Interrogating multi-featured arrays

• US 6,406,849 B1
• Filed: 10/29/1999
• Issued: 06/18/2002
• Est. Priority Date: 10/29/1999
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Sillman, Debra A., Schleifer, Kyle J., White, Elecia C., Ladd, Charles S., Dorsel, Andreas N.
• Primary Examiner(s): Marschel, Ardin H.
• Application Number:
  US09/430,214
• Time in Patent Office: 963 Days
• Field of Search: 435/4, 435/6, 435/7.1, 435/7.92, 435/283.1, 435/286.1, 435/287.1, 435/287.2, 435/288.7, 436/172, 356/317-320, 356/323, 356/326, 356/375, 356/380, 356/398, 356/400, 356/401, 356/244, 356/246, 422/50, 422/52, 422/55, 422/68.1, 422/82.05, 422/82.08
• US Class Current: 435/6.19
• CPC Class Codes: G01N 21/274 Calibration, base line adjustment, drift correction
• 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 2201/1242 Validating, e.g. range invalidation, suspending operation

Abstract

A method, apparatus for executing the method, and computer program products for use in such an apparatus. The method includes scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple array features. Signals from respective scanned sites emitted in response to the interrogating light are detected. The interrogating light power is altered for a first site on the array package during the array scan, based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined value absent the altering (which allows for protecting a detector against expected overly bright sites), or is altered during the array scan based on the detected interrogating light power (which allows for compensating for light source drift during an array scan).

Claims

1. A method comprising:

(a) scanning an interrogating light across an addressable array of multiple features of different moieties, which interrogating light is generated from a variable optical attenuator through which light from a light source has passed and which optical attenuator is responsive to a control signal to alter the power of the interrogating light;

(b) detecting signals from respective features emitted in response to the interrogating light;

(c) detecting a power of the interrogating light from the variable optical attenuator; and

(d) adjusting the attenuator control signal to alter interrogating light power, based on the detected power.

2. A method according to claim 1 wherein the multiple features comprise polynucleotides of different sequences.

3. A method according to claim 1 wherein the multiple features comprise DNA of different sequences.

4. A method according to claim 1 wherein the detected signals are fluorescent emissions from the features.

5. A method according to claim 1 wherein the power is detected and altered during step (a).

6. A method according to claim 5 wherein the interrogating light additionally scans across sites other than on the array, and wherein the interrogating light power is decreased when the interrogating light has scanned off the array.

7. A method according to claim 5 wherein the interrogating light is scanned row by row across the array features, and wherein the interrogating light power is altered during a transition of the interrogating light from one row to another.

8. A method comprising:

(a) scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple features of the array;

(b) detecting signals from respective scanned sites emitted in response to the interrogating light; and

(c) altering the interrogating light power for a first site on the array package during the array scan based on location of the first site;

wherein the interrogating light power is reduced based on location of the first site.

9. A method according to claim 8 wherein the multiple features comprise polynucleotides of different sequences.

10. A method according to claim 8 wherein the multiple features comprise DNA of different sequences.

11. A method according to claim 8 additionally comprising reading an identification carried on the array package and determining the location of the first site based on the read identification.

12. A method according to claim 11 wherein the identification is machine read.

13. A method comprising:

(a) scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple features of the array;

(b) detecting signals from respective scanned sites emitted in response to the interrogating light; and

(c) altering the interrogating light power for a first site on the array package during the array scan based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined range absent the altering;

the method additionally comprising, prior to steps (a) through (c), performing a pre-scan which includes;

scanning an interrogating light across multiple sites on the array package using a lower sensitivity than that used in step (a); and

detecting signals from respective scanned sites emitted in response to the interrogating light;

wherein the interrogating light power is altered based on the determination that the emitted signal from the first site will be outside a predetermined range, which is based on the emitted signal obtained from the first site during the pre-scan.

14. A method comprising:

(a) scanning an interrogating light across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple features of the array;

(b) detecting signals from respective scanned sites emitted in response to the interrogating light; and

(c) altering the interrogating light power for a first site on the array package during the array scan based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined range absent the altering;

wherein the interrogating light power is reduced based on a determination that the emitted signal from the first site will exceed a predetermined value;

and wherein the first site is not an array feature.

15. An apparatus for interrogating an addressable array of multiple features of different moieties, comprising:

(a) a light source and a variable optical attenuator through which light from the source passes to provide an interrogating light, and which optical attenuator is responsive to a control signal to alter the power of the interrogating light;

(b) a scanning system which scans the interrogating light across the addressable array;

(c) a signal detector to detect signals from respective features emitted in response to the interrogating light;

(b) a power detector to detect the power of the interrogating light from the variable optical attenuator; and

(c) a system controller which adjusts the optical attenuator control signal to alter interrogating light power, based on the detected power.

16. An apparatus according to claim 15 wherein the power detector and system controller co-operate to detect and adjust interrogating light power prior to scanning each of multiple arrays.

17. An apparatus according to claim 15 wherein the power detector and system controller co-operate to detect and adjust interrogating light power during scanning of the interrogating light across the array.

18. An apparatus according to claim 15 wherein the system controller decreases the power when the scanning system causes the interrogating light to scan off the array.

19. An apparatus according to claim 18 wherein the scanning system causes the interrogating light to scan row by row across the array features, and wherein the power is adjusted during a transition of the interrogating light from one row to another.

20. An apparatus for interrogating an addressable array of multiple features of different moieties, carried by an array package, comprising:

(a) a light system which provides an interrogating light of variable power in response to a control signal;

(b) a scanning system which scans the interrogating light across multiple sites on the array package, which scanned sites include multiple features of the array;

(c) a signal detector which detects signals from respective sites emitted in response to the interrogating light; and

(d) a system controller which adjusts the interrogating light power for a first site on the array package during the array scan based on location of the first site.

21. An apparatus according to claim 20 wherein the system controller reduces the interrogating light power for the first site.

22. A method according to claim 20 additionally comprising a reader to machine read an identification carried on the array package, and wherein the system controller determines the location of the first site based on the read identification.

23. An apparatus according to claim 20 wherein the light system includes a light source and an optical attenuator through which light from the source passes to provide the interrogating light, and wherein the control signal comprises a signal for the optical attenuator which provides variable attenuation in response to the characteristic of the control signal.

24. An apparatus for interrogating an addressable array of multiple features of different moieties, carried by an array package, comprising:

(a) a light system which provides an interrogating light of variable power in response to a control signal;

(b) a scanning system which scans the interrogating light across multiple sites on the array package, which scanned sites include multiple features of the array;

(c) a signal detector which detects signals from respective sites emitted in response to the interrogating light; and

(d) a system controller which adjusts the interrogating light power for a first site on the array package during the array scan based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined range absent alteration;

wherein adjustment is based on the determination by the system controller, which is based on the emitted signal detected from the first site;

and wherein the system controller, prior to the array scan, additionally causes the apparatus to execute a pre-scan which includes;

scanning the interrogating light across multiple sites on the array package using a lower sensitivity than that used in step (a); and

detecting at the detector, signals from respective scanned sites emitted in response to the interrogating light;

wherein the determination made by the system controller that the emitted signal from the first site during a scan is outside a predetermined range, is based on the emitted signal obtained from the first site during the pre-scan.

25. An apparatus for interrogating an addressable array of multiple features of different moieties, carried by an array package, comprising:

(a) a light system which provides an interrogating light of variable power in response to a control signal characteristic;

(b) a scanning system which scans the interrogating light across multiple sites on the array package, which scanned sites include multiple features of the array;

(c) a signal detector which detects signals from respective sites emitted in response to the interrogating light; and

(d) a system controller which calibrates interrogating light power in response to the control signal characteristic, and which adjusts the interrogating light power for a first site on the array package during the array scan using the calibration, based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined range;

wherein the controller repeats the calibration prior to each scanning of an array package.

26. An apparatus for interrogating an addressable array of multiple features of different moieties, carried by an array package, comprising:

(a) a light system which provides an interrogating light of variable power in response to a control signal characteristic;

(b) a scanning system which scans the interrogating light across multiple sites on the array package, which scanned sites include multiple features of the array;

(c) a signal detector which detects signals from respective sites emitted in response to the interrogating light; and

(d) a system controller which calibrates interrogating light power in response to the control signal characteristic, and which adjusts the interrogating light power for a first site on the array package during the array scan using the calibration, based on location of the first site.

27. A computer program product for use on an apparatus for interrogating an addressable array of multiple features of different moieties by means of an interrogating light generated from a variable optical attenuator through which light from a light source has passed, and which optical attenuator is responsive to a control signal to alter the power of the interrogating light, the program product comprising:

a computer readable storage medium having a computer program stored thereon which, when loaded into a computer of the apparatus performs the steps of;

(a) causing the interrogating light to scan across the addressable array;

(b) receiving an indication of interrogating light power from the variable optical attenuator; and

(d) adjusting the attenuator control signal to alter interrogating light power, based on the detected power.

28. A computer program product according to claim 27 wherein the attenuator control signal is adjusted to decrease light power when the interrogating light has scanned off the array.

29. A computer program product for use on an apparatus for interrogating an addressable array of multiple features of different moieties by means of an interrogating light generated from a light system which provides an interrogating light of variable power in response to a control signal, the program product comprising:

a computer readable storage medium having a computer program stored thereon which, when loaded into a computer of the apparatus performs the steps of;

(a) causing the interrogating light to scan across multiple sites on an array package including an addressable array of multiple features of different moieties, which scanned sites include multiple features of the array; and

(b) adjusting the control signal to alter the interrogating light power for a first site on the array package during the array scan, based on location of the first site or on a determination that the emitted signal from the first site will be outside a predetermined range.

30. A computer program product according to claim 29 wherein the interrogating light power is reduced based on a determination that the emitted signal from the first site will exceed a predetermined value.

31. A computer program product according to claim 29 wherein the adjustment is based on location of the first site.

32. A computer program product according to claim 29 wherein the determination is based on an emitted signal detected from the first site.