Abstract: Provided herein are methods of assaying a methylated DNA-binding protein comprising contacting methylated DNA-binding proteins with labeled oligonucleotides, obtaining sample partitions for oligonucleotides with different methylation states, and quantifying the labeled oligonucleotides in the partitions.

Abstract: In an aspect, a method for detecting the presence or absence of cancer, comprising: (a) obtaining the polynucleotide sample from the subject; (b) partitioning the polynucleotide sample based on methylation status into plurality of partitioned sets to generate partitioned polynucleotides; (c) fragmenting the partitioned polynucleotides from at least one of the plurality of partitioned sets to generate fragmented polynucleotides; (d) tagging the fragmented polynucleotides to generate tagged polynucleotides; (e) concatenating the tagged polynucleotides to generate concatenated polynucleotides; (f) processing the concatenated polynucleotides to generate processed polynucleotides, wherein the processing comprises amplification; (g) sequencing the processed polynucleotides to generate a set of sequencing reads; (h) analyzing the set of sequencing reads to detect a methylation status of a plurality of genomic regions; and (i) detecting the presence or absence of cancer from the methylation status of the plurality of

Abstract: In an aspect, a method for detecting the presence or absence of tumor in a polynucleotide sample obtained from a subject comprising: (i) adding carrier nucleic acid molecules to the polynucleotide sample to generate a first sample; wherein the set of carrier nucleic acid molecules comprises at least one subset of unmethylated carrier nucleic acid molecules and/or at least one subset of methylated carrier nucleic acid molecules and at least one end of the carrier nucleic acid molecules is modified to prevent ligation; (ii) partitioning the first sample into at least two partitioned sets using capturing agent that binds selectively to methylated polynucleotides; (iii) processing the partitioned sample to generate processed sample, wherein the processing comprises: tagging, amplifying and enriching; (iv) sequencing the processed sample to generate a set of sequencing reads; and (v) analyzing a plurality of sequencing reads to detect the presence or absence of tumor.

Abstract: In an aspect, the present disclosure provides a method for analyzing nucleic acid molecules in a sample of polynucleotides, comprising: (a) adding a subset of fragment size control molecules to the nucleic acid molecules, thereby producing a first spike-in sample; (b) extracting nucleic acids from the first spike-in sample; (c) processing at least a subset of the extracted nucleic acids, thereby producing a processed sample, wherein the processing comprises partitioning, tagging, and/or amplifying at least a subset of the first spike-in sample; (d) enriching for at least a subset of the processed sample, thereby producing an enriched sample; (e) sequencing at least a subset of the enriched sample to generate sequence reads; (0 analyzing the sequence reads to generate fragment size scores of the subset of fragment size control molecules; and (g) comparing the fragment size scores with fragment size thresholds.