Methods and systems for targeted detection of circulating tumor DNA (ctDNA) molecules are disclosed herein. A cell-free nucleic acid may be subjected to conditions to increase its methylation level, thereby yielding a hypermethylated cell-free nucleic acid, and subsequently identifying a sequence of the hypermethylated cell-free nucleic acid.

Methods and systems for targeted detection of circulating tumor DNA (ctDNA) molecules are disclosed herein. A cell-free nucleic acid may be subjected to conditions to increase its methylation level, thereby yielding a hypermethylated cell-free nucleic acid, and subsequently identifying a sequence of the hypermethylated cell-free nucleic acid.

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.

The present invention relates to methods and kits for the detection of 5-hydroxymethylcytosine (5hmC) and/or 5-methylcytosine (5meC). In some embodiments, the present invention relates to methods and kits for detection of 5hmC and/or 5meC in nucleic acid (e.g., DNA, RNA). In some embodiments, the present invention relates to detection of 5hmC in genomic DNA, e.g., mammalian genomic DNA.

The present invention relates to methods and kits for the detection of 5-hydroxymethylcytosine (5hmC) and/or 5-methylcytosine (5meC). In some embodiments, the present invention relates to methods and kits for detection of 5hmC and/or 5meC in nucleic acid (e.g., DNA, RNA). In some embodiments, the present invention relates to detection of 5hmC in genomic DNA, e.g., mammalian genomic DNA.

Provided is a method for modifying a ssRNA at the 3′ end, the method including contacting the strand with a ssRNA 2′-O-methyltransferase in the presence of a co-factor, under conditions which allow for the transfer by the ssRNA 2′-O-methyltransferase of a part of the co-factor onto the 3′ end of the ssRNA to form a modified ssRNA, wherein the ssRNA bears 2′-OH group at 3′ terminal nucleotide and wherein the part of the co-factor transferred includes a reporter group or a functional group.

Provided is a method for modifying a ssRNA at the 3′ end, the method including contacting the strand with a ssRNA 2′-O-methyltransferase in the presence of a co-factor, under conditions which allow for the transfer by the ssRNA 2′-O-methyltransferase of a part of the co-factor onto the 3′ end of the ssRNA to form a modified ssRNA, wherein the ssRNA bears 2′-OH group at 3′ terminal nucleotide and wherein the part of the co-factor transferred includes a reporter group or a functional group.

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.