Detection of HPV

• US 20070111200A1
• Filed: 09/27/2004
• Published: 05/17/2007
• Est. Priority Date: 09/25/2003
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Third Wave Technologies Incorporated (Hologic Incorporated)
• Inventors: Agarwal, Poonam, Ip, Hon, Elagin, Vecheslav, Hudson, Angela, Sander, Tamara, Olson-Munoz, Marilyn, Tyler, Ilse, Curtis, Michelle, Olson, Sarah, Garsha, Michelle, Kwiatkowski, Robert
• Granted Patent: US 7,527,948 B2
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2561/109 Invader technology

Abstract

The present invention provides compositions and methods for the detection and characterization of HPV sequences. More particularly, the present invention provides compositions, methods and kits for using invasive cleavage structure assays (e.g. the INVADER assay) to screen nucleic acid samples, e.g., from patients, for the presence of any one of a collection of HPV sequences. The present invention also provides compositions, methods and kits for screening sets of HPV sequences in a single reaction container.

Claims

1. A method for detecting at least one HPV sequence in a sample, comprising using a first and a second oligonucleotide, wherein said oligonucleotides are configured to form an invasive cleavage structure with a target sequence comprising said at least one HPV sequence.

2. The method of claim 1, wherein said first oligonucleotide comprises a 5′

portion and a 3′

portion, wherein said 3′

portion is configured to hybridize to said target sequence, and wherein said 5′

portion is configured to not hybridize to said target sequence.

3. The method of claim 1, wherein said second oligonucleotide comprises a 5′

portion and a 3′

portion, wherein said 5′

portion is configured to hybridize to said target sequence, and wherein said 3′

portion is configured to not hybridize to said target sequence.

4. The method of claim 1, wherein said oligonucleotides are selected from the group consisting of SEQ ID NOS. 1-5,7-62, 64-67, 69-70, 73-116 and 122-193.

5. A method for detecting the presence or absence of HPV nucleic acid in a sample, comprising:

a) providing;

i) a sample comprising nucleic acids; and

ii) an invasive cleavage assay configured to detect at least one HPV nucleic acid;

b) exposing said sample to said detection assay under conditions such that said at least one HPV nucleic acid can be detected, and c) detecting the presence or absence of HPV nucleic acid in a sample.

6. The method of claim 5, wherein said detecting comprises identifying one or more strains of HPV present in the sample.

7. The method of claim 6, wherein said HPV strain is HPV 16, 16Ty2, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 58 iso, 59, 66, 67, 68, 68var, 69, 70, or 82.

8. The method of claim 5, wherein said nucleic acid is amplified prior to said exposure step.

9. A method for detecting the presence or absence of HPV nucleic acid in a sample, said method comprising:

a) treating said sample using a first oligonucleotide and a second oligonucleotide, wherein said oligonucleotides are configured to form an invasive cleavage reaction; and

b) detecting the presence or absence of HPV nucleic acid.

10. The method of claim 9, wherein said oligonucleotides are selected from the group consisting of SEQ ID NOS. 1-5,7-62, 64-67, 69-70, 73-116 and 122-193.

11. The method of claim 9, wherein said oligonucleotides comprise two or more mismatches with HPV nucleic acid.

12. The method of claim 11, wherein said oligonucleotides hybridize preferentially to non-HPV nucleic acid sequences.

13. The method of claim 9, wherein said oligonucleotides are configured such that a stable duplex between said oligonucleotides and said HPV nucleic acid is not formed.

14. A kit comprising a non-amplified oligonucleotide detection assay configured for detecting at least one HPV sequence.

15. The kit of claim 14, wherein said non-amplified oligonucleotide detection assay comprises first and second oligonucleotides configured to form an invasive cleavage structure in combination with a target sequence comprising said at least one HPV sequence.

16. The kit of claim 15, wherein said first oligonucleotide comprises a 5′

portion and a 3′

portion, wherein said 3′

portion is configured to hybridize to said target sequence, and wherein said 5′

portion is configured to not hybridize to said target sequence.

17. The kit of claim 15, wherein said second oligonucleotide comprises a 5′

portion and a 3′

portion, wherein said 5′

portion is configured to hybridize to said target sequence, and wherein said 3′

portion is configured to not hybridize to said target sequence.

18. A kit comprising oligonucleotide detection assays configured for detecting a HPV sequence, wherein said kit comprises one or more oligonucleotides selected from the group consisting of SEQ ID NOS. 1-193.

19. The kit of claim 18, wherein multiple HPV strains can be detected simultaneously by combining one or more of said oligonucleotides into one reaction.

20. The kit of claim 18, wherein none of said oligonucleotides are completely complementary to HPV nucleic acid sequences.

21. The kit of claim 20, wherein said oligonucleotides comprise sequences not completely complementary to any target sequence that is detected.

22. The kit of claim 18, wherein all high-risk HPV strains can be detected in 4 or fewer reactions.

23. The kit of claim 18, wherein all high-risk HPV strains can be detected in 3 or fewer reactions.

24. A kit comprising oligonucleotide detection assays configured for detecting all high-risk HPV strains.

25. The kit of claim 24, wherein said oligonucleotides are not fully complementary to nucleic acid sequences of said HPV strains.

26. The kit of claim 24, wherein said oligonucleotides hybridize to multiples regions of a single HPV nucleic acid.

27. The kit of claim 24, wherein said oligonucleotides are selected from the group consisting of SEQ ID NOS. 77-193.

28. A method of detecting a target sequence by using mismatch probe sequences, comprising:

a) providing a sample suspected of containing a target nucleic acid;

b) exposing said sample to one or more oligonucleotides that contain a region that is complementary to said target nucleic acid, said region having a first portion completely complementary to said target nucleic acid, a second portion contiguous to said first portion that is not complementary to said target nucleic acid, and a third portion contiguous to said second portion that is completely complementary to said target nucleic acid; and

c) detecting said target nucleic acid under conditions such that no sequences that are completely complementary to said one or more oligonucleotides are detected.

29. The method of claim 28, wherein said region of said one or more oligonucleotides contains two or more mismatches to said target nucleic acid.

30. The method of claim 28, wherein said region of said one or more oligonucleotides contains three or more mismatches to said target nucleic acid.

31. The method of claim 28, wherein said region contains no more than ten contiguous nucleotides that are completely complementary to said target nucleic acid.

32. The method of claim 28, wherein said region contains no more than seven contiguous nucleotides that are completely complementary to said target nucleic acid.

33. The method of claim 28, wherein at least one of said one or more oligonucleotides is generated by extending a primer in an enzymatic extension reaction using said target nucleic acid as a template.

34. The method of claim 28, wherein said target nucleic acid comprises a viral target nucleic acid.

35. The method of claim 34, wherein said viral target nucleic acid comprises an HPV target nucleic acid.

36. The method of claim 34, wherein said target nucleic acid comprises a conserved region of a viral genome.

37. The method of claim 28, wherein said one or more oligonucleotides comprise two oligonucleotides configured to form an invasive cleavage structure on said target nucleic acid.

38. The method of claim 28, wherein said one or more oligonucleotides comprise two oligonucleotides configured to ligate to each other in the presence of said target nucleic acid.

39. The method of claim 28, wherein said one or more oligonucleotides comprise two oligonucleotides configured to amplify a sequence contained in said target nucleic acid in a polymerase chain reaction.