Method for identifying suitable nucleic acid probe sequences for use in nucleic acid arrays

• US 7,894,998 B2
• Filed: 06/26/2002
• Issued: 02/22/2011
• Est. Priority Date: 06/26/2002
• Status: Active Grant

• Current Assignee: Agilent Technologies, Inc.
• Original Assignee: Agilent Technologies, Inc.
• Inventors: Kincaid, Robert
• Primary Examiner(s): Dejong; Eric S
• Application Number:
  US10/184,501
• Publication Number:
  US 20040002070A1
• Time in Patent Office: 3,163 Days
• Field of Search: 702/19, 702/20, 435/6
• US Class Current: 702/20
• 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

Abstract

Methods of identifying regions of a nucleic acid sequence suitable for use as probes in nucleic acid arrays, as well as compositions of matter for practicing such methods, are provided. The subject methods include: (a) providing a set of known, undesirable probe sequences; (b) comparing a nucleic acid sequence to each member of the set; and (c) identifying regions of the nucleic acid sequence that substantially match a sequence of a member of the probe set as undesirable regions. The subject methods also include marking the undesirable regions of the nucleic acid sequence to identify regions of the nucleic acid sequence that are suitable for use as probes in a nucleic acid array. The subject invention also includes an algorithm and kits for carrying out the subject methods. Also provided are nucleic acid arrays produced with the identified suitable probes, and methods for using the same.

Claims

1. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:

(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence;

(b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set;

(c) marking regions of said nucleic acid sequence that have no more than 5 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence;

(d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and

(e) synthesizing at least one of said identified candidate probe sequences.

2. The method according to claim 1, further comprising computationally analyzing one or more of said candidate probe sequences for suitability for use as probes for said nucleic acid sequence in a nucleic acid array.

3. The method according to claim 2, further comprising adding any candidate probe sequences found unsuitable to said set of known, undesirable probe sequences.

4. The method according to claim 1, further comprising synthesizing and testing one or more of said candidate probe sequences in an array hybridization assay for suitability for use as probes for said nucleic acid sequence in a nucleic acid array.

5. The method according to claim 4, further comprising adding said candidate probe sequences found unsuitable to said set of known, undesirable probe sequences.

6. The method according to claim 4, wherein said step of testing comprises determining at least one of the signal strength, binding specificity, melting temperature and hybridization energies of said synthesized candidate probe sequences.

7. The method according to claim 1, further comprising expanding said set of known, undesirable probe sequences with an additional sequence.

8. The method according to claim 1, further comprising testing an identified candidate probe sequence.

9. The method according to claim 8, further comprising adding a tested candidate probe sequence to said set of known, undesirable probe sequences.

10. The method according to claim 8, wherein said testing is accomplished using experimental analysis.

11. The method according to claim 8, wherein said testing is accomplished using computational analysis.

12. The method according to claim 8, wherein said testing is based at least in part on a particular sample type.

13. The method of claim 8, wherein said format is a computer readable format.

14. The method of claim 8, wherein said method further comprises employing said identified candidate probe sequences in the manufacture of a nucleic acid array.

29. The method of claim 1, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence are computer readable formats and said comparing, marking and identifying steps are performed by a processor.

30. The method of claim 29, further comprising presenting said identified candidate probe sequences in text format to a user.

35. The method of claim 1, wherein regions of said nucleic acid sequence that are marked are prevented from being used to generate candidate probes.

38. The method of claim 1, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence is a text format.

15. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:

(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequence that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence;

(b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set; and

(c) marking regions of said nucleic acid sequence that have no more than 2 mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence;

(d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and

(e) synthesizing at least one of said identified candidate probe sequences.

16. The method according to claim 15, further comprising computationally analyzing one or more of said candidate probe sequences.

17. The method according to claim 15, further comprising synthesizing and testing one or more of said candidate probe sequences in an array hybridization assay.

18. The method according to claim 17, wherein said step of testing comprises determining at least one of the signal strength, binding specificity, melting temperature and hybridization energies of said synthesized candidate probe sequences.

19. The method according to claim 15, further comprising testing an identified candidate probe sequence.

20. The method according to claim 19, wherein said testing is accomplished using experimental analysis.

21. The method of claim 19, wherein said method further comprises employing said identified candidate probe sequences in the manufacture of a nucleic acid array.

31. The method of claim 15, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence are computer readable formats and said comparing, marking and identifying steps are performed by a processor.

32. The method of claim 15, further comprising presenting said identified candidate probe sequences in text format to a user.

36. The method of claim 15, wherein regions of said nucleic acid sequence that are marked are prevented from being used to generate candidate probes.

39. The method of claim 15, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence is a text format.

22. A method of identifying candidate probe sequences for a nucleic acid sequence for use as probes in a nucleic acid array, said method comprising:

(a) providing a set of known, undesirable probe sequences present in a format representative of the nucleotide sequences of said known, undesirable probe sequences, wherein said set of undesirable probe sequences comprises probe sequences that do not meet a predetermined specificity of binding affinity for said nucleic acid sequence;

(b) comparing said nucleic acid sequence present in a format representative of the nucleotide sequence of said nucleic acid sequence to each member of said set; and

(c) marking regions of said nucleic acid sequence that have no mismatches with a sequence of a member of said set as undesirable regions for candidate probe sequences for said nucleic acid sequence;

(d) identifying candidate probe sequences for said nucleic acid sequence for use as probes in a nucleic acid array from unmarked regions of said nucleic acid sequence; and

(e) synthesizing at least one of said identified candidate probe sequences.

23. The method according to claim 22, further comprising further computationally analyzing one or more of said candidate probe sequences.

24. The method according to claim 22, further comprising synthesizing and testing one or more of said candidate probe sequences in an array hybridization assay.

25. The method according to claim 24, wherein said step of testing comprises determining at least one of the signal strength, binding specificity, melting temperature and hybridization energies of said synthesized candidate probe sequences.

26. The method according to claim 22, further comprising testing an identified candidate probe sequence.

27. The method according to claim 26, wherein said testing is accomplished using experimental analysis.

28. The method of claim 26, wherein said method further comprises employing said identified candidate probe sequences in the manufacture of a nucleic acid array.

33. The method of claim 22, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence are computer readable formats and said comparing, marking and identifying steps are performed by a processor.

34. The method of claim 33, further comprising presenting said identified candidate probe sequences in text format to a user.

37. The method of claim 22, wherein regions of said nucleic acid sequence that are marked are prevented from being used to generate candidate probes.

40. The method of claim 22, wherein said format of said known, undesirable probe sequences and said format of said nucleic acid sequence is a text format.