Compositions and reaction mixtures for the detection of nucleic acids from multiple types of human papillomavirus

• US 9,328,392 B2
• Filed: 08/04/2014
• Issued: 05/03/2016
• 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): Babic, Christopher M
• Assistant Examiner(s): PRIEST, AARON A
• Application Number:
  US14/451,259
• Publication Number:
  US 20150094235A1
• Time in Patent Office: 638 Days
• Field of Search: None
• US Class Current: 1/1
• 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 mixture of oligomers for detecting multiple types of human papillomavirus (HPV) nucleic acids, wherein the mixture includes first amplification oligomers, comprising a target binding region and a 5′

promoter sequence, and second amplification oligomers, comprising a target binding region, wherein pairs of the first and second amplification oligomers hybridize to opposing strands of HPV nucleic acids for transcription mediated amplification of HPV nucleic acids between pairs of hybridized first and second amplification oligomers, wherein;

(a) the first amplification oligomers comprise nucleic acid sequences selected from the group consisting of SEQ ID Nos. 18, 20, 22, 24, 28, 30, 32, 34, 36, RNA equivalents thereof, complements thereof, and combinations thereof; and

(b) the second amplification oligomers comprise nucleic acid sequences selected from the group consisting of SEQ ID Nos. 38, 39, 40, 41, RNA equivalents thereof, complements thereof, and combinations thereof.

2. The mixture of oligomers of claim 1, in which one or more individual oligomers comprises at least one 2′

-methoxy RNA group, at least one 2′

fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, at least one methylphosphonate linkage or any combination thereof.

3. The mixture of oligomers of claim 1 contained in a kit.

4. The mixture of oligomers of claim 1, further comprising at least two detection probe oligomers comprising sequences selected from the group consisting of SEQ ID NO:

11 to SEQ ID NO;

17, SEQ ID NO;

44 to SEQ ID NO;

54 and SEQ ID NO;

58, which includes the complementary oligomer sequences or RNA equivalents of the specified sequences.

5. The mixture of oligomers of claim 4, wherein each oligomer sequence includes a label joined directly or indirectly to the oligomer.

6. The mixture of oligomers of claim 4, wherein each oligomer sequence includes a label that is a chemiluminescent compound.

7. The mixture of oligomers of claim 4, wherein each oligomer sequence has a backbone comprising at least one 2′

-methoxy RNA group.

8. The mixture of claim 1, wherein the first amplification oligomers are at least three amplification oligomers comprising nucleic acid sequences selected from the group consisting of SEQ ID Nos. 18, 20, 22, 24, 28, 30, 32, 34, 36, RNA equivalents thereof, complements thereof, and combinations thereof and the second amplification oligomers are at least three amplification oligomers comprising nucleic acid sequences selected from the group consisting of SEQ ID Nos. 38, 39, 40, 41, RNA equivalents thereof, complements thereof, and combinations thereof.

9. The mixture of at least two oligomers of claim 1, further comprising at least two capture oligomers selected from SEQ ID Nos. 2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer, and SEQ ID Nos. 1, 3, 5, 7 and 9, including RNA equivalents thereof, complements thereof, and combinations thereof.

10. The mixture of oligomers of claim 9, wherein at least one oligomer comprises at least one 2′

-methoxy RNA group, at least one 2′

fluoro-substituted RNA group, at least one peptide nucleic acid linkage, at least one phosphorothioate linkage, or at least one methylphosphonate linkage.

11. The mixture of oligomers of claim 9 contained in a kit.