Disclosed is a diagnostic panel of methylated genomic loci encoding microRNA (mgmiR) markers that demonstrated 90% sensitivity and 100% specificity in the detection of head and neck squamous cell carcinoma (HNSCC). These results represent the first use of quantitative MS-PCR for the detection of mgmiRs. In addition, this panel demonstrates the ability to detect hypermethylation in the adjacent mucosa of cancer patients, suggesting its utility in early detection. This panel is also capable of detecting cancer by using saliva, blood and FNA tissue samples.

Disclosed herein are methods and compositions for generating a single-stranded break in a target sequence, which facilitates targeted integration of one or more exogenous sequences.

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.

The present disclosure provided methods, devices, and systems for CRISPR-based screening and detection of HPV-related diseases. In particular, the present disclosure provides a CRISPR-Cas assay for rapid, enhanced screening of cervical intraepithelial neoplasia (CIN) and cancer, which can also be applied to screening for other HPV-related anogenital or head and neck cancers, whose origin is based on infections with high-risk strains of human papillomavirus (hr-HPV).

A diagnostic kit for simultaneously detecting at least seven silent sexually transmitted diseases (SSTDs) having a diagnostic strip which has detection zones with at least eight probes with SEQ ID NOs: 3, 6, 9, 12, 15, 18, 21, 24; at least 14 primers with SEQ ID NOs: 1, 2, 4, 5, 7, 8, 10, 11, 13, 14, 16, 17, 19, 20, 22, 23; an instruction manual; a nucleotide sequence set for simultaneously detecting at least seven silent sexually transmitted diseases (SSTDs); use of the kit to detect at least the following pathogens: Herpes Virus type 1, Herpes Virus type 2, Chlamydia trachomatis, Ureaplasma urealitycum, Mycoplasma hominis, Mycoplasma genitalium, and Human papillomavirus (HPV); a method for simultaneously detecting at least seven silent sexually transmitted diseases (SSTDs).

Methods are provided to improve the positive predictive value for cancer detection using cell-free nucleic acid samples. Various embodiments are directed to applications (e.g., diagnostic applications) of the analysis of the fragmentation patterns and size of cell-free DNA, e.g., plasma DNA and serum DNA, including nucleic acids from pathogens, including viruses. Embodiments of one application can determine if a subject has a particular condition. For example, a method of present disclosure can determine if a subject has cancer or a tumor, or other pathology. Embodiments of another application can be used to assess the stage of a condition, or the progression of a condition over time. For example, a method of the present disclosure may be used to determine a stage of cancer in a subject, or the progression of cancer in a subject over time (e.g., using samples obtained from a subject at different times).

The present invention relates to primers, kits, PCR assay methods and methods for in vitro and non-invasive diagnosis of HPV positive head and neck squamous cell carcinoma. The invention provides inexpensive, rapid, non-invasive and objective determination whether a person is affected with HPV positive head and neck squamous cell carcinoma. Non-requirement of trained personnel for sample collection provides a huge advantage and can lead to real-time disease monitoring.

The present disclosure provides reactive quencher dyes that can be used in the detection and/or quantification of desirable target molecules, such as proteins, nucleic acids and various cellular organelles. These dyes are essentially non-fluorescent but are efficient quenchers of various fluorescent dyes. Also, provided are methods of using the dyes, bio-probes incorporating dyes and methods of using the bio-probes. The quencher dyes described herein are modified to provide beneficial properties.

Methods, systems, and software are provided for determining whether a subject is afflicted with an oncogenic pathogen. Nucleic acids from a biological sample of the subject are hybridized to a probe set that includes probes for human genomic loci and for genomic loci of oncogenic pathogens. Sequence reads of the hybridized nucleic acid are obtained and it’s determined whether each sequence read aligns to a human reference genome. For each sequence read that fails to align to the human reference genome, it’s determined whether the sequence read aligns to a reference genome of an oncogenic pathogen. Sequence reads that both (i) fail to align to the human reference genome and (ii) align to a reference genome of an oncogenic pathogen are tracked, thereby obtaining a sequence read count for the oncogenic pathogen. The sequence read count is used to ascertain whether the subject is afflicted with the oncogenic pathogen.

Provided herein are methods and systems for identifying chimeric nucleic acid fragments, e.g., organism-pathogen chimeric nucleic acid fragments and chromosomal rearrangement chimeric nucleic acid fragments. Also provided herein are methods and systems relating to determining a pathogen integration profile or a chromosomal rearrangement in a biological sample and determining a classification of pathology based at least in part on a pathogen integration profile or a chromosomal rearrangement in a biological sample. In certain aspects of the present disclosure, cell-free nucleic acid molecules from a biological sample are analyzed.