Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxymethylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.

Provided herein are methods for monitoring false negative and/or false positive detection of modified nucleosides in DNA in a sample using a base-pairing conversion procedure. The methods use nucleosides having known nucleoside identity and known modification status in adapters ligated to the DNA. In certain aspects, the disclosure relates to methods for improving the quality control of such methods.

Provided herein are methods for monitoring false negative and/or false positive detection of modified nucleosides in DNA in a sample using a base-pairing conversion procedure. The methods use nucleosides having known nucleoside identity and known modification status in adapters ligated to the DNA. In certain aspects, the disclosure relates to methods for improving the quality control of such methods.

The invention relates to a method of eluting nucleic acid from a swab. The invention also relates to a kit for eluting nucleic acid from a swab and an elution solution.

The invention relates to a method of eluting nucleic acid from a swab. The invention also relates to a kit for eluting nucleic acid from a swab and an elution solution.

This invention features systems and methods for the detection of analytes, and their use in the treatment and diagnosis of disease.

The present disclosure provides methods of detecting analytes such as RNA and/or DNA, extracting analytes such as RNA and/or DNA, improving library construction for nucleic acid sequencing, and reducing the level of embedding agent in analyte samples such as RNA and/or DNA samples that are extracted from embedded samples such as paraffin-embedded samples.

The present disclosure provides methods of detecting analytes such as RNA and/or DNA, extracting analytes such as RNA and/or DNA, improving library construction for nucleic acid sequencing, and reducing the level of embedding agent in analyte samples such as RNA and/or DNA samples that are extracted from embedded samples such as paraffin-embedded samples.

Methods are provided for the epigenetic analysis of cell-free DNA using organic boranes to convert oxidized 5-methylcytosine residues in the cell-free DNA to dihydrouracil (DHU) residues. Cell-free DNA is contacted with an organic borane selected to successively bring about reduction, deamination, and decarboxylation of oxidized 5-methylcytosine residues such as 5-carboxylcytosine and 5-formylcytosine, resulting in DHU residues in place thereof. Following amplification, the treated cell-free DNA is sequenced, with the DHU residues read as thymine residues. Reaction mixtures, kits and additional methods are also provided, as are related methods for the epigenetic analysis of DNA, including cell-free DNA.

The invention provides compositions and methods for preparing high-quality labeled DNA for use in array-based comparative genomic hybridization in amounts sufficient therefor starting with a low amount of input genomic DNA, such as 50-250 nanograms input genomic DNA.