Oligonucleotides for use in determining the presence of human papilloma virus in a test sample

• US 20050260562A1
• Filed: 06/26/2003
• Published: 11/24/2005
• Est. Priority Date: 11/15/1995
• Status: Active Grant

• Current Assignee: Nick M. Carter, Patricia Gordon, Philip W. Hammond, Steven T. Brentano
• Original Assignee: Nick M. Carter, Patricia Gordon, Philip W. Hammond, Steven T. Brentano
• Inventors: Brentano, Steven T., Hammond, Philip W., Gordon, Patricia, Carter, Nick M.
• Granted Patent: US 7,355,034 B2
• Time in Patent Office: Days
• US Class Current: 435/5
• CPC Class Codes: C12Q 1/6865 Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 1/708 for papilloma
• CPC Class Codes: C12Q 2600/112 Disease subtyping, staging or classification
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

The present invention describes oligonucleotides targeted to HPV Type 16 and/or Type 18 nucleic acid sequences which are particularly useful to aid in detecting HPV type 16 and or 18. The oligonucleotides can aid in detecting HPV Type 16 and/or Type 18 in different ways such as by acting as hybridization assay probes, helper probes, and/or amplification primers.

Claims

1. A hybridization assay probe for use in determining the presence of HPV Type 18 nucleic acid in a sample, said probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a first nucleic acid target region selected from the group consisting of SEQ ID NO:

45, SEQ ID NO;

46, SEQ ID NO;

47, SEQ ID NO;

48, SEQ ID NO;

57, SEQ ID NO;

58, SEQ ID NO;

59, SEQ ID NO;

60, SEQ ID NO;

65, SEQ ID NO;

66, SEQ ID NO;

67, SEQ ID NO;

68, SEQ ID NO;

73, SEQ ID NO;

74, SEQ ID NO;

75, SEQ ID NO;

76, SEQ ID NO;

77, SEQ ID NO;

78, SEQ ID NO;

79, SEQ i) NO;

80, SEQ ID NO;

81, SEQ ID NO;

82, SEQ ID NO;

83 and SEQ ID NO;

84, wherein said probe forms a detectable probe;

target duplex with said first target region under selective stringency hybridization conditions, and wherein said probe does not form a detectable probe;

non-target duplex with nucleic acid from HPV Type 6, 11, 31, 33, 35, 39, 45, 51, 52 and/or 58 under said conditions.

2. A nucleic acid hybrid formed between said probe and said first target region of claim 1.

3. A probe mix comprising:

said probe of claim 1;

and

a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO;

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

4. A kit comprising:

said probe of claim 1;

and

a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO;

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

5. A kit comprising:

said probe of claim 1;

and

an amplification oligonucleotide for use in amplifying HPV Type 18 nucleic acid in a sample, said amplification oligonucleotide being up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a nucleic acid target region selected from the group consisting of SEQ ID NO;

41, SEQ ID NO;

42, SEQ ID NO;

43, SEQ ID NO;

44, SEQ ID NO;

49, SEQ ID NO;

50, SEQ ID NO;

51, SEQ ID NO;

52, SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55, SEQ ID NO;

56, SEQ ID NO;

69, SEQ ID NO;

70, SEQ ID NO;

71, SEQ ID NO;

72, SEQ ID NO;

101, SEQ ID NO;

102, SEQ ID NO;

103, SEQ ID NO;

104, SEQ ID NO;

105, SEQ ID NO;

106, SEQ ID NO;

107, SEQ ID NO;

108, SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

11, SEQ ID NO;

112, SEQ ID NO;

113, SEQ ID NO;

114, SEQ ID NO;

115 and SEQ ID NO;

116, wherein said amplification oligonucleotide optionally includes a base sequence that is recognized by an RNA polymerase.

6. The kit of claim 5 further comprising a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO:

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

7. A kit comprising:

said probe of claim 1;

and

a set of amplification oligonucleotides for use in amplifying HPV Type 18 nucleic acid in a sample, said set including first and second amplification oligonucleotides, wherein each of said first and second amplification oligonucleotides is up to 100 bases in length and has a base region that is at least 70% complementary to an at least 10 contiguous base region present in a nucleic acid target region selected from the group consisting of SEQ ID NO;

41, SEQ ID NO;

42, SEQ ID NO;

43, SEQ ID NO;

44, SEQ ID NO;

49, SEQ ID NO;

50, SEQ ID NO;

51, SEQ ID NO;

52, SEQ ID NO;

53, SEQ BD NO;

54, SEQ ID NO;

55, SEQ ID NO;

56, SEQ ID NO;

69, SEQ ID NO;

70, SEQ ID NO;

71, SEQ ID NO;

72, SEQ ID NO;

101, SEQ BD NO;

102, SEQ ID NO;

103, SEQ ID NO;

104, SEQ ID NO;

105, SEQ ID NO;

106, SEQ ID NO;

107, SEQ ID NO;

108, SEQ ID NO;

109, SEQ ID NO;

10, SEQ ID NO;

111, SEQ ID NO;

112, SEQ ID NO;

113, SEQ ID NO;

114, SEQ ID NO;

115 and SEQ ID NO;

116, wherein at least one of said first and second amplification oligonucleotides optionally includes a base sequence that is recognized by an RNA polymerase.

8. The kit of claim 7 further comprising a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO:

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

9. A method for determining the presence of HPV Type 18 nucleic acid in a sample, said method comprising the steps of:

providing to a sample said probe of claim 1 under said conditions; and

determining whether said probe;

target duplex has formed as an indication of the presence of HPV Type 18 nucleic acid in said sample.

10. The method of claim 9 further comprising providing to said sample a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO:

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

11. The method of claim 9 further comprising providing to said sample an amplification oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a nucleic acid target region selected from the group consisting of SEQ ID NO:

41, SEQ ID NO;

42, SEQ ID NO;

43, SEQ ID NO;

44, SEQ ID NO;

49, SEQ ID NO;

50, SEQ ID NO;

51, SEQ ID NO;

52, SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55, SEQ ID NO;

56, SEQ ID NO;

69, SEQ ID NO;

70, SEQ ID NO;

71, SEQ ID NO;

72, SEQ ID NO;

101, SEQ ID NO;

102, SEQ ID NO;

103, SEQ ID NO;

104, SEQ ID NO;

105, SEQ ID NO;

106, SEQ ID NO;

107, SEQ ID NO;

108, SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

11, SEQ ID NO;

112, SEQ ID NO;

113, SEQ ID NO;

114, SEQ ID NO;

115 and SEQ ID NO;

116, wherein said amplification oligonucleotide optionally includes a base sequence that is recognized by an RNA polymerase.

12. The method of claim 11 further comprising providing to said sample a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ ID NO:

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.

13. The method of claim 9 further comprising providing to said sample a set of amplification oligonucleotides, said set including first and second amplification oligonucleotides, wherein each of said first and second amplification oligonucleotides is up to 100 bases in length and has a base region that is at least 70% complementary to an at least 10 contiguous base region present in a nucleic acid target region selected from the group consisting of SEQ ID NO:

41, SEQ ID NO;

42, SEQ ID NO;

43, SEQ ID NO;

44, SEQ ID NO;

49, SEQ ID NO;

50, SEQ ID NO;

51, SEQ ID NO;

52, SEQ ID NO;

53, SEQ ID NO;

54, SEQ ID NO;

55, SEQ ID NO;

56, SEQ ID NO;

69, SEQ ID NO;

70, SEQ ID NO;

71, SEQ ID NO;

72, SEQ ID NO;

101, SEQ ID NO;

102, SEQ ID NO;

103, SEQ ID NO;

104, SEQ ID NO;

105, SEQ ID NO;

106, SEQ ID NO;

107, SEQ ID NO;

108, SEQ ID NO;

109, SEQ ID NO;

110, SEQ ID NO;

11, SEQ ID NO;

112, SEQ ID NO;

113, SEQ ID NO;

114, SEQ ID NO;

115 and SEQ ID NO;

116, wherein at least one of said amplification oligonucleotides optionally includes a base sequence that is recognized by an RNA polymerase.

14. The method of claim 13 further comprising providing to said sample a helper probe, said helper probe comprising an oligonucleotide up to 100 bases in length and having a base region that is at least 70% complementary to an at least 10 contiguous base region present in a second nucleic acid target region selected from the group consisting of SEQ BD NO:

61, SEQ ID NO;

62, SEQ ID NO;

63, SEQ ID NO;

64, SEQ ID NO;

117, SEQ ID NO;

118, SEQ ID NO;

119, SEQ ID NO;

120, SEQ ID NO;

121, SEQ ID NO;

122, SEQ ID NO;

123, SEQ ID NO;

124, SEQ ID NO;

125, SEQ ID NO;

126, SEQ ID NO;

127 and SEQ ID NO;

128, wherein said helper probe binds to said second target region under said conditions, thereby facilitating hybridization of said probe to said first target region.