	US 11,913,080 B2
	Compositions and methods for the selective detection of tumor-derived viral DNA
Gaorav Gupta, Chapel Hill, NC (US); Bhishamjit S. Chera, Chapel Hill, NC (US); and Sunil Kumar, Chapel Hill, NC (US)
Assigned to The University of North Carolina at Chapel Hill, Chapel Hill, NC (US)
Filed by The University of North Carolina at Chapel Hill, Chapel Hill, NC (US)
Filed on Feb. 15, 2022, as Appl. No. 17/671,789.
Application 17/671,789 is a continuation of application No. 17/203,068, filed on Mar. 16, 2021, granted, now 11,254,989.
Claims priority of provisional application 62/990,438, filed on Mar. 16, 2020.
Prior Publication US 2022/0259681 A1, Aug. 18, 2022
Int. Cl. C12Q 1/68 (2018.01); C12Q 1/6888 (2018.01); C12Q 1/70 (2006.01); C12Q 1/686 (2018.01); C12Q 1/6853 (2018.01)

CPC C12Q 1/6888 (2013.01) [C12Q 1/686 (2013.01); C12Q 1/6853 (2013.01); C12Q 1/70 (2013.01); C12Q 1/701 (2013.01); C12Q 1/708 (2013.01)]

19 Claims

1. A composition for detecting tumor-derived Human Papilloma Virus type 18 (HPV18) in a sample from a subject, comprising at least a triad of modified oligonucleotide primer/probe sets selected from the group consisting of:

Set 1: SEQ ID NO:80, SEQ ID NO:81, and SEQ ID NO:82,

Set 2: SEQ ID NO:83, SEQ ID NO:84, and SEQ ID NO:85,

Set 3: SEQ ID NO:86, SEQ ID NO:87, and SEQ ID NO:88,

Set 4: SEQ ID NO:89, SEQ ID NO:90, and SEQ ID NO:91,

Set 5: SEQ ID NO:92, SEQ ID NO:93, and SEQ ID NO:94,

Set 6: SEQ ID NO:95, SEQ ID NO:96, and SEQ ID NO:97,

Set 7: SEQ ID NO:98, SEQ ID NO:99, and SEQ ID NO:100,

Set 8: SEQ ID NO:101, SEQ ID NO:102, and SEQ ID NO:103,

Set 9: SEQ ID NO:104, SEQ ID NO:105, and SEQ ID NO:106,

Set 10: SEQ ID NO:107, SEQ ID NO:108, and SEQ ID NO:109,

Set 11: SEQ ID NO:110, SEQ ID NO:111, and SEQ ID NO:112,

Set 12: SEQ ID NO:113, SEQ ID NO:114, and SEQ ID NO:115,

Set 13: SEQ ID NO:116, SEQ ID NO:117, and SEQ ID NO:118,

Set 14: SEQ ID NO:119, SEQ ID NO:120, and SEQ ID NO:121,

Set 15: SEQ ID NO:122, SEQ ID NO:123, and SEQ ID NO:124,

Set 16: SEQ ID NO:125, SEQ ID NO:126, and SEQ ID NO:127,

Set 17: SEQ ID NO:128, SEQ ID NO:129, and SEQ ID NO:130, and

Set 18: SEQ ID NO:131, SEQ ID NO:132, and SEQ ID NO:133,

wherein a first primer/probe set of the triad is configured to produce a first amplicon signal,

wherein a second primer/probe set of the triad is configured to produce a second amplicon signal,

wherein a third primer/probe set of the triad is configured to produce a third amplicon signal, and

wherein the primer/probe set of the triad with the smallest set number corresponds to the first primer/probe set and the primer/probe set of the triad with the largest set number corresponds to the third primer/probe set.