Methods designing multiple mRNA transcript nucleic acid probe sequences for use in nucleic acid arrays

• US 7,029,854 B2
• Filed: 11/22/2002
• Issued: 04/18/2006
• Est. Priority Date: 11/22/2002
• Status: Expired due to Fees

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Shannon, Karen W., Webb, Peter G., Collins, Patrick J., Butler, Keith C., Tang, Sandra L.
• Primary Examiner(s): Martinell, James
• Application Number:
  US10/303,151
• Publication Number:
  US 20040101845A1
• Time in Patent Office: 1,243 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 702/19, 702/20
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e.g., by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

Claims

1. A method of identifying a nucleic acid sequence for a substrate surface immobilized probe for two or more different mRNA transcripts encoded by the same genomic coding sequence, said method comprising:

(a) selecting at least one consensus sequence for said two or more different mRNA transcripts that are transcribed from said same genomic coding sequence;

(b) identifying a plurality of candidate sequences for said at least one consensus sequence; and

(c) choosing a probe sequence from said plurality to identify said nucleic acid sequence for said substrate surface immobilized probe.

2. The method according to claim 1, wherein said consensus sequence is selected by identifying a genomic region that includes an exon sequence found in each of said two or more mRNA transcripts.

3. The method according to claim 1, wherein said selecting step (a) provides two or more consensus sequences and said method further comprises picking the most 3′

consensus sequence from said two or more consensus sequences as the consensus sequence employed in said step (b).

4. The method according to claim 1, wherein said probe sequence for said consensus sequence is chosen using a probe design protocol.

5. The method according to claim 4, wherein said probe design protocol comprises:

(a) identifying a plurality of candidate probe sequences for said consensus sequence using at least one selection criterion;

(b) empirically evaluating each of said candidate probe sequences under a plurality of different experimental conditions to obtain a collection of empirical data values for each of said candidate nucleic acid probe sequences for each of said plurality of different experimental conditions;

(c) clustering said candidate probe sequences into two or more groups of candidate probe sequences using each candidate probe sequences collection of empirical data values;

(d) selecting one of said two or more groups using at least one criterion; and

(e) choosing a candidate probe sequence from said selected group as said suitable nucleic acid sequence.

6. The method according to claim 1, wherein at least some of said steps are carried out by a computational analysis system.

7. A computational analysis system comprising a computer-readable medium according to claim 6.

8. A kit for identifying a sequence of a nucleic acid that is suitable for use as a substrate surface immobilized probe that can hybridize to two or more different target nucleic acids that correspond to the same genomic coding sequence, said kit comprising:

(a) a computer readable medium according to claim 6; and

(b) instructions for using said algorithm to identify said suitable sequence.

9. A computer-readable medium having recorded thereon a program that identifies a sequence of a nucleic acid according to the method of claim 1.

10. A method of producing a nucleic acid array, said method comprising:

producing at least two different probe nucleic acids immobilized on a surface of a solid support, wherein at least one of said at least two different probe nucleic acids has a sequence of nucleotides identified according to the method of claim 1.

11. The method according to claim 10, wherein said at least two different probe nucleic acids are produced on said surface of said solid support by synthesizing said probe nucleic acids on said surface.

12. The method according to claim 10, wherein said at least two different probe nucleic acids are produced on said surface of said solid support by depositing said at least two different probe nucleic acids onto said surface of said solid support.

13. A nucleic acid array produced according to the method of claim 10.

14. A method of detecting the presence of a nucleic acid analyte in a sample, said method comprising:

(a) contacting a nucleic acid array according to claim 13 having a nucleic acid probe that specifically binds to said nucleic acid analyte with a sample suspected of comprising said analyte under conditions sufficient for binding of said analyte to said nucleic acid ligand on said array to occur; and

(b) detecting the presence of binding complexes on the surface of said array to detect the presence of said analyte in said sample.

15. The method according to claim 14, wherein said method further comprises a data transmission step in which a result from a reading of the array is transmitted from a first location to a second location.

16. The method according to claim 15, wherein said second location is a remote location.

17. A method comprising receiving a transmitted result of a reading of an array obtained according to the method claim 14.

18. The method according to claim 1, wherein said at least one consensus sequence shares 100% sequence identity with at least a portion of each of said two or more different mRNA transcripts.

19. The method according to claim 1, wherein said consensus sequence ranges from about 200 to about 6,000 nucleotides in length.