Computer-aided probability base calling for arrays of nucleic acid probes on chips

• US 6,546,340 B2
• Filed: 03/20/2001
• Issued: 04/08/2003
• Est. Priority Date: 09/14/1995
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Lipshutz, Robert J., Walker, Michael G.
• Primary Examiner(s): Brusca, John S.
• Application Number:
  US09/814,144
• Publication Number:
  US 20020058261A1
• Time in Patent Office: 749 Days
• Field of Search: 702/20, 435/6
• US Class Current: 702/20
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: Y10S 435/973 Simultaneous determination of more than one analyte

Abstract

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to calculate probabilities for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes on biological chips. Additionally, information from multiple experiments is utilized to improve the accuracy of calling unknown bases.

Claims

1. A computer program product that calls an unknown base in a sample nucleic acid sequence, comprising:

computer code that defines a set of potential base calls, said base calls including at least one of A, C, G, T(U), deletion, insertion, and a plurality of ambiguous calls;

computer code that inputs a plurality of measurements for hybridization between a plurality of probes and said sample nucleic acid sequence or nucleic acid derived from said sample nucleic acid sequence;

computer code that determines a plurality of probabilities, each of said probabilities reflecting the likelihood that one of the potential base calls is correct, said probabilities being calculated according to a distribution model, said hybridization measurements and sequences of said plurality of probes;

computer code that calls the unknown base according to the probabilities of said potential base calls; and

a computer readable medium that stores the computer codes.

2. The computer program product of claim 1, wherein the unknown base is called according to the highest probability, said highest probability indicates a confidence that the unknown base is called correctly.

3. The computer program product of claim 1, wherein each nucleic acid probe has a different base at an interrogation position.

4. The computer program product of claim 3, wherein each probability indicates the likelihood that the unknown base is complementary to a base at the interrogation position in the corresponding nucleic acid probe.

5. The computer program product of claim 1, wherein a plurality of measurements for each hybridization are inputted.

6. The computer program product of claim 4, wherein a mean of said plurality of measurements for each hybridization is determined.

7. The computer program product of claim 4, further comprising computer code that calculates a standard deviation of said plurality of measurements for each hybridization.

8. The computer program product of claim 1, further comprising computer code that compares the highest probability to a probability threshold.

9. The computer program product of claim 8, wherein the unknown base is called according to the nucleic acid probe associated with the highest probability if the highest probability exceeds the probability threshold.

10. The computer program product of claim 8, further comprising:

computer code that produces a sum of the highest probability and a next highest probability;

computer code that compares the sum to the probability threshold; and

computer code that calls the unknown base according to the nucleic acid probes associated with the highest and next highest probabilities if the sum exceeds the probability threshold.

11. The computer program product of claim 1, wherein the sum indicates a confidence that the unknown base is called correctly if the sum exceeds the probability threshold.

12. An apparatus that calls an unknown base in a sample nucleic acid sequence, comprising:

means for defining a set of potential base calls, said base calls including at least one of A, C, G, T(U), deletion, insertion, and a plurality of ambiguous calls;

means for inputting a plurality of measurements for hybridization between a plurality of probes and said sample nucleic acid sequence or nucleic acid derived from said sample nucleic acid sequence;

means for determining a plurality of probabilities, each of said probabilities reflecting the likelihood that one of the potential base calls is correct, said probabilities being calculated according to a distribution model, said hybridization measurements and sequences of said plurality of probes; and

means for calling the unknown base according to the probabilities of said potential base calls.

13. The apparatus of claim 12, wherein the unknown base is called according to the highest probability, said highest probability indicates a confidence that the unknown base is called correctly.

14. The apparatus of claim 12, wherein each nucleic acid probe has a different base at an interrogation position.

15. The apparatus of claim 14, wherein each probability indicates the likelihood that the unknown base is complementary to a base at the interrogation position in the corresponding nucleic acid probe.

16. The apparatus of claim 12, wherein a plurality of measurements for each hybridization are inputted.

17. The apparatus of claim 16, wherein a mean of said plurality of measurements for each hybridization is determined.

18. The apparatus of claim 16, further comprising means for calculating a standard deviation of said plurality of measurements for each hybridization.

19. The apparatus of claim 12, further comprising means for comparing the highest probability to a probability threshold.

20. The apparatus of claim 19, wherein the unknown base is called according to the nucleic acid probe associated with the highest probability if the highest probability exceeds the probability threshold.

21. The apparatus of claim 19, further comprising:

means for producing a sum of the highest probability and a next highest probability;

means for comparing the sum to the probability threshold; and

means for calling the unknown base according to the nucleic acid probes associated with the highest and next highest probabilities if the sum exceeds the probability threshold.

22. The apparatus of claim 12, wherein the sum indicates a confidence that the unknown base is called correctly if the sum exceeds the probability threshold.