Methods and systems for hpv detection and quantification
AssigneeBoard of Regents, The University of Texas System
InventorsMaura GILLISON, Weihong XIAO
Life of this patent
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Abstract
Disclosed are methods and systems for detection and quantification of human papilloma virus (HPV) DNA. Aspects of the disclosure are directed to detection of HPV DNA from cell-free biological samples (e.g., serum, plasma). Disclosed are methods for detecting and quantifying HPV DNA from one or more high-risk types including HPV16, HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV58, HPV59, HPV56, and HPV68. The present disclosure includes compositions (e.g., primers, probes) useful for amplification and detection of HPV DNA.
Claims170
A method for detecting HPV DNA in a biological sample from a subject, the method comprising:
- (a) amplifying HPV DNA from the biological sample using at least six primer pairs each configured to amplify a different HPV type of a set of high-risk HPV types;
- and
- (b) detecting which HPV types of the set of high-risk HPV types are present in the biological sample;
- wherein the set of high-risk HPV types comprises six or more of HPV16, HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV58, HPV59, HPV56, and HPV68.
The method of claim 19 or 20, wherein the detecting of (b) comprises using a first probe comprising SEQ ID NO:29.
The method of any of claims 38-40, wherein the seventh primer pair comprises a seventh forward primer comprising SEQ ID NO:13 and a seventh reverse primer comprising SEQ ID NO:
- 14.
A method for detecting HPV DNA in a biological sample from a subject, the method comprising:
- (a) amplifying HPV DNA from the biological sample using at least six primer pairs comprising at least six of (i) SEQ ID NOs:1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:
- 15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26;
- and
- (b) detecting the HPV DNA in the biological sample using at least six probes comprising at least six of SEQ ID NOs:29-41.
A method for preparing amplified HPV DNA from a biological sample from a subject, the method comprising amplifying HPV DNA from the biological sample using at least six primer pairs comprising at least six of (i) SEQ ID NOs:
- 1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
The method of any of claims 116-117117, wherein the at least six primer pairs comprise at least eight primer pairs comprising at least eight of (i) SEQ ID NOs:1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:
- 15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:
- 19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
The method of any of claims 116-118118, wherein the at least six primer pairs comprise at least nine primer pairs comprising at least nine of (i) SEQ ID NOs:
- 1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:
- 11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:
- 15 and 16, (viv) SEQ ID NOs:
- 17 and 18, (x) SEQ ID NOs:19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
The method of any of claims 116-119119, wherein the at least six primer pairs comprise at least ten primer pairs comprising at least ten of (i) SEQ ID NOs:
- 1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:
- 11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
The method of any of claims 116-120120, wherein the at least six primer pairs comprise at least eleven primer pairs comprising at least eleven of (i) SEQ ID NOs:1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:
- 11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:
- 15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
A kit for detecting HPV DNA from a subject comprising at least six primer pairs comprising at least six of (i) SEQ ID NOs:
- 1 and 2, (ii) SEQ ID NOs:3 and 4, (iii) SEQ ID NOs:5 and 6, (iv) SEQ ID NOs:7 and 8, (v) SEQ ID NOs:9 and 10, (vi) SEQ ID NOs:11 and 12, (vii) SEQ ID NOs:13 and 14, (viii) SEQ ID NOs:15 and 16, (viv) SEQ ID NOs:17 and 18, (x) SEQ ID NOs:
- 19 and 20, (xi) SEQ ID NOs:21 and 22, (xii) SEQ ID NOs:23 and 25, and (xiii) SEQ ID NOs:24 and 26.
A method for detecting HPV DNA in a biological sample from a subject, the method comprising:
- (a) amplifying HPV DNA from the biological sample using at least six primer pairs each configured to amplify a different HPV type of a set of high-risk HPV types;
- and
- (b) detecting which HPV types of the set of high-risk HPV types are present in the biological sample;
- wherein the set of high-risk HPV types comprises six or more of HPV16, HPV18, HPV31, HPV33, HPV35, HPV39, HPV45, HPV51, HPV52, HPV58, HPV59, HPV56, and HPV68.
Dependencies are inferred from the claim text.