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

• US 6,957,149 B2
• Filed: 04/01/2003
• Issued: 10/18/2005
• Est. Priority Date: 09/14/1995
• Status: Expired due to Fees

• 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:
  US10/405,962
• Publication Number:
  US 20040002819A1
• Time in Patent Office: 931 Days
• Field of Search: 702/20, 365/94, 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 method of calling an unknown base in a sample nucleic acid sequence, comprising:

inputting a plurality of probe intensities, each of the probe intensities corresponding to a nucleic acid probe;

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

calling the unknown base according to the probabilities of the potential base calls.

2. The method of claim 1, where the distribution model is a signal distribution model.

3. The method of claim 2, where the signal distribution model is the normal distribution function.

4. The method of claim 2, where the signal distribution model is the Student'"'"'s t distribution.

5. The method of claim 1, wherein the unknown base is called according to the highest probability.

6. The method of claim 5, further comprising comparing the highest probability to a probability threshold.

7. The method of claim 6, wherein the unknown base is called according to the highest probability if the highest probability exceeds the probability threshold.

8. The method of claim 1, wherein the highest probability indicates a confidence that the unknown base is called correctly.

9. The method of claim 1, wherein each nucleic acid probe has a different base at an interrogation position.

10. The method of claim 9, 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.

11. The method of claim 1, wherein a plurality of measurements for each probe intensity are inputted.

12. The method of claim 11, wherein a mean of the plurality of measurements for each probe intensity is determined.

13. The method of claim 11, wherein a standard deviation of the plurality of measurements for each probe intensity is calculated.

14. A computer program on computer readable media that calls an unknown base in a sample nucleic acid sequence, comprising:

code that receives as input a plurality of probe intensities, each of the probe intensities corresponding to a nucleic acid probe;

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

code that calls the unknown base according to the probabilities of the potential base calls.

15. The computer program of claim 14, where the distribution model is a signal distribution model.

16. The computer program of claim 15, where the signal distribution model is the normal distribution function.

17. The computer program of claim 15, where the signal distribution model is the Student'"'"'s t distribution.

18. The computer program of claim 14, wherein the unknown base is called according to the highest probability.

19. The computer program of claim 18, further comprising comparing the highest probability to a probability threshold.

20. The computer program of claim 19, wherein the unknown base is called according to the highest probability if the highest probability exceeds the probability threshold.

21. The computer program of claim 14, wherein the highest probability indicates a confidence that the unknown base is called correctly.

22. The computer program of claim 14, wherein each nucleic acid probe has a different base at an interrogation position.

23. The computer program of claim 22, 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.

24. The computer program of claim 14, wherein a plurality of measurements for each probe intensity are inputted.

25. The computer program of claim 24, wherein a mean of the plurality of measurements for each probe intensity is determined.

26. The computer program of claim 24, wherein a standard deviation of the plurality of measurements for each probe intensity is calculated.