Chemical array reading

• US 7,269,518 B2
• Filed: 04/30/2003
• Issued: 09/11/2007
• Est. Priority Date: 04/30/2003
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Corson, John F.
• Primary Examiner(s): Brusca; John S.
• Assistant Examiner(s): Lin; Jerry
• Application Number:
  US10/427,876
• Publication Number:
  US 20040219536A1
• Time in Patent Office: 1,595 Days
• Field of Search: 702/19, 702/22, 435/6
• US Class Current: 702/22
• CPC Class Codes: B01J 2219/00378 Piezoelectric or ink jet dispensers
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00657 One-dimensional arrays
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00664 Three-dimensional arrays
• CPC Class Codes: B01J 2219/00675 In-situ synthesis on the substrate
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00707 separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00731 Saccharides
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• 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 21/6456 : Spatial resolved fluorescence measurements; Imaging
• CPC Class Codes: G01N 2201/1242 : Validating, e.g. range invalidation, suspending operation

Abstract

A method in which a chemical array is read on an array reader and the results saved in a memory linked with a performance characteristic of the array reader. Alternatively or additionally results from reading an array and a linked performance characteristic of a reader which performed the reading are retrieved from a memory. Computer program products and apparatus are also provided.

Claims

1. A method comprising:

(i) reading a chemical array on an array reader, wherein the chemical array comprises biopolymer features and was exposed to a sample, and saving results of the reading in a memory, wherein the saved results are linked with a performance characteristic of the array reader which performed the reading, and processing the saved results using the linked performance characteristic of the reader which performed the reading;

or

(ii) retrieving from a memory the results from reading an array, the results being linked with a performance characteristic of a reader which performed the reading, wherein the array comprises biopolymer features and was exposed to a sample, and processing the retrieved results using the retrieved performance characteristic of the reader which performed the reading; and

, based on said processing, a human user who is interpreting the results of the reading assesses whether one or more targets is present in the sample or whether an organism from which the sample was obtained exhibits a particular condition,

wherein the performance characteristic comprises one or more of a reader accuracy or a reader responsivity of the reader which performed the reading and wherein processing includes rejecting or flagging as suspect a result from one or more of the features based on a predetermined performance characteristic or generating error bars or confidence intervals for a result from one or more of the features.

2. A method according to claim 1 wherein in (i) the reader detects light emitted in response to illumination.

3. A method according to claim 1 wherein in (i) an array identifier associated with the chemical array is read;

and wherein the read results and performance characteristic of the array reader are both saved in the memory linked with the identifier.

4. A method according to claim 2 wherein the reader includes a memory in which the performance characteristic is saved, the method additionally comprising retrieving the performance characteristic from the memory prior to the saving with the linked results from the reading.

5. A method according to claim 2 additionally comprising measuring the performance characteristic prior to the saving with the linked results from the reading.

6. A method according to claim 2 additionally wherein the performance characteristic comprises reader accuracy.

7. A method according to claim 2 additionally wherein the performance characteristic comprises reader responsivity.

8. A method according to claim 2 additionally wherein the performance characteristic comprises a sample parameter.

9. A method comprising forwarding the saved results and linked performance characteristic obtained by a method of claim 2 to a remote location.

10. A method comprising receiving the saved results and linked performance characteristic obtained by a method of claim 2 from a remote location.

11. A method according to claim 1 wherein the results from reading an array and a linked performance characteristic of a reader which performed the reading are retrieved from a memory.

12. A method according to claim 11 wherein a result from one or more features is flagged based on the retrieved performance characteristic.

13. A method according to claim 11 wherein a result from one or more features is rejected based on the retrieved performance characteristic.

14. A method according to claim 11 wherein the performance characteristic comprises reader accuracy.

15. A method according to claim 11 wherein the performance characteristic comprises reader responsivity.

16. A method according to claim 12 wherein the performance characteristic comprises reader channel cross-talk.

17. A computer program product comprising a computer readable medium carrying a computer program which executes a method of claim 1.

18. A computer program product comprising a computer readable medium carrying a computer program which executes a method of claim 3.

19. A computer program product comprising a computer readable medium carrying a computer program which executes a method of claim 11.

20. A chemical array reading system comprising:

an array reader having a detector;

a memory;

a processor unit which receives results from reading an array from the array reader and which executes a method of claim 1.

21. A chemical array reading system comprising:

an array reader having a detector;

a memory;

a processor unit which receives results from reading an array from the array reader and which executes a method of claim 2.

22. A method comprising:

reading a chemical array on an array reader, wherein the chemical array comprises biopolymer features and was exposed to a sample, and saving results of the reading in a memory wherein the results are linked with a performance characteristic of the array reader which performed the reading;

or

retrieving from a memory the results from reading an array and a performance characteristic of a reader which performed the reading, the results being linked with the performance characteristic and wherein the array comprises biopolymer features and was exposed to a sample; and

, based on said processing, a human user who is interpreting the results of the reading assesses whether one or more targets is present in the sample or whether an organism from which the sample was obtained exhibits a particular condition,

wherein the performance characteristic comprises one or more of a reader accuracy in detected signal or ratios of detected signals in different channels, a reader responsivity, or a physical characteristic of an array being read selected from the group consisting of flatness characteristics of any sample used to measure the variations of detected signal value per actual signal value over a space to be read or the flatness of the array being read.

23. A method comprising:

reading a chemical array on an array reader, wherein the chemical array comprises biopolymer features and was exposed to a sample and wherein the reader detects light emitted in response to illumination, and saving results of the reading in a memory wherein the results are linked with a performance characteristic of the array reader which performed the reading and processing the saved results using the linked performance characteristic;

or

retrieving from a memory the results from reading an array and a performance characteristic of a reader which performed the reading, the results being linked to the performance characteristic and processing the retrieved results using the retrieved performance characteristic, wherein the array comprises biopolymer features and was exposed to a sample; and

, based on said processing, a human user who is interpreting the results of the reading assesses whether one or more targets is present in the sample or whether an organism from which the sample was obtained exhibits a particular condition,

wherein the performance characteristic comprises one or more of a reader accuracy, a reader responsivity or reader channel cross-talk and wherein processing includes rejecting or flagging as suspect a result from one or more features based on a predetermined performance characteristic or generating error bars or confidence intervals for a result from one or more features.