Computer-aided visualization and analysis system for sequence evaluation

• US 6,242,180 B1
• Filed: 09/23/1998
• Issued: 06/05/2001
• Est. Priority Date: 10/21/1994
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Chee, Mark S.
• Primary Examiner(s): Brusca, Ph.D, John S.
• Assistant Examiner(s): KIM, YOUNG J
• Application Number:
  US09/158,765
• Time in Patent Office: 986 Days
• Field of Search: 435/6, 702/27, 706/47
• US Class Current: 435/6.11
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B82Y 30/00 Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: G01N 15/1433 using image recognition
• CPC Class Codes: G16B 25/00 : ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/20 : Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
• CPC Class Codes: G16B 30/00 : ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 : Sequence assembly

Abstract

A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Claims

1. A computer implemented method of calling unknown bases in a sample nucleic acid sequence, comprising:

inputting a plurality of probe intensities, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence;

calling bases of the sample nucleic acid sequence according to the plurality of probe intensities;

identifying a mutant base call that has indicated that a base at a position in the sample nucleic acid sequence is suspected as being a mutation;

analyzing probe intensities of at least one position that is near the position of the suspected mutation; and

changing the mutant base call to a nonmutant base call if the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation.

2. The method of claim 1, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

3. The method of claim 1, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a position that is adjacent to the position of the suspected mutation.

4. The method of claim 3, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

5. The method of claim 1, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a plurality of positions near the suspected mutation.

6. The method of claim 5, wherein the plurality of probe intensities surround the suspected mutation equal to the length of the nucleic acid probes.

7. The method of claim 6, wherein the probe intensities of the plurality of positions are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

8. A computer program product that calls unknown bases in a sample nucleic acid sequence, comprising:

computer code that receives a plurality of probe intensities, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence;

computer code that calls bases of the sample nucleic acid sequence according to the plurality of probe intensities;

computer code that identifies a mutant base call that has indicated that a base at a position in the sample nucleic acid sequence is suspected as being a mutation;

computer code that analyzes probe intensities of at least one position that is near the position of the suspected mutation;

computer code that changes the mutant base call to a nonmutant base call if the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation; and

a computer readable medium that stores the computer codes.

9. The computer program product of claim 8, wherein the computer readable medium is a memory, hard drive, floppy disk, CD-ROM, flash memory, or tape.

12. The computer program product of claim 8, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

13. The computer program product of claim 8, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a position that is adjacent to the position of the suspected mutation.

14. The computer program product of claim 13, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

15. The computer program product of claim 8, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a plurality of positions near the suspected mutation.

16. The computer program product of claim 15, wherein the plurality of probe intensities surround the suspected mutation equal to the length of the nucleic acid probes.

17. The computer program product of claim 16, wherein the probe intensities of the plurality of positions are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

10. A computer system, comprising:

a processor;

a computer readable medium coupled to the processor that stores a computer program, the computer program including;

computer code that receives a plurality of probe intensities, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence;

computer code that calls bases of the sample nucleic acid sequence according to the plurality of probe intensities;

computer code that identifies a mutant base call that has indicated that a base at a position in the sample nucleic acid sequence is suspected as being a mutation;

computer code that analyzes probe intensities of at least one position that is near the position of the suspected mutation;

computer code that changes the mutant base call to a nonmutant base call if the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation.

11. The computer system of claim 10, wherein the computer readable medium is a memory, hard drive, floppy disk, CD-ROM, flash memory, or tape.

18. The computer program product of claim 10, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

19. The computer program product of claim 10, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a position that is adjacent to the position of the suspected mutation.

20. The computer program product of claim 19, wherein the probe intensities of at least one position that is near the position of the suspected mutation are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.

21. The computer program product of claim 10, wherein analyzing probe intensities of at least one position that is near the position of the suspected mutation includes analyzing a plurality of positions near the suspected mutation.

22. The computer program product of claim 21, wherein the plurality of probe intensities surround the suspected mutation equal to the length of the nucleic acid probes.

23. The computer program product of claim 22, wherein the probe intensities of the plurality of positions are inconsistent with a mutation if the probe intensities do not indicate lower hybridization affinity than is expected.