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.

Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

Methods, compositions and kits are provided to amplify the amount of genomic methylated DNA can by subsequently analyzed and/or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase/polymerase is used.

Methods and kits for detecting the presence of at least one target DNA sequence with or without a modification in a DNA molecule are provided.

Methods and kits for detecting the presence of at least one target DNA sequence with or without a modification in a DNA molecule are provided.

Disclosed is an epigenetic biomarker that comprises clustered methylated genomic DNA which can self-assemble to form complexes that have distinct physicochemical properties relative to genomic DNA that lacks such clusters. Also disclosed are methods, systems, compositions and kits that takes advantage of these physicochemical properties for detecting clustered methylated genomic DNA including for determining likelihood of the presence of cancer.

Disclosed is an epigenetic biomarker that comprises clustered methylated genomic DNA which can self-assemble to form complexes that have distinct physicochemical properties relative to genomic DNA that lacks such clusters. Also disclosed are methods, systems, compositions and kits that takes advantage of these physicochemical properties for detecting clustered methylated genomic DNA including for determining likelihood of the presence of cancer.

Disclosed herein are methods for performing a medical procedure by determining the mutation and DNA modification status of a biological sample from a subject with respect to a single sample. Also disclosed herein are methods for diagnosis by determining whether a DNA of a biological sample contains nucleobase modifications and mutations, by assessing the DNA modification and mutation status with respect to a single sample.

Disclosed herein are methods for performing a medical procedure by determining the mutation and DNA modification status of a biological sample from a subject with respect to a single sample. Also disclosed herein are methods for diagnosis by determining whether a DNA of a biological sample contains nucleobase modifications and mutations, by assessing the DNA modification and mutation status with respect to a single sample.

The current disclosure relates to methods, compositions and kits for detecting modified adenosine in a target RNA molecule. Aspects relate to a method for detecting modified adenosine in a target ribonucleic acid (RNA) comprising contacting the target RNA with an adenosine deaminase enzyme (adenosine deaminase, RNA-specific) to generate a target RNA with deaminated adenosines and sequencing the target RNA with deaminated adenosines; wherein the modified adenosine is detected when the nucleotide sequence is adenosine.