There is described herein, a method of capturing and analyzing cell-free methylated DNA in a sample. The method involves subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA. A predetermined amount of control synthetic DNA fragments are added to the sample. The control synthetic DNA fragments each have a known nucleic acid sequence that does not align to a target genome sequence, and at least some of the control synthetic DNA fragments are methylated. The sample is denatured, and cell-free methylated DNA and the control synthetic DNA fragments are captured using a binder selective for methylated polynucleotides. The captured DNA is amplified and sequenced.

There is described herein, a method of capturing and analyzing cell-free methylated DNA in a sample. The method involves subjecting the sample to library preparation to permit subsequent sequencing of the cell-free methylated DNA. A predetermined amount of control synthetic DNA fragments are added to the sample. The control synthetic DNA fragments each have a known nucleic acid sequence that does not align to a target genome sequence, and at least some of the control synthetic DNA fragments are methylated. The sample is denatured, and cell-free methylated DNA and the control synthetic DNA fragments are captured using a binder selective for methylated polynucleotides. The captured DNA is amplified and sequenced.

The present invention provides modified single primer extension-based methods for generating an amplified library of fragments of a target gene or genome of interest from a sample of fragmented DNA, wherein the library is suitable for use in detecting, quantifying and/or sequencing the target gene or genome of interest. The present invention also provides compositions for use in such methods. In some embodiments the present invention provides methods and compositions specifically for detecting, quantifying and/or sequencing circulating tumor derived HPV DNA.

The present invention provides modified single primer extension-based methods for generating an amplified library of fragments of a target gene or genome of interest from a sample of fragmented DNA, wherein the library is suitable for use in detecting, quantifying and/or sequencing the target gene or genome of interest. The present invention also provides compositions for use in such methods. In some embodiments the present invention provides methods and compositions specifically for detecting, quantifying and/or sequencing circulating tumor derived HPV DNA.

A method for detecting minimal residual disease in a subject following a cancer surgery is disclosed. The method includes obtaining a sample from the subject. The sample includes a surgical drainage. The method also includes isolating an amount of tumor-associated genetic material from the sample, sequencing the amount of tumor-associated genetic material to detect and quantify at least one tumor-associated mutation or variant in the amount of tumor-associated genetic material, and providing the at least one quantity of the at least one tumor-associated mutation or variant to a practitioner.

A method for detecting minimal residual disease in a subject following a cancer surgery is disclosed. The method includes obtaining a sample from the subject. The sample includes a surgical drainage. The method also includes isolating an amount of tumor-associated genetic material from the sample, sequencing the amount of tumor-associated genetic material to detect and quantify at least one tumor-associated mutation or variant in the amount of tumor-associated genetic material, and providing the at least one quantity of the at least one tumor-associated mutation or variant to a practitioner.

The invention relates to methods for purifying and isolating at least one RNA molecule which interacts with an RNA-binding protein (RBP). The invention also provides nucleic acid adaptors and primers for use in such methods.

The invention relates to methods for purifying and isolating at least one RNA molecule which interacts with an RNA-binding protein (RBP). The invention also provides nucleic acid adaptors and primers for use in such methods.

Provided herein are modified Archaeal family B polymerases derived from the Archaeal microorganism Thermococcus sp. EP1 that exhibit improved incorporation of nucleotide analogues utilized in DNA sequences.

Provided herein are modified Archaeal family B polymerases derived from the Archaeal microorganism Thermococcus sp. EP1 that exhibit improved incorporation of nucleotide analogues utilized in DNA sequences.