Detection of nucleic acids from multiple types of human papillomavirus

• US 10,465,255 B2
• Filed: 09/18/2017
• Issued: 11/05/2019
• Est. Priority Date: 12/08/2004
• Status: Active Grant

• Current Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Original Assignee: Gen-Probe Incorporated (Hologic Incorporated)
• Inventors: Norman, Sylvia A., Bungo, Jennifer J., Hanna, William L., Rao, Neeraj P.
• Primary Examiner(s): Priest, Aaron A
• Application Number:
  US15/707,679
• Publication Number:
  US 20180002768A1
• Time in Patent Office: 778 Days
• Field of Search: None
• CPC Class Codes: C07K 14/005 from viruses
• CPC Class Codes: C12N 2710/20022 New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Nucleic acid oligonucleotide sequences are disclosed which include amplification oligomers and probe oligomers which are useful for detecting multiple types of human papillomaviruses (HPV) associated with cervical cancer. Methods for detecting multiple HPV types in biological specimens by amplifying HPV nucleic acid sequences in vitro and detecting the amplified products are disclosed.

Claims

1. A combination of oligomers for detecting human papillomavirus (HPV) types in group D, the combination comprising:

a first amplification oligomer comprising a target-specific sequence and a 5′

promoter sequence, wherein the first amplification oligomer target-specific sequence consists of SEQ ID NO;

35 or SEQ ID NO;

37, or an RNA equivalent thereof; and

a second amplification oligomer comprising a target-specific sequence consisting of SEQ ID NO;

41, or an RNA equivalent thereof.

2. The oligomer combination of claim 1, wherein the nucleotide sequence of the first amplification oligomer consists of SEQ ID NO:

34 or SEQ ID NO;

36, or an RNA equivalent thereof.

3. The oligomer combination of claim 1, wherein the first amplification oligomer target-specific sequence consists of SEQ ID NO:

35, or an RNA equivalent thereof.

4. The oligomer combination of claim 3, further comprising a third amplification oligomer comprising a target-specific sequence and a 5′

promoter sequence, wherein the third amplification oligomer target-specific sequence consists of SEQ ID NO;

37, or an RNA equivalent thereof.

5. The oligomer combination of claim 4, wherein

the nucleotide sequence of the first amplification oligomer consists of SEQ ID NO:

34, or an RNA equivalent thereof, and

the nucleotide sequence of the third amplification oligomer consists of SEQ ID NO;

36, or an RNA equivalent thereof.

6. The oligomer combination of claim 1, further comprising a detection probe oligomer comprising a target-specific sequence selected from the group consisting of SEQ ID NO:

15, SEQ ID NO;

16, SEQ ID NO;

17, complements thereof, and RNA equivalents thereof.

7. The oligomer combination of claim 6, wherein the detection probe oligomer further comprises a detectable label.

8. The oligomer combination of claim 6, wherein the detection probe oligomer target-specific sequence comprises at least one 2′

-methoxy RNA group.

9. The oligomer combination of claim 6, wherein the combination comprises first and second detection probe oligomers, each of the first and second detection probe oligomers comprising a target-specific sequence selected from the group consisting of SEQ ID NO:

15, SEQ ID NO;

16, SEQ ID NO;

17, complements thereof, and RNA equivalents thereof.

10. The oligomer combination of claim 9, wherein

(i) the first detection probe oligomer target-specific sequence consists of SEQ ID NO:

15, the complement thereof, or an RNA equivalent thereof, and

(ii) the second detection probe oligomer target-specific sequence consists of SEQ ID NO;

16, the complement thereof, or an RNA equivalent thereof.

11. The oligomer combination of claim 1, wherein the oligomer combination is contained in an amplification reaction mixture.

12. The oligomer combination of claim 6, wherein the oligomer combination is contained in an amplified product detection reaction mixture.

13. The oligomer combination of claim 1, wherein the oligomer combination is contained in a kit.

14. A method for of determining the presence or absence of a human papillomavirus (HPV) nucleic acid type in group D in a sample, comprising the steps of:

(a) contacting a sample, said sample suspected of containing a target nucleic acid of an HPV type in group D, with a combination of amplification oligomers that amplify a target region of said target nucleic acid, wherein

(i) a first amplification oligomer comprises a target-specific sequence and a 5′

promoter sequence, wherein the first amplification oligomer target-specific sequence consists of SEQ ID NO;

35 or SEQ ID NO;

37, or an RNA equivalent thereof; and

(ii) a second amplification oligomer comprises a target-specific sequence consisting of SEQ ID NO;

41, or an RNA equivalent thereof;

(b) performing an amplification reaction using the amplification oligomers, wherein if the target nucleic acid of the HPV type in group D is present in the sample, an amplification product is produced; and

(c) detecting the amplification product.

15. The method of claim 14, wherein the first amplification oligomer target-specific sequence consists of SEQ ID NO:

35, or an RNA equivalent thereof.

16. The method of claim 15, wherein the combination of amplification oligomers further comprises a third amplification oligomer comprising a target-specific sequence and a 5′

promoter sequence, wherein the third amplification oligomer target-specific sequence consists of SEQ ID NO;

37, or an RNA equivalent thereof.

17. The method of claim 14, wherein the detecting step (c) comprises contacting the amplification product, if present, with a detection probe oligomer that binds specifically to the amplification product and results in a signal to indicate the presence in the sample of the HPV nucleic acid type in group D.

18. The method of claim 17, wherein the detection probe oligomer comprises a target-specific sequence selected from the group consisting of SEQ ID NO:

15, SEQ ID NO;

16, SEQ ID NO;

17, complements thereof, and RNA equivalents thereof.

19. The method of claim 14, further comprising a step of separating any target nucleic acid of the HPV type in group D from other components in the sample by (i) contacting the HPV target nucleic acid in the sample with a capture oligomer and (ii) separating a complex that includes the capture oligomer and the HPV target nucleic acid from other sample components before the amplifying step (b).

20. The method of claim 14, wherein the amplification reaction of step (b) is a transcription-associated amplification reaction.