Detection of nucleic acids from multiple types of human papillomavirus

• US 10,047,407 B2
• Filed: 06/23/2015
• Issued: 08/14/2018
• 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:
  US14/747,974
• Publication Number:
  US 20150292046A1
• Time in Patent Office: 1,148 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 detection probe oligomer for selectively detecting HPV types in group C1 in the presence of HPV types from one or more of groups A1, A2, B, C2, and D, wherein the detection probe oligomer comprises:

(i) a target-specific sequence consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs;

13, 46, 45, complements thereof, and RNA equivalents thereof; and

(ii) a detectable label.

2. The detection probe oligomer of claim 1, wherein the detectable label is joined directly to the oligomer.

3. The detection probe oligomer of claim 1, wherein the detection probe oligomer nucleotide sequence has a backbone comprising at least one 2′

-methoxy RNA group.

4. The detection probe oligomer of claim 1, wherein the detection probe oligomer is contained in a kit.

20. The detection probe oligomer of claim 1, wherein the detection probe oligomer is contained in a probe reagent comprising one or more of:

lithium succinate, lithium lauryl sulfate, lithium chloride, mercaptoethanesulfonate, EDTA, ethanol, a detection probe oligomer that detects HPV sequences in group A1, a detection probe oligomer that detects HPV sequences in group A2, a detection probe oligomer that detects HPV sequences in group C2, and/or a detection probe oligomer that detects HPV sequences in group D.

21. The detection probe oligomer of claim 1, wherein the detectable label is a chemiluminescent compound.

5. A method of determining the presence or absence of a human papillomavirus (HPV) nucleic acid type in group C1 in a sample, comprising the steps of:

(a) contacting a sample with a detection probe oligomer comprising;

(i) a target-specific sequence consisting of a nucleotide sequence selected from the group consisting of SEQ ID NOs;

13, 46, 45, complements thereof, and RNA equivalents thereof; and

(ii) a detectable label; and

(b) performing a detection reaction to detect a signal from the detectable label, wherein the signal indicates the presence of a human papillomavirus (HPV) nucleic acid type in group C1 in the sample.

6. The method of claim 5, further comprising a step of separating the human papillomavirus (HPV) nucleic acid type in group C1 from other components in the sample by contacting the human papillomavirus (HPV) nucleic acid type in group C1 with a capture oligomer and separating a complex that includes the capture oligomer and the human papillomavirus (HPV) nucleic acid type in group C1 from other components in the sample before the detection reaction.

7. The method of claim 6, wherein the capture oligomer is present in a mixture of capture oligomers made up of at least two oligomers in which individual oligomer sequences are selected from the group consisting of SEQ ID Nos. 1 to 10, which includes the complementary oligomer sequences or RNA equivalents of the specified sequences.

8. The method of claim 6, wherein the capture oligomer is present in a mixture of capture oligomers made up of:

at least two oligomers selected from SEQ ID Nos. 2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer;

oligomers of SEQ ID Nos. 2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer;

at least two oligomers selected from SEQ ID Nos. 1, 3, 5, 7 and 9;

or

oligomers of SEQ ID Nos. 1, 3, 5, 7 and 9.

9. The method of claim 5, wherein before or during the detection reaction step (b) there is an amplifying step, wherein the sample is contacted with a mixture of amplification oligomers and reagents for amplifying a human papillomavirus (HPV) nucleic acid type in group C1 comprising a target sequence.

10. The method of claim 9, wherein the amplifying step uses a transcription-associated amplification method.

11. The method of claim 5, wherein the detecting step uses a mixture of detection probe oligomers.

12. The method of claim 9, wherein the amplifying step uses an amplification process that is substantially isothermal.

13. The method of claim 9, wherein the mixture of amplification oligomers comprises SEQ ID NO:

29, SEQ ID NO;

31, and SEQ ID NO;

39.

14. The method of claim 5, wherein the sample is a biological sample.

15. The method of claim 6, wherein the target sequence is separated from a biological sample.

16. The method of claim 5, wherein the sample in step (a) is a biological sample.

17. The method of claim 5, wherein the human papillomavirus (HPV) nucleic acid type in group C1 is specifically detected in the presence of one or more of a human papillomavirus (HPV) nucleic acid type A1, A2, B, C2 and/or D.

18. The method of claim 9, wherein the amplifying step produces an amplicon comprising a detection probe oligomer target sequence.

19. The method of claim 18, wherein the amplicon is an RNA transcript.