Computer-aided visualization and analysis system for sequence evaluation

• US 6,607,887 B2
• Filed: 02/27/2001
• Issued: 08/19/2003
• Est. Priority Date: 10/21/1994
• Status: Expired due to Fees

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Chee, Mark S.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Kim, Young
• Application Number:
  US09/796,071
• Publication Number:
  US 20020012925A1
• Time in Patent Office: 903 Days
• Field of Search: 435/6, 536/23.1, 702/27
• US Class Current: 435/6.12
• 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 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 and sample sequences in another area on a display device.

Claims

1. A method of identifying an unknown base in a sample nucleic acid sequence, comprising:

inputting probe intensities for a plurality of nucleic acid probes that differ by a base at an interrogation position corresponding to the unknown base, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence;

analyzing the probe intensities and at least one probe intensity from a nucleic acid probe with an interrogation position corresponding to a position near the unknown base in the sample nucleic acid sequence; and

generating a base call identifying the unknown base according to results of analyzing the probe intensities and the at least one probe intensity.

2. The method of claim 1, wherein if the at least one probe intensity is not lower as is expected for a mutation, the base call identifies the unknown base as a nonmutant base.

3. The method of claim 1, wherein if the at least one probe intensity is lower as is expected for a mutation, the base call identifies the unknown base as a mutant base.

4. The method of claim 3, wherein the mutant is identified by the one of the plurality of nucleic acid probes with the highest probe intensity.

5. The method of claim 1, wherein the position near the unknown base in the sample nucleic acid sequence is adjacent to the unknown base.

6. The method of claim 1, wherein the interrogation position is at an internal position of the nucleic acid probes.

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

computer code that receives probe intensities for a plurality of nucleic acid probes that differ by a base at an interrogation position corresponding to the unknown base, each probe intensity indicating hybridization affinity between a nucleic acid probe and the sample nucleic acid sequence;

computer code that analyzes the probe intensities and at least one probe intensity from a nucleic acid probe with an interrogation position corresponding to a position near the unknown base in the sample nucleic acid sequence;

computer code that generates a base call identifying the unknown base according to results of analyzing the probe intensities and the at least one probe intensity; and

a computer readable medium that stores the computer codes.

8. The computer program product of claim 7, wherein the computer readable medium is a memory, hard drive, floppy disk, CD-ROM, flash memory, or tape.

9. The computer program product of claim 7, wherein if the at least one probe intensity is not lower as is expected for a mutation, the base call identifies the unknown base as a nonmutant base.

10. The computer program product of claim 7, wherein if the at least one probe intensity is lower as is expected for a mutation, the base call identifies the unknown base as a mutant base.

11. The computer program product of claim 10, wherein the mutant is identified by the one of the plurality of nucleic acid probes with the highest probe intensity.

12. The computer program product of claim 7, wherein the position near the unknown base in the sample nucleic acid sequence is adjacent to the unknown base.

13. The computer program product of claim 7, wherein the interrogation position is at an internal position of the nucleic acid probes.