The present disclosure provides compositions, methods, systems, and devices for polynucleotide processing and analyte characterization from a single cell. Such polynucleotide processing may be useful for a variety of applications, including cell lineage analysis. Cell lineage analysis may comprise the use of one or more lineage tracing nucleic acid molecules. The disclosed methods may comprise using a lineage tracing nucleic acid molecule to identify a biological particle with one or more progenitor cells.

The present disclosure relates to methodology for fast and cost-effective identification of the source of DNA samples. DNA samples obtained from unknown or unrecognized tissues or cell types are analyzed according to the methodology described herein, yielding an identification of the tissue and/or cell type source. Identification is based on sequential biochemical procedures including methylation sensitive/dependent restriction and polymerase chain reaction, followed by analysis of the data. All biochemical steps are performed in a single test tube. The disclosure has immediate applications in forensic science for identification of the tissue source of DNA obtained from biological stains. The disclosure also has immediate applications in cancer diagnosis for identification.

The present disclosure relates to methodology for fast and cost-effective identification of the source of DNA samples. DNA samples obtained from unknown or unrecognized tissues or cell types are analyzed according to the methodology described herein, yielding an identification of the tissue and/or cell type source. Identification is based on sequential biochemical procedures including methylation sensitive/dependent restriction and polymerase chain reaction, followed by analysis of the data. All biochemical steps are performed in a single test tube. The disclosure has immediate applications in forensic science for identification of the tissue source of DNA obtained from biological stains. The disclosure also has immediate applications in cancer diagnosis for identification.

In certain embodiments, this application discloses methods for detecting lung cancer. The method includes characterization of cells extracted from human sputum, which is a valuable tissue surrogate and source of upper respiratory cells that become cancerous early in 5 the process of lung cancer development. The method includes the staining of extracted cells with fluorescent reporters that produce a specific pattern in the nuclei of labeled cells, which can be made visible by light microscopy. The pattern is relevant to a type of epigenetic coding of DNA known as DNA methylation, which changes in specific cells of the lung during cancer development, in comparison to normal respiratory cells.

In certain embodiments, this application discloses methods for detecting lung cancer. The method includes characterization of cells extracted from human sputum, which is a valuable tissue surrogate and source of upper respiratory cells that become cancerous early in 5 the process of lung cancer development. The method includes the staining of extracted cells with fluorescent reporters that produce a specific pattern in the nuclei of labeled cells, which can be made visible by light microscopy. The pattern is relevant to a type of epigenetic coding of DNA known as DNA methylation, which changes in specific cells of the lung during cancer development, in comparison to normal respiratory cells.

The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

The present invention is generally directed to compositions, methods, and systems for performing single-molecule, real-time analysis of a variety of different biological reactions, and for determining various characteristics of the different biological reactions. The ability to analyze such reactions provides an opportunity to study those reactions as well as to potentially identify factors and/or approaches for impacting such reactions, e.g., to stimulate, enhance, or inhibit such reactions.

This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.

This invention provides methods of derivatizing a double-stranded DNA comprising contacting double-stranded DNA with a CpG methyltransferase and an s-adenosylmethionine analog. This invention also provides methods of sequencing DNA to determine methylation patterns.

The present invention relates to the field of pharmacogenomics and in particular to detecting the presence or absence of hypermethylated DNA. The detection of CpG methylation in marker DNA is useful for the diagnosis of cancers and the invention provides improved methods for this purpose. These improved methods allow in particular for a more sensitive detection of methylated marker DNA with high backgrounds of unmethylated marker DNA.