Fragmentation for measuring methylation and disease

A method for measuring methylation of a CpG site in a genome of a subject using cell-free DNA molecules, the method comprising:

• analyzing a plurality of cell-free DNA molecules from a biological sample of the subject, wherein the plurality of cell-free DNA molecules is not treated using a process that differentially modifies nor differentially recognizes DNA molecules depending on their methylation status, wherein the analyzing includes at least one selected from a group consisting of massively parallel sequencing and PCR that provides sequence reads of the plurality of cell-free DNA molecules, and wherein analyzing each cell-free DNA molecule of the plurality of cell-free DNA molecules includes:
• determining, using one or more of the sequence reads, a genomic position in a reference genome corresponding to at least one end of the cell-free DNA molecule;
• determining, using the sequence reads, a first amount of the plurality of cell-free DNA molecules from the biological sample ending at a first position within a window around the CpG site, the first position being between-1 to +1 position of the window, the CpG site having a 0 position being C;
• determining one or more other amounts of the plurality of cell-free DNA molecules, and wherein the first amount, the one or more other amounts, or both include one or more cell-free DNA molecules of the plurality of cell-free DNA molecules that end at a position (1) that is in a region including the CpG site and (2) that is other than the 0 position for the CpG site or any other CpG site;
• and
• determining, using the first amount and the one or more other amounts, a classification for methylation of the CpG site in the genome of the subject.