Oligonucleotides for use in determining the presence of human papilloma virus in a test sample

• US 7,355,034 B2
• Filed: 06/26/2003
• Issued: 04/08/2008
• Est. Priority Date: 11/15/1995
• Status: Expired due to Fees

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Brentano, Steven T., Hammond, Philip W., Gordon, Patricia, Carter, Nick M.
• Primary Examiner(s): Benzion; Gary
• Assistant Examiner(s): Calamita; Heather
• Application Number:
  US10/607,416
• Publication Number:
  US 20050260562A1
• Time in Patent Office: 1,748 Days
• Field of Search: None
• US Class Current: 536/24.3
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention describes oligonucleotides targeted to HPV Type 16 and/or Type 18 nucleic acid sequences which are particularly useful to aid in detecting HPV type 16 and or 18. The oligonucleotides can aid in detecting HPV Type 16 and/or Type 18 in different ways such as by acting as hybridization assay probes, helper probes, and/or amplification primers.

Claims

1. A hybridization assay probe for use in determining the presence of HPV Type 18 nucleic acid in a sample, wherein the base sequence of said probe is up to 100 bases in length and consists of a target binding region having no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48 and, optionally, additional nucleotides that are non-complementary to a nucleic acid derived from HPV Type 18 adjacent the complement of said target binding region, wherein said probe forms a detectable probe;

target duplex with a target nucleic acid sequence derived from HPV Type 18 under selective stringency hybridization conditions, and wherein said probe does not form a detectable probe;

non-target duplex with nucleic acid from HPV Type 16 under said conditions.

2. A nucleic acid hybrid formed between said probe and said target nucleic acid sequence of claim 1.

3. A probe mix comprising:

said probe of claim 1; and

a helper probe, wherein the base sequence of said helper probe has no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124, wherein said helper probe binds to nucleic acid derived from HPV Type 18 under said conditions, thereby facilitating hybridization of said probe to said target nucleic acid sequence.

4. A kit comprising:

said probe of claim 1; and

a helper probe, wherein the base sequence of said helper probe has no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124, wherein said helper probe binds to nucleic acid derived from HPV Type 18 under said conditions, thereby facilitating hybridization of said probe to said target nucleic acid sequence.

5. A kit comprising:

said probe of claim 1; and

a set of first and second amplification oligonucleotides for use in amplifying HPV Type 18 nucleic acid in a sample, wherein;

the base sequence of said first amplification oligonucleotide consists of a first base region selected from the group consisting of SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55 and SEQ ID NO;

56 and, optionally, a second base region that is recognized by an RNA polymerase; and

the base sequence of said second amplification oligonucleotide consists of a first base region selected from the group consisting of SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

111 and SEQ ID NO;

112 and, optionally, a second base region that is recognized by an RNA polymerase.

6. The kit of claim 5 further comprising a helper probe, wherein the base sequence of said helper probe has no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO:

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124, wherein said helper probe binds to nucleic acid derived from HPV Type 18 under said conditions, thereby facilitating hybridization of said probe to said target nucleic acid sequence.

7. A method for determining the presence of HPV Type 18 nucleic acid in a sample, said method comprising the steps of:

providing to a sample said probe of claim 1 under said conditions; and

determining whether said probe;

target duplex has formed as an indication of the presence of HPV Type 18 nucleic acid in said sample.

8. The method of claim 7 further comprising providing to said sample a helper probe, wherein the base sequence of said helper probe has no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO:

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124, wherein said helper probe binds to nucleic acid derived from HPV Type 18 under said conditions, thereby facilitating hybridization of said probe to said target nucleic acid sequence.

9. The method of claim 7 further comprising providing to said sample a set of first and second amplification oligonucleotides, wherein:

the base sequence of said first amplification oligonucleotide consists of a first base region selected from the group consisting of SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55 and SEQ ID NO;

56 and, optionally, a second base region that is recognized by an RNA polymerase; and

the base sequence of said second amplification oligonucleotide consists of a first base region selected from the group consisting of SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

111 and SEQ ID NO;

112, and, optionally, a second base region that is recognized by an RNA polymerase.

10. The method of claim 9 further comprising providing to said sample a helper probe, wherein the base sequence of said helper probe has no more than a 10% base difference with a base sequence selected from the group consisting of SEQ ID NO:

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124, wherein said helper probe binds to nucleic acid derived from HPV Type 18 under said conditions, thereby facilitating hybridization of said probe to said target nucleic acid sequence.

11. The probe of claim 1, wherein said target binding region of said probe consists of a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48.

12. The probe of claim 1, wherein the base sequence of said probe consists of a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48.

13. The probe of claim 1, wherein said probe is labeled with a reporter group moiety.

14. The probe mix of claim 3, wherein:

said target binding region of said probe consists of a base sequence selected from the group consisting of SEQ ID NO;

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48; and

the base sequence of said helper probe consists of a base sequence selected from the group consisting of SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124.

15. The probe mix of claim 14, wherein the base sequence of said probe consists of a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48.

16. The kit of claim 4, wherein:

said target binding region of said probe consists of a base sequence selected from the group consisting of SEQ ID NO;

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48; and

the base sequence of said helper probe consists of a base sequence selected from the group consisting of SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123 and SEQ ID NO;

124.

17. The kit of claim 16, wherein the base sequence of said probe consists of a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48.

18. The kit of claim 5, wherein:

said target binding region of said probe consists of a base sequence selected from the group consisting of SEQ ID NO;

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48;

said first base region of said first amplification oligonucleotide consists of a base sequence selected from the group consisting of SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55 and SEQ ID NO;

56; and

said first base region of said second amplification oligonucleotide consists of a base sequence selected from the group consisting of SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

111 and SEQ ID NO;

112.

19. The kit of claim 18, wherein the base sequence of said probe consists of a base sequence selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47 and SEQ ID NO;

48.

20. The kit of claim 5, wherein at least one of said first and second amplification oligonucleotides further consists of said second base region.