Fragmentation for measuring methylation and disease

Abstract

A method for measuring a fractional concentration of DNA from a first tissue type in a biological sample of a subject, the biological sample comprising cell-free DNA, the method comprises analysing a plurality of cell-free DNA molecules from the biological sample of the subject by (a) determining a genomic position in a reference genome corresponding to at least one end of the cell-free DNA molecule, (b) identifying a first set of CpG sites that all have a first differential methylation for the first tissue type in the reference genome, wherein the first set of CpG sites includes one or more CpG sites, (c) determining a first amount of cell-free DNA molecules ending at one of 0 or -1 position of any one of the first set of CpG sites or alternatively, (c) determining an end sequence motif of at least one end of the cell-free DNA molecule, wherein an end of the cell-free DNA molecule has a first position at an outermost position, a second position that is next to the first position, and a third position that is next to the second position; and (d) determining the fractional concentration of DNA from the first tissue type in the biological sample by comparing the first amount to a calibration value, wherein the calibration value is determined from one or more calibration samples having known fractional concentrations of DNA from the first tissue type.