The present invention relates to a method for detecting an integration pattern of a virus in a host genome. In particular, a method is provided encompassing selective cleavage of circularized DNA fragments carrying viral DNA with an RNA-guided endonuclease and at least one guide RNA or at least one pool of guide RNAs, followed by inverse PCR, in particular inverse long-range PCR, and sequencing. The invention further relates to kits for performing the method and application of the method.

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.

The first object of the invention is primer sets for amplifying the nucleotide sequence of the L2 gene of human papillomavirus type 16 or L1 gene of human papillomavirus type 18. The second object of the invention is a method for detecting HPV16 or HPV18 viruses. Another object of the invention is a method of detecting HPV16 and HPV18 infections. A fourth object of the invention is a kit for detecting HPV16 or HPV18 infections.

The present invention provides modified single primer extension-based methods for generating an amplified library of fragments of a target gene or genome of interest from a sample of fragmented DNA, wherein the library is suitable for use in detecting, quantifying and/or sequencing the target gene or genome of interest. The present invention also provides compositions for use in such methods. In some embodiments the present invention provides methods and compositions specifically for detecting, quantifying and/or sequencing circulating tumor derived HPV DNA.

Provided is a method and a kit for detection of human papillomaviruses. Specifically, provided is a method for detecting at least 65 human papillomavirus genotypes. Also provided is a kit for detection of human papillomaviruses, which comprises one or more reagents capable of detecting at least 65 human papillomavirus genotypes.

A method for detecting minimal residual disease in a subject following a cancer surgery is disclosed. The method includes obtaining a sample from the subject. The sample includes a surgical drainage. The method also includes isolating an amount of tumor-associated genetic material from the sample, sequencing the amount of tumor-associated genetic material to detect and quantify at least one tumor-associated mutation or variant in the amount of tumor-associated genetic material, and providing the at least one quantity of the at least one tumor-associated mutation or variant to a practitioner.

A composition for binding to human papillomavirus type 16 (HPV16)-positive tumor cells, the composition including a DNA aptamer. The DNA aptamer includes one of SEQ ID NO: 1 and SEQ ID NO: 2.

The present invention relates to methods of diagnosing and/or treating head and neck squamous cell carcinoma (HNSCC) in a subject. The present invention further relates to methods of diagnosing and/or treating head and neck squamous cell carcinoma (HNSCC) in a subject, wherein the subject has been diagnosed as being positive for human papillomavirus (HPV

Disclosed herein are methods for molecularly characterizing cervical cell samples as being negative for intraepithelial lesion or malignancy (NILM), low-grade squamous intraepithelial lesion (LSIL), or high-grade squamous intraepithelial lesion (HSIL).

There is described herein a method for capturing circulating tumor DNA (ctDNA) of interest from an animal sample, preferably a mammalian sample, further preferably a human patient sample, comprising cell-free DNA (cfDNA), the method comprising: adding to the patient sample a library of nucleic acid hybrid capture probes, wherein the library of 5 probes is complementary to both strands of the double stranded ctDNA of interest and the probes are tagged for capture; allowing the probes to hybridize to the ctDNA; and capturing the hybridized ctDNA using the tag on the probes. Libraries of probes for use with these methods are also described.