Compositions and methods for the selective detection of tumor-derived viral DNA
AssigneeThe University of North Carolina at Chapel Hill
InventorsGaorav Gupta, Bhishamjit S. Chera, Sunil Kumar
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Abstract
The present disclosure provides methods and compositions of modified oligonucleotide primer and probe combinations, structurally modified with locked nucleic acids, quenchers, and dyes, effective to detect tumor-derived Human Papilloma Virus (HPV) and tumor-derived Epstein-Barr virus (EBV) and, especially, to distinguish viral DNA derived from tumors from viral DNA derived from infectious viral particles.
Claims5
A composition for detecting tumor-derived Human Papilloma Virus type 31 (HPV31) in a sample from a subject, comprising at least a triad of modified oligonucleotide primer and probe sets selected from the group consisting of:
- Set 1:
- SEQ ID NO:
- 134, SEQ ID NO:
- 135, and SEQ ID NO:
- 136,
- Set 2:
- SEQ ID NO:
- 137, SEQ ID NO:
- 138, and SEQ ID NO:
- 139,
- Set 3:
- SEQ ID NO:
- 140, SEQ ID NO:
- 141, and SEQ ID NO:
- 142,
- Set 4:
- SEQ ID NO:
- 143, SEQ ID NO:
- 144, and SEQ ID NO:
- 145,
- Set 5:
- SEQ ID NO:
- 146, SEQ ID NO:
- 147, and SEQ ID NO:
- 148,
- Set 6:
- SEQ ID NO:
- 149, SEQ ID NO:
- 150, and SEQ ID NO:
- 151,
- Set 7:
- SEQ ID NO:
- 152, SEQ ID NO:
- 153, and SEQ ID NO:
- 154,
- Set 8:
- SEQ ID NO:
- 155, SEQ ID NO:
- 156, and SEQ ID NO:
- 157,
- Set 9:
- SEQ ID NO:
- 158, SEQ ID NO:
- 159, and SEQ ID NO:
- 160,
- Set 10:
- SEQ ID NO:
- 161, SEQ ID NO:
- 162, and SEQ ID NO:
- 163,
- Set 11:
- SEQ ID NO:
- 164, SEQ ID NO:
- 165, and SEQ ID NO:
- 166,
- Set 12:
- SEQ ID NO:
- 167, SEQ ID NO:
- 168, and SEQ ID NO:
- 169,
- Set 13:
- SEQ ID NO:
- 170, SEQ ID NO:
- 171, and SEQ ID NO:
- 172,
- Set 14:
- SEQ ID NO:
- 173, SEQ ID NO:
- 174, and SEQ ID NO:
- 175,
- Set 15:
- SEQ ID NO:
- 176, SEQ ID NO:
- 177, and SEQ ID NO:
- 178,
- Set 16:
- SEQ ID NO:
- 179, SEQ ID NO:
- 180, and SEQ ID NO:
- 181, and
- Set 17:
- SEQ ID NO:
- 182, SEQ ID NO:
- 183, and SEQ ID NO:
- 184,
- wherein the first primer and probe set of the triad is configured to produce a first amplicon signal,
- wherein the second primer and probe set of the triad is configured to produce a second amplicon signal,
- wherein the third primer and probe set of the triad is configured to produce a third amplicon signal, and
- wherein the primer and probe set of the triad with the smallest set number corresponds to the first primer and probe set, and the primer and probe set of the triad with the largest set number corresponds to the third primer and probe set.
Dependencies are inferred from the claim text.