Separation of human papillomavirus nucleic acids from biological samples

• US 10,640,836 B2
• Filed: 07/20/2018
• Issued: 05/05/2020
• 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:
  US16/040,847
• Publication Number:
  US 20190002995A1
• Time in Patent Office: 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 mixture 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, wherein the mixture includes;

at least two oligomers selected from SEQ ID NOs;

2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer, wherein at least one of the at least two oligomers is SEQ ID NO;

4 or 10 joined to the ligand moiety;

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, wherein at least one of the at least two oligomers is SEQ ID NO;

3 or 9;

or

oligomers of SEQ ID NOs;

1, 3, 5, 7 and 9.

2. The mixture of oligomers of claim 1, wherein at least one oligomer comprises a backbone that includes 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.

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

6. The mixture of oligomers of claim 1, wherein the mixture includes oligomers of SEQ ID NOs:

2 and 6 with a ligand moiety joined to each oligomer.

7. The mixture of oligomers of claim 1, wherein the mixture includes oligomers of SEQ ID NOs:

2 and 4 with a ligand moiety joined to each oligomer.

8. The mixture of oligomer of claim 1, wherein the mixture includes oligomers of SEQ ID NOs:

6 and 8 with a ligand moiety joined to each oligomer.

9. The mixture of oligomers of claim 1, wherein the mixture includes oligomers of SEQ ID NOs:

4, 6, 8 and 10 with a ligand moiety joined to each oligomer.

10. The mixture of oligomers of claim 1, wherein the mixture includes oligomers of SEQ ID NOs:

2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer.

4. A method of separating a human papillomavirus (HPV) nucleic acid from other components present within a biological sample, comprising the steps of:

contacting nucleic acid in a biological sample containing RNA of at least one of HPV types 33, 51, 52, 56, 58, and 66 with a capture oligomer comprising an oligomer sequence selected from the group consisting of SEQ ID NOs;

3, 4, 9, and 10, which includes the complementary oligomer sequences or RNA equivalents of the specified sequences.

5. The method of claim 4, 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, wherein at least one of the at least two oligomers is SEQ ID NO;

4 or 10 joined to the ligand moiety;

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, wherein at least one of the at least two oligomers is SEQ ID NO;

3 or 9;

or

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

11. The method of claim 5, wherein the capture oligomer is present in a mixture of capture oligomers made up of oligomers of SEQ ID NOs:

2 and 4 with a ligand moiety joined to each oligomer.

12. The method of claim 5, wherein the capture oligomer is present in a mixture of capture oligomers made up of oligomers of SEQ ID NOs:

4, 6, 8 and 10 with a ligand moiety joined to each oligomer.

13. The method of claim 5, wherein the capture oligomer is present in a mixture of capture oligomers made up of oligomers of SEQ ID NOs:

2, 4, 6, 8 and 10 with a ligand moiety joined to each oligomer.