical analysis comprises generating a confidence interval.

19. The method of claim 17 further comprising determining outlier signals and excluding said outlier signals from said statistical analysis.

20. The method of claim 12, wherein said subpopulations of sensor elements have at least ten-fold sensor redundancy.

21. The method of claim 12, wherein said target analyte comprises a nucleic acid.

22. A method of increasing signal to noise in a sensor array, said method comprising:

(a) providing an array comprising a population of sensor elements at a density of at least 20,000 sensor elements per 1 mm², said population of sensor elements comprising different subpopulations of redundant sensor elements;

(b) contacting said array with a sample comprising a plurality of analytes under conditions wherein said plurality of analytes binds to sensor elements in said different subpopulations, thereby producing signals at separate redundant sensor elements;

(c) detecting the signals from the separate redundant sensor elements within each different subpopulation; and

(d) combining the signals detected at the separate redundant sensor elements within each different subpopulation so as to increase the signal as compared to the noise.

23. The method of claim 22, wherein said combining comprises summing said signals detected at separate redundant sensor elements.

24. The method of claim 22 further comprising performing a statistical analysis on the signals detected at the separate redundant sensor elements, thereby determining statistical validity of said signals.

25. The method of claim 24, wherein the step of performing a statistical analysis comprises generating a confidence interval.

26. The method of claim 24 further comprising determining outlier signals and excluding said outlier signals from said statistical analysis.

27. The method of claim 22 further comprising obtaining at least a first control signal and adjusting the baseline of said signals detected at the separate redundant sensor elements against said first control signal.

28. The method of claim 22, wherein said subpopulations of sensor elements have at least five-fold sensor redundancy.

29. The method of claim 22, wherein the redundant sensor elements comprise nucleic acids.

30. The method of claim 22, wherein immersing the surface of said array with a sample comprising a plurality of analytes.

31. The method of claim 22, wherein said subpopulations of sensor elements have at least ten-fold sensor redundancy.

32. The method of claim 22, wherein said analytes comprise nucleic acids.