Compositions, reaction mixtures and methods for detecting nucleic acids from multiple types of human papillomavirus

• US 8,835,114 B2
• Filed: 09/30/2013
• Issued: 09/16/2014
• 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:
  US14/041,970
• Publication Number:
  US 20140038173A1
• Time in Patent Office: 351 Days
• Field of Search: None
• US Class Current: 435/6.1
• 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 method of detecting the presence of human papillomavirus (HPV) nucleic acid present in a biological sample, comprising the steps of:

(a) contacting HPV nucleic acid in a biological sample with a combination of amplification oligonucleotides that amplify a HPV target sequence in an E6/E7 target region sequence, comprising one of the following combinations of amplification oligonucleotides;

(1) amplification oligonucleotides comprising oligonucleotide sequences consisting of SEQ ID Nos. 21, 23, 25, 29, 31, 33, 35, 37, 38, 39, 40, 41, and 42, sequences that are completely complementary thereto, RNA equivalents thereof, or RNA equivalents of the sequences that are completely complementary thereto;

or

(2) amplification oligonucleotides comprising oligonucleotide sequences consisting of SEQ ID Nos. 19, 21, 23, 25, 29, 31, 33, 35, 37, 38, 39, 40 and 41, sequences that are completely complementary thereto, RNA equivalents thereof, and RNA equivalents of the sequences that are completely complementary thereto;

(b) producing amplified product from the HPV nucleic acid by using the amplification oligonucleotides and a nucleic acid polymerase in an in vitro amplification reaction; and

(c) detecting the amplified product to indicate the presence in the sample of an HPV nucleic acid in the biological sample.

2. The method of claim 1, further comprising a separating step before step (b), wherein the separating step separates at least one HPV RNA from other components in the biological sample by contacting HPV RNA in the biological sample with a capture oligonucleotide that hybridizes to the HPV RNA and separating a complex that includes the capture oligonucleotide and HPV RNA from other components in the biological sample.

3. The method of claim 2, wherein the separating step uses a mixture of at least two capture oligonucleotides wherein each oligonucleotide sequence is selected from the group consisting of SEQ ID Nos. 1 to 10 and RNA equivalents of the sequences identified by SEQ ID Nos. 1 to 10, wherein a capture oligonucleotide sequence consisting of SEQ ID Nos. 2, 4, 6, 8 or 10 is joined to a ligand moiety.

4. The method of claim 3, wherein the mixture of at least two capture oligonucleotides is made up of:

at least two capture oligonucleotides consisting of sequences selected from SEQ ID Nos. 2, 4, 6, 8 and 10, wherein each capture oligonucleotide is joined to a ligand moiety;

or

at least two oligonucleotides consisting of sequences selected from SEQ ID Nos. 1, 3, 5, 7 and 9.

5. The method of claim 1, wherein the in vitro amplification reaction is a substantially isothermal amplification reaction.

6. The method of claim 5, wherein the in vitro amplification reaction is a transcription-associated amplification reaction.

7. The method of claim 1, wherein the detecting step uses a mixture of probe oligonucleotides selected from the group consisting of:

a mixture of probe oligonucleotides comprising oligonucleotide sequences selected from the group consisting of SEQ ID Nos. 11 to 17, complete complements thereof, RNA equivalents thereof, and RNA equivalents of the complete complements thereof, wherein each probe oligonucleotide optionally includes a label joined directly or indirectly to the oligonucleotide;

a mixture of probe oligonucleotides comprising oligonucleotide sequences selected from the group consisting of SEQ ID Nos. 11 to 15 and 17, complete complements thereof, RNA equivalents thereof, and RNA equivalents of the complete complements thereof, wherein each probe oligonucleotide optionally includes a label joined directly or indirectly to the oligonucleotide;

a mixture of probe oligonucleotides comprising oligonucleotide sequences selected from the group consisting of SEQ ID Nos. 11 to 15 and 17 with at least one of SEQ ID Nos. 44 to 54 or 58, complete complements thereof, RNA equivalents thereof, and RNA equivalents of the complete complements thereof, wherein each probe oligonucleotide optionally includes a label joined directly or indirectly to the oligonucleotide;

or

a mixture of probe oligonucleotides comprising oligonucleotide sequences selected from the group consisting of SEQ ID Nos. 11, 12, 14, 15, 17, 44, 45 and 52, complete complements thereof, RNA equivalents thereof, and RNA equivalents of the complete complements thereof, wherein each probe oligonucleotide optionally includes a label joined directly or indirectly to the oligonucleotide.

8. The method of claim 1, wherein the contacting step further includes introducing a non-HPV internal control sequence into the sample, the amplifying step further includes amplifying the non-HPV internal control sequence to produce an amplified internal control sequence, and the detecting step further includes detecting the amplified internal control sequence to produce a signal that indicates that the method steps have been performed appropriately.

9. The method of claim 1, further comprising performing a second reaction that includes the steps of:

contacting nucleic acid in the biological sample with a mixture of amplification oligonucleotides that amplify a HPV 16 target sequence and that amplify a HPV 18 target sequence, wherein both the HPV 16 target sequence and the HPV 18 target sequence are in an E6/E7 target region sequence;

amplifying the HPV 16 target sequence or the HPV 18 target sequence that is present in the sample by using the mixture of amplification oligonucleotides and a nucleic acid polymerase in vitro to produce an HPV 16 amplified product, an HPV 18 amplified product, or both an HPV 16 amplified product and an HPV 18 amplified product, depending on which HPV type or types are present in the sample; and

detecting the HPV 16 amplified product, the HPV 18 amplified product, or both the HPV 16 amplified product and the HPV 18 amplified product, depending on which HPV type or types are present in the sample by using a mixture of detection probes made up of a detection probe specific for detection of HPV 16 and a detection probe specific for HPV 18 amplified sequences, thereby detecting the presence of HPV 16, HPV 18, or both HPV 16 and HPV 18 in the sample.

10. The method of claim 9, wherein the mixture of amplification oligonucleotides consists of SEQ ID Nos. 18, 28, and 39, and wherein the mixture of detection probes consists of SEQ ID Nos. 11 and 13, sequences that are completely complementary to SEQ ID Nos. 11 and 13, RNA equivalents of SEQ ID Nos. 11 and 13, or RNA equivalents of the sequences completely complementary to SEQ ID Nos. 11 and 13, wherein each detection probe optionally includes a label joined directly or indirectly to the oligonucleotide.

11. The method of claim 9, wherein the mixture of amplification oligonucleotides consists of SEQ ID Nos. 19, 29, and 39, and wherein the mixture of detection probes consists of SEQ ID Nos. 11 and 13, sequences that are completely complementary to SEQ ID Nos. 11 and 13, RNA equivalents of SEQ ID Nos. 11 and 13, or RNA equivalents of the sequences completely complementary to SEQ ID Nos. 11 and 13, wherein each detection probe optionally includes a label joined directly or indirectly to the oligonucleotide.