METHODS AND SYSTEMS FOR ANALYZING METHYLATED POLYNUCLEOTIDES

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 genomic regions.